scholarly journals Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1535
Author(s):  
Kanoko Nokihara ◽  
Yoshihiro Okada ◽  
Shinichiro Ohata ◽  
Yuki Monden
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Transcriptome Analysis ◽  
Growth Stage ◽  
Gene Expression Analysis ◽  
Molecular Mechanisms ◽  
Cellular Processes ◽  
Significant Difference ◽  
Insect Metamorphosis ◽  
Key Genes

Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato.

Screening of cervical cancer-related hub genes based on comprehensive bioinformatics analysis

2021 ◽  
pp. 1-13
Author(s):  
Simei Tu ◽  
Hao Zhang ◽  
Xiaocheng Yang ◽  
Wen Wen ◽  
Kangjing Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cervical Cancer ◽  
Molecular Mechanisms ◽  
Disease Free Survival ◽  
The Cancer Genome Atlas ◽  
Mrna Levels ◽  
Hub Genes ◽  
Normal Tissues ◽  
Significant Difference ◽  
Core Genes

BACKGROUND: Since the molecular mechanisms of cervical cancer (CC) have not been completely discovered, it is of great significance to identify the hub genes and pathways of this disease to reveal the molecular mechanisms of cervical cancer. OBJECTIVE: The study aimed to identify the biological functions and prognostic value of hub genes in cervical cancer. METHODS: The gene expression data of CC patients were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. The core genes were screened out by differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). R software, the STRING online tool and Cytoscape software were used to screen out the hub genes. The GEPIA public database was used to further verify the expression levels of the hub genes in normal tissues and tumour tissues and determine the disease-free survival (DFS) rates of the hub genes. The protein expression of the survival-related hub genes was identified with the Human Protein Atlas (HPA) database. RESULTS: A total of 64 core genes were screened, and 10 genes, including RFC5, POLE3, RAD51, RMI1, PALB2, HDAC1, MCM4, ESR1, FOS and E2F1, were identified as hub genes. Compared with that in normal tissues, RFC5, POLE3, RAD51,RMI1, PALB2, MCM4 and E2F1 were all significantly upregulated in cervical cancer, ESR1 was significantly downregulated in cervical cancer, and high RFC5 expression in CC patients was significantly related to OS. In the DFS analysis, no significant difference was observed in the expression level of RFC5 in cervical cancer patients. Finally, RFC5 protein levels verified by the HPA database were consistently upregulated with mRNA levels in CC samples. CONCLUSIONS: RFC5 may play important roles in the occurrence and prognosis of CC. It could be further explored and validated as a potential predictor and therapeutic target for CC.

scholarly journals Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 525 ◽  
Author(s):  
Samar Tareen ◽  
Michiel Adriaens ◽  
Ilja Arts ◽  
Theo de Kok ◽  
Roel Vink ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Weight Loss ◽  
Adipose Tissue ◽  
Molecular Mechanisms ◽  
Dietary Intervention ◽  
Network Biology ◽  
Analysis Tool ◽  
Cellular Processes ◽  
Time Series Gene Expression

Obesity is a global epidemic identified as a major risk factor for multiple chronic diseases and, consequently, diet-induced weight loss is used to counter obesity. The adipose tissue is the primary tissue affected in diet-induced weight loss, yet the underlying molecular mechanisms and changes are not completely deciphered. In this study, we present a network biology analysis workflow which enables the profiling of the cellular processes affected by weight loss in the subcutaneous adipose tissue. Time series gene expression data from a dietary intervention dataset with two diets was analysed. Differentially expressed genes were used to generate co-expression networks using a method that capitalises on the repeat measurements in the data and finds correlations between gene expression changes over time. Using the network analysis tool Cytoscape, an overlap network of conserved components in the co-expression networks was constructed, clustered on topology to find densely correlated genes, and analysed using Gene Ontology enrichment analysis. We found five clusters involved in key metabolic processes, but also adipose tissue development and tissue remodelling processes were enriched. In conclusion, we present a flexible network biology workflow for finding important processes and relevant genes associated with weight loss, using a time series co-expression network approach that is robust towards the high inter-individual variation in humans.

scholarly journals Expression analysis of defense-related genes in cucumber (Cucumis sativus L.) against Phytophthora melonis

2020 ◽  
Author(s):  
Lida Hashemi ◽  
Ahmad Reza Golparvar ◽  
Mehdi Nasr Esfahani ◽  
Maryam Golabadi
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Molecular Mechanisms ◽  
Crown Rot ◽  
Economic Losses ◽  
Post Inoculation ◽  
Expression Ratio ◽  
Phytophthora Melonis ◽  
Maximum Expression

AbstractPhytophthora melonis is the causal agent of damping-off or crown rot, one of the most destructive cucumber diseases that causes severe economic losses in Iran and some other parts of the world. Despite intense research efforts made in the past years, no permanent cure currently exists for this disease. With the aim to understand the molecular mechanisms of defense against P. melonis, root collars and leaves of four cucumber genotypes consisting of resistant Ramezz; moderately resistant Baby and very susceptible Mini 6-23 and Extrem, were monitored for quantitative gene expression analysis of five antifungal and/or anti-oomycete genes (CsWRKY20, CsLecRK6.1, PR3, PR1-1a and LOX1) at three points after inoculation with P. melonis. The gene expression analysis indicated that P. melonis strongly enhanced the expression of these genes after inoculation in both leaves and root collars. Further, not only the transcript levels of these genes were significantly higher in the resistant and moderately resistance genotypes, but also the time point of the highest relative expression ratio for the five genes was different in the four cucumber genotypes. CsWRKY20 and PR3 showed the maximum expression in Ramezz at 48 hours post inoculation (hpi) while CsLecRK6.1, and LOX1 showed the highest expression at 72 hpi. In addition, PR1-1a showed the maximum expression in the Baby at 72 hpi. Root collars responded faster than leaves and some responses were more strongly up-regulated in root collars than in leaves. The genes found to be involved in disease resistance in two different organs of cucumber after pathogen infection. The results suggest that increased expression of these genes led to activation of defense pathways and could be responsible for a reduced P. melonis colonization capacity in Ramezz and Baby. Overall, this work represents a valuable resource for future functional genomics studies to unravel the molecular mechanisms of C. sativus- P. melonis interaction.

crooked legs encodes a family of zinc finger proteins required for leg morphogenesis and ecdysone-regulated gene expression during Drosophila metamorphosis

Development ◽  
1998 ◽  
Vol 125 (9) ◽  
pp. 1733-1745 ◽  
Author(s):  
P.P. D'Avino ◽  
C.S. Thummel
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Genetic Locus ◽  
Regulatory Genes ◽  
Protein Isoforms ◽  
Sequence Motif ◽  
Specific Effects ◽  
Insect Metamorphosis ◽  
Adult Head ◽  
Regulated Gene Expression

Drosophila imaginal discs undergo extensive pattern formation during larval development, resulting in each cell acquiring a specific adult fate. The final manifestation of this pattern into adult structures is dependent on pulses of the steroid hormone ecdysone during metamorphosis, which trigger disc eversion, elongation and differentiation. We have defined genetic criteria that allow us to screen for ecdysone-inducible regulatory genes that are required for this transformation from patterned disc to adult structure. We describe here the first genetic locus isolated using these criteria: crooked legs (crol). crol mutants die during pupal development with defects in adult head eversion and leg morphogenesis. The crol gene is induced by ecdysone during the onset of metamorphosis and encodes at least three protein isoforms that contain 12–18 C2H2 zinc fingers. Consistent with this sequence motif, crol mutations have stage-specific effects on ecdysone-regulated gene expression. The EcR ecdysone receptor, and the BR-C, E74 and E75 early regulatory genes, are submaximally induced in crol mutants in response to the prepupal ecdysone pulse. These changes in gene activity are consistent with the crol lethal phenotypes and provide a basis for understanding the molecular mechanisms of crol action. The genetic criteria described here provide a new direction for identifying regulators of adult tissue development during insect metamorphosis.

scholarly journals Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sujeenthar Tharmalingam ◽  
Sandhya Khurana ◽  
Alyssa Murray ◽  
Jeremy Lamothe ◽  
T. C. Tai
Keyword(s):  
Gene Expression ◽  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Adrenal Glands ◽  
Genetic Model ◽  
Pathway Enrichment Analysis ◽  
Wistar Kyoto ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Prenatal glucocorticoid exposure is associated with the development of hypertension in adults. We have previously demonstrated that antenatal dexamethosone (DEX) administration in Wistar-Kyoto dams results in offspring with increased blood pressure coupled with elevated plasma epinephrine levels. In order to elucidate the molecular mechanisms responsible for prenatal DEX-mediated programming of hypertension, a whole-transcriptome analysis was performed on DEX programmed WKY male adrenal glands using the Rat Gene 2.0 microarray. Differential gene expression (DEG) analysis of DEX-exposed offspring compared with saline-treated controls revealed 142 significant DEGs (109 upregulated and 33 downregulated genes). DEG pathway enrichment analysis demonstrated that genes involved in circadian rhythm signaling were most robustly dysregulated. RT-qPCR analysis confirmed the increased expression of circadian genes Bmal1 and Npas2, while Per2, Per3, Cry2 and Bhlhe41 were significantly downregulated. In contrast, gene expression profiling of Spontaneously Hypertensive (SHR) rats, a genetic model of hypertension, demonstrated decreased expression of Bmal1 and Npas2, while Per1, Per2, Per3, Cry1, Cry2, Bhlhe41 and Csnk1D were all upregulated compared to naïve WKY controls. Taken together, this study establishes that glucocorticoid programmed adrenals have impaired circadian signaling and that changes in adrenal circadian rhythm may be an underlying molecular mechanism responsible for the development of hypertension.

scholarly journals Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shan Lin ◽  
Zhicheng Zou ◽  
Cuibing Zhou ◽  
Hancheng Zhang ◽  
Zhiming Cai
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Purine Metabolism ◽  
Expression Data ◽  
Rna Seq ◽  
Metabolism Pathway ◽  
Caterpillar Fungus ◽  
Regulated Gene Expression ◽  
Late Stages

Caterpillar fungus is a well-known fungal Chinese medicine. To reveal molecular changes during early and late stages of adenosine biosynthesis, transcriptome analysis was performed with the anamorph strain of caterpillar fungus. A total of 2,764 differentially expressed genes (DEGs) were identified (p≤0.05, |log2 Ratio| ≥ 1), of which 1,737 were up-regulated and 1,027 were down-regulated. Gene expression profiling on 4–10 d revealed a distinct shift in expression of the purine metabolism pathway. Differential expression of 17 selected DEGs which involved in purine metabolism (map00230) were validated by qPCR, and the expression trends were consistent with the RNA-Seq results. Subsequently, the predicted adenosine biosynthesis pathway combined with qPCR and gene expression data of RNA-Seq indicated that the increased adenosine accumulation is a result of down-regulation of ndk, ADK, and APRT genes combined with up-regulation of AK gene. This study will be valuable for understanding the molecular mechanisms of the adenosine biosynthesis in caterpillar fungus.

scholarly journals The Ubiquitin Carboxyl Hydrolase BAP1 Forms a Ternary Complex with YY1 and HCF-1 and Is a Critical Regulator of Gene Expression

2010 ◽  
Vol 30 (21) ◽  
pp. 5071-5085 ◽  
Author(s):  
Helen Yu ◽  
Nazar Mashtalir ◽  
Salima Daou ◽  
Ian Hammond-Martel ◽  
Julie Ross ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ternary Complex ◽  
Transcriptional Control ◽  
Molecular Mechanisms ◽  
Mitochondrial Protein ◽  
Coiled Coil ◽  
Dependent Manner ◽  
Cellular Processes ◽  
Rich Domain

ABSTRACT The candidate tumor suppressor BAP1 is a deubiquitinating enzyme (DUB) involved in the regulation of cell proliferation, although the molecular mechanisms governing its function remain poorly defined. BAP1 was recently shown to interact with and deubiquitinate the transcriptional regulator host cell factor 1 (HCF-1). Here we show that BAP1 assembles multiprotein complexes containing numerous transcription factors and cofactors, including HCF-1 and the transcription factor Yin Yang 1 (YY1). Through its coiled-coil motif, BAP1 directly interacts with the zinc fingers of YY1. Moreover, HCF-1 interacts with the middle region of YY1 encompassing the glycine-lysine-rich domain and is essential for the formation of a ternary complex with YY1 and BAP1 in vivo. BAP1 activates transcription in an enzymatic-activity-dependent manner and regulates the expression of a variety of genes involved in numerous cellular processes. We further show that BAP1 and HCF-1 are recruited by YY1 to the promoter of the cox7c gene, which encodes a mitochondrial protein used here as a model of BAP1-activated gene expression. Our findings (i) establish a direct link between BAP1 and the transcriptional control of genes regulating cell growth and proliferation and (ii) shed light on a novel mechanism of transcription regulation involving ubiquitin signaling.

Gene Expression Levels Of Imatinib Transporters and Molecular Response To Imatinib Therapy In Chronic Myeloid Leukemia Patients

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4959-4959
Author(s):  
Hemant Malhotra ◽  
Pratibha Sharma ◽  
Shipra Bhargava ◽  
Bharti Malhotra ◽  
Madhu Kumar
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Conflicts Of Interest ◽  
Imatinib Therapy ◽  
Molecular Response ◽  
Transcript Expression ◽  
Analysis Study ◽  
Expression Levels ◽  
Significant Difference

Abstract Imatinib mesylate (IM) is the standard first-line treatment for most CML patients. After an initial response, approximately 30 to 40% patients develop resistance to the drug. Various mechanisms of resistance to Imatinib therapy have been identified. One of the mechanisms proposed is varying expression levels of the drug transporters. In the present study, we determined the relative expression levels of Imatinib transporter genes (hOCT1, ABCB1, ABCG2) in CML patients by quantitative real time polymerase chain reaction (qRT-PCR) and correlated these levels with molecular response. One hundred and ten CML patients were considered for gene expression analysis study for hOCT1 gene and eighty seven CML patients were considered for gene expression analysis study for ABCB1 and ABCG2 genes. CML patients who were on IM therapy for more than 2 years were divided into two groups: Responders: patients who achieve a Complete Molecular response (CMR) or a Major Molecular Response (MMR) [bcr/abl: abl ratio <1% as assessed by RQ-PCR] and Non-responders: those without CMR or MMR (bcr/abl: abl ratio =/> 1% as assessed by RQ-PCR). The relative transcript expression levels of the three genes were compared between responders and non-responders. No significant difference in the expression levels of hOCT1, ABCB1 and ABCG2 was found between the two categories - responders versus non-responders (p value > 0.05). The median transcript expression levels of hOCT1, ABCB1 and ABCG2 genes in responders were 30.63, 10.14 and 0.59 versus 40.13, 8.34 and 0.53 in non-responders, respectively. We conclude that, in our study, the mRNA expression levels of IM transporter genes did no correlate with molecular response in CML patients. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Effects of L-Theanine on Posttraumatic Stress Disorder Induced Changes in Rat Brain Gene Expression

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Tomás Eduardo Ceremuga ◽  
Stephanie Martinson ◽  
Jason Washington ◽  
Robert Revels ◽  
Jessica Wojcicki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Posttraumatic Stress Disorder ◽  
Posttraumatic Stress ◽  
Molecular Mechanisms ◽  
Stress Disorder ◽  
Traumatic Event ◽  
Pcr Analysis ◽  
Sprague Dawley ◽  
Significant Difference ◽  
Induced Changes

Posttraumatic stress disorder (PTSD) is characterized by the occurrence of a traumatic event that is beyond the normal range of human experience. The future of PTSD treatment may specifically target the molecular mechanisms of PTSD. In the US, approximately 20% of adults report taking herbal products to treat medical illnesses. L-theanine is the amino acid in green tea primarily responsible for relaxation effects. No studies have evaluated the potential therapeutic properties of herbal medications on gene expression in PTSD. We evaluated gene expression in PTSD-induced changes in the amygdala and hippocampus of Sprague-Dawley rats. The rats were assigned to PTSD-stressed and nonstressed groups that received either saline, midazolam, L-theanine, or L-theanine + midazolam. Amygdala and hippocampus tissue samples were analyzed for changes in gene expression. One-way ANOVA was used to detect significant difference between groups in the amygdala and hippocampus. Of 88 genes examined, 17 had a large effect size greater than 0.138. Of these, 3 genes in the hippocampus and 5 genes in the amygdala were considered significant (P<0.05) between the groups. RT-PCR analysis revealed significant changes between groups in several genes implicated in a variety of disorders ranging from PTSD, anxiety, mood disorders, and substance dependence.

scholarly journals Transcriptome analysis of sevoflurane exposure effects at the different brain regions

2020 ◽  
Author(s):  
Hiroto Yamamoto ◽  
Yutaro Uchida ◽  
Tomoki Chiba ◽  
Ryota Kurimoto ◽  
Takahide Matsushima ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Neural Development ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Ontology Term ◽  
Whole Brain ◽  
Differently Expressed Genes

AbstractBackgroundsSevoflurane is a most frequently used volatile anaesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in whole brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis.MethodsEight-week old mice were exposed to sevoflurane. RNA from four medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted. Their gene ontology terms and the transcriptome array data of the cerebral cortex of sleeping mice were analysed using Metascape, and the gene expression patterns were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes.ResultsThe gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in the whole brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anaesthetized mice. Sevoflurane induced Klf4 upregulation in the whole brain. The transcriptional analysis result suggests that KLF4 is a potential transcriptional regulator of angiogenesis and neural development.ConclusionsKlf4 was upregulated by sevoflurane inhalation in whole brain. KLF4 might promote angiogenesis and cause the appearance of undifferentiated neural cells by transcriptional regulation. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.

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