Using Gene Expression to Assess the Status of Fish from Anthropogenically Influenced Estuarine Wetlands

2011 ◽  
Vol 46 (1) ◽  
pp. 69-77 ◽  
Author(s):  
Doris E. Vidal-Dorsch ◽  
Steven M. Bay ◽  
Monica A. Mays ◽  
Darrin J. Greenstein ◽  
Diana Young ◽  
...  
Keyword(s):  
Gene Expression ◽  
Estuarine Wetlands ◽  
The Status

A Review on Important Histone Acetyltransferase (HAT) Enzymes as Targets for Cancer Therapy

2019 ◽  
Vol 15 (2) ◽  
pp. 120-130
Author(s):  
Mohammad Ghanbari ◽  
Reza Safaralizadeh ◽  
Kiyanoush Mohammadi
Keyword(s):  
Gene Expression ◽  
Histone Acetyltransferase ◽  
Critical Role ◽  
Cancer Treatments ◽  
Control Of Gene Expression ◽  
Post Translational Modifications ◽  
Therapeutic Drugs ◽  
The Status ◽  
Acetyl Group ◽  
Increase Gene Expression

At the present time, cancer is one of the most lethal diseases worldwide. There are various factors involved in the development of cancer, including genetic factors, lifestyle, nutrition, and so on. Recent studies have shown that epigenetic factors have a critical role in the initiation and development of tumors. The histone post-translational modifications (PTMs) such as acetylation, methylation, phosphorylation, and other PTMs are important mechanisms that regulate the status of chromatin structure and this regulation leads to the control of gene expression. The histone acetylation is conducted by histone acetyltransferase enzymes (HATs), which are involved in transferring an acetyl group to conserved lysine amino acids of histones and consequently increase gene expression. On the basis of similarity in catalytic domains of HATs, these enzymes are divided into different groups such as families of GNAT, MYST, P300/CBP, SRC/P160, and so on. These enzymes have effective roles in apoptosis, signaling pathways, metastasis, cell cycle, DNA repair and other related mechanisms deregulated in cancer. Abnormal activation of HATs leads to uncontrolled amplification of cells and incidence of malignancy signs. This indicates that HAT might be an important target for effective cancer treatments, and hence there would be a need for further studies and designing of therapeutic drugs on this basis. In this study, we have reviewed the important roles of HATs in different human malignancies.

scholarly journals Decrosslinking enables visualization of RNA-guided endonuclease–in situ labeling signals for DNA sequences in plant tissues

2019 ◽  
Vol 71 (6) ◽  
pp. 1792-1800
Author(s):  
K Nagaki ◽  
N Yamaji
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Glass Slide ◽  
Plant Tissues ◽  
Visualization Method ◽  
Caspase 9 ◽  
Coordinate Gene Expression ◽  
Target Dna ◽  
The Status

Abstract Information about the positioning of individual loci in the nucleus and the status of epigenetic modifications at these loci in each cell contained in plant tissue increases our understanding of how cells in a tissue coordinate gene expression. To obtain such information, a less damaging method of visualizing DNA in tissue that can be used with immunohistochemistry is required. Recently, a less damaging DNA visualization method using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/associated caspase 9) system, named RNA-guided endonuclease–in situ labeling (RGEN-ISL), was reported. This system made it possible to visualize a target DNA locus in a nucleus fixed on a glass slide with a set of simple operations, but it could not be applied to cells in plant tissues. In this work, we have developed a modified RGEN-ISL method with decrosslinking that made it possible to simultaneously detect the DNA loci and immunohistochemistry signals, including histone modification, in various types of plant tissues and species.

scholarly journals Transcriptomic profiling of peripheral blood nucleated cells in dogs with and without clinical signs of chronic mitral valve disease

2014 ◽  
Vol 58 (1) ◽  
pp. 135-140
Author(s):  
Magdalena Garncarz ◽  
Magdalena Hulanicka ◽  
Marta Parzeniecka-Jaworska ◽  
Jacek Garncarz ◽  
Michał Jank
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Mitral Valve ◽  
Peripheral Blood ◽  
Mitral Valve Disease ◽  
Clinical Signs ◽  
Valve Disease ◽  
Non Invasive ◽  
The Status ◽  
Healthy Dogs

Abstract The aim of the study was to demonstrate differences in the gene expression of signalling pathways between healthy dogs and dogs with chronic mitral valve disease in different heart failure groups. Blood samples were collected from 49 dogs of various breeds between 1.4 and 15.2 years of age. Isolated RNA samples were analysed for quality and integrity and the gene expression profile was determined. The study demonstrated that nucleated cells from peripheral blood can be used to assess the status of heart failure in dogs. Furthermore, significant differences in the expression of the genes were noticed between healthy dogs and dogs with clinical signs of chronic mitral valve disease. This is a preliminary non-invasive study showing the feasibility of genetic testing from peripheral blood nucleated cells, which at the same time has made it possible to set the future directions of genetic studies in clinical cases of canine chronic mitral valve disease.

scholarly journals Response of DREB transcription factor to drought stress based on DNA methylation in wheat

2020 ◽  
Author(s):  
Yanqiu Zhu ◽  
Huihui Wang ◽  
Wenjing Jia ◽  
Xiaoyan Wei ◽  
Zhikun Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Drought Stress ◽  
Promoter Methylation ◽  
Resistance Mechanism ◽  
Dreb Transcription Factor ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background: The growth and development of wheat are seriously influenced by drought stress, and the research on drought resistance mechanism of wheat is very important. Dehydration responsive element binding protein (DREB) plays an important role in plant response to drought stress, but epigenetic regulation for gene expression of DREB transcription factor is less studied, especially the regulatory role of DNA methylation has not been reported.Results: In this research, DREB2, DREB6 and Wdreb2 were cloned from wheat in this study, their CDS sequence was composed of 732bp, 837bp or 1035bp, respectively, one 712bp intron was found in DREB6. Although AP2/EREBP domain of DREB2, DREB6 and Wdreb2 had 73.25% identity, they belong to different types of DREB transcription factor, and the expression of Wdreb2 was significantly higher, yet was the lowest in DREB2. Under drought stress, the expression of DREB2, DREB6 and Wdreb2 could be induced, but had different trends along with the increase of stress time, and their expression had tissue specificity, was obviously higher in leaf. Promoter of DREB2, DREB6 and Wdreb2 in leaf was further studied, some elements related to adverse stress were found, and the promoter of DREB2 and Wdreb2 was slightly methylated, but DREB6 promoter was mildly methylated. Compared with the control, the level of promoter methylation decreased in DREB2 and DREB6 as stressed for 2h, then increased along with the increase of stress time, which was opposite in Wdreb2 promoter, the status of promoter methylation also had significant change under drought stress. Further analysis showed that promoter methylation of DREB6 or Wdreb2 was negatively correlated with their expression, especially was significant in Wdreb2. Conclusions: DREB2, DREB6 and Wdreb2 might function differently in response to drought stress, and promoter methylation had more significant effects on gene expression of Wdreb2 and DREB6.

scholarly journals Mir-485-3p and Mir-654-3p Expression in Bone Marrow Mesenchymal Stromal Cells in Patients with Monoclonal Gammopathies Is Related to the Status of the Disease

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3155-3155
Author(s):  
Carlos Fernandez de Larrea ◽  
Tania Diaz ◽  
Alfons Navarro ◽  
Ester Lozano ◽  
Mari-Pau Mena ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Bone Marrow ◽  
Mesenchymal Stromal Cells ◽  
Mirna Expression ◽  
Stromal Cells ◽  
Plasma Cells ◽  
Differentially Expressed ◽  
Monoclonal Gammopathies ◽  
The Status

Abstract Background: Crosstalk between malignant plasma cells and surrounding cells in the bone marrow (BM), such as mesenchymal stromal cells (MSCs), endothelial cells and immune cells, is crucial for pathogenesis of multiple myeloma (MM) and in asymptomatic monoclonal gammopathies. In these diseases, microRNAs (miRNAs) could be useful as biomarkers for diagnosis, prognosis and evaluation of treatment response. miRNAs can be released to the serum and transferred among MM cells and BM-MSCs as cell-cell communication. Previously, we have showed a serum 14-miRNA signature associated with complete remission (CR) after autologous stem-cell transplantation (ASCT). In this sense, patients in CR with partial recovery of two normal serum miRNA levels, similar to those with monoclonal gammopathy of undetermined significance (MGUS), was associated with better prognosis. The aim of this study was to analyze the miRNAs profile in mesenchymal stromal cells derived from bone marrow of patients with multiple myeloma in different status of the disease, comparing with MGUS controls. Methods: We analyzed samples from 95 patients with MGUS (N=23), MM at diagnosis (N=14), relapsed/refractory MM (N=14), MM in partial response (PR) or very good partial response (VGPR) (N=15), MM in CR (N=24) and healthy donors (N=5). Mononuclear cells from BM samples were cultured in DMEM containing 10% FBS. After a week, non-adherent cells were removed, whereas BM-MSCs were selected by their adherence to the plastic and their phenotype was confirmed by multiparametric flow cytometry. In a first screening phase, we analyzed 670 microRNAs in 20 primary BM-MSC from patients with MGUS (N=4), symptomatic MM (N=8) and MM in CR (N=8). miRNAs differentially expressed were identified according to a supervised analysis using significance analysis of microarrays (SAM) and Student's t-test based on multivariate permutation (with random variance model). miRNAs differentially expressed between groups of patients were validated in the whole cohort of BM-MSC from patients. Paired malignant plasma cells (CD38+) miRNA expression from patients with symptomatic MM as well as miRNA in serum samples paired with BM-MSC samples were also compared. RmiR package was used to identify miRNA targets, cross-correlating the miRNA expression data from the present study with our findings on the gene expression signature (Affymetrix Human Genome U219 array) in 12 BM-MSCs from patients (4 MGUS, 4 symptomatic MM and 4 in CR), based on the predicted targets from TargetScan and miRBase databases. Results: In the screening phase, we identified a miRNA profile of 10 miRNAs (miR-663b, miR-654-3p, miR-206, miR-411*, miR-885-5p, miR-668, miR-638, miR-485-3p, miR-744* and miR-199a) differentially expressed between patients with symptomatic MM and MM in CR (adjusted p-value <0.0001). In the validation phase, miR-485-3p and miR-654-3p resulted differentially expressed in the three groups of patients: MGUS, symptomatic MM and patients in CR (ANOVA test: p=0.0101 and p=0.0228, respectively). The levels of these miRNAs were significantly decreased in patients with MM than in those with MGUS, and these levels seemed to recover when patients achieved CR. These two miRNAs (miR-485-3p and miR-654-3p) were also correlated with all degrees of response in MM and with asymptomatic gammopathies (ANOVA test: p=0.0154 and p=0.0487, respectively). Moreover, paired cross-correlation among these two miRNAs expression with our results in mRNA gene expression profile data showed 324 for miR-485-3p and 265 for miR-654-3p genes (correlation index < -0.8) (Figure 1A and 1B). miR-485-3p and miR-654-3p showed a higher expression in BM-MSC than in MM CD38+ cells, suggesting MSC as cell of origin for these miRNAs. Serum expression of these two miRNAs was concordant with the observed in BM-MSC, with higher in patients in CR and MGUS than in those with symptomatic MM (Figure 1C and 1D). miRNA expression in BM-MSC supernatant as well as the identification of the biological role and validation of the miRNA targets are ongoing. Conclusion: miR-485-3p and miR-654-3p expression in mesenchymal stromal cells from bone marrow in patients with multiple myeloma and asymptomatic monoclonal gammopathies is related to the status of the disease and the response to treatment. These miRNAs are also expressed in serum, resulting in potential biomarkers for disease activity and risk of progression. Disclosures Rosinol: Janssen, Celgene, Amgen, Takeda: Honoraria. Bladé:Janssen: Honoraria.

scholarly journals Peptide Regulation of Gene Expression: A Systematic Review

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 7053
Author(s):  
Vladimir Khatskelevich Khavinson ◽  
Irina Grigor’evna Popovich ◽  
Natalia Sergeevna Linkova ◽  
Ekaterina Sergeevna Mironova ◽  
Anastasiia Romanovna Ilina
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Epigenetic Mechanism ◽  
Short Peptides ◽  
Gene Promoters ◽  
Amino Acid Residues ◽  
Sequence Recognition ◽  
Wide Range ◽  
The Status ◽  
Synthetic Reactions

Peptides are characterized by their wide range of biological activity: they regulate functions of the endocrine, nervous, and immune systems. The mechanism of such action of peptides involves their ability to regulate gene expression and protein synthesis in plants, microorganisms, insects, birds, rodents, primates, and humans. Short peptides, consisting of 2–7 amino acid residues, can penetrate into the nuclei and nucleoli of cells and interact with the nucleosome, the histone proteins, and both single- and double-stranded DNA. DNA–peptide interactions, including sequence recognition in gene promoters, are important for template-directed synthetic reactions, replication, transcription, and reparation. Peptides can regulate the status of DNA methylation, which is an epigenetic mechanism for the activation or repression of genes in both the normal condition, as well as in cases of pathology and senescence. In this context, one can assume that short peptides were evolutionarily among the first signaling molecules that regulated the reactions of template-directed syntheses. This situation enhances the prospects of developing effective and safe immunoregulatory, neuroprotective, antimicrobial, antiviral, and other drugs based on short peptides.

scholarly journals Response of wheat DREB transcription factor to drought stress based on DNA methylation

2021 ◽  
Author(s):  
Yanqiu Zhu ◽  
Huihui Wang ◽  
Wenjing Jia ◽  
Xiaoyan Wei ◽  
Zhikun Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Drought Stress ◽  
Promoter Methylation ◽  
Expression Patterns ◽  
Dreb Transcription Factor ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background: The growth and development of wheat are seriously influenced by drought, dehydration responsive element binding protein (DREB) plays an important role in the response of plant to drought stress, but epigenetic regulation for gene expression of DREB transcription factor is less studied, especially the regulatory role of DNA methylation has not been reported.Results: In this research, DREB2, DREB6 and Wdreb2 were cloned from wheat AK58, and one 712-bp intron was identified in DREB6. Although AP2/EREBP domains of DREB2, DREB6 and Wdreb2 showed 73.25% identity, they belong to different types of DREB transcription factor. Under drought stress, different transcript expression patterns of DREB2, DREB6 and Wdreb2 were observed, and their expression had tissue specificity, was obviously higher in leaves. Promoters of DREB2, DREB6 and Wdreb2 were further studied, some elements related to stresses were found, and the promoters of DREB2 and Wdreb2 were slightly methylated, but DREB6 promoter was moderately methylated. Compared with the control, the level of promoter methylation in DREB2 and DREB6 decreased after 2 h stress treatment, and then increased, which was opposite in Wdreb2 promoter, the status of promoter methylation in DREB2, DREB6 and Wdreb2 also had significant changes under drought stress. Further analysis showed that promoter methylation of DREB6 and Wdreb2 was negatively correlated with their expression, especially in Wdreb2. Conclusions: Our data suggest the different functions of DREB2, DREB6 and Wdreb2 in response to drought stress, and demonstrate the strong effects of promoter methylation on the regulation of Wdreb2 and DREB6 gene expression.

scholarly journals BAX Redistribution Induces Apoptosis Resistance and Selective Stress Sensitivity in Human HCC

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1437
Author(s):  
Kathrin Funk ◽  
Carolin Czauderna ◽  
Ramona Klesse ◽  
Diana Becker ◽  
Jovana Hajduk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Expression Profiles ◽  
Tumor Biology ◽  
Gene Expression Profiles ◽  
Parp Inhibition ◽  
Molecular Characteristics ◽  
Apoptosis Resistance ◽  
Molecular Features ◽  
The Status

Cancer therapies induce differential cell responses, ranging from efficient cell death to complete stress resistance. The BCL-2 proteins BAX and BAK govern the cellular decision between survival and mitochondrial apoptosis. Therefore, the status of BAX/BAK regulation can predict the cellular apoptosis predisposition. Relative BAX/BAK localization was analyzed in tumor and corresponding non-tumor samples from 34 hepatocellular carcinoma (HCC) patients. Key transcriptome changes and gene expression profiles related to the status of BAX regulation were applied to two independent cohorts including over 500 HCC patients. The prediction of apoptotic response was tested using cell lines and polyclonal tumor isolates. Cellular protection from BAX was confirmed by challenging cells with mitochondrial BAX. We discovered a subgroup of HCC with selective protection from BAX-dependent apoptosis. BAX-protected tumors showed enrichment of signaling pathways associated with oxidative stress response and DNA repair as well as increased genetic heterogeneity. Gene expression profiles characteristic to BAX-specific protection are enriched in poorly differentiated HCCs and show significant association to the overall survival of HCC patients. Consistently, addiction to DNA repair of BAX-protected cancer cells caused selective sensitivity to PARP inhibition. Molecular characteristics of BAX-protected HCC were enriched in cells challenged with mitochondrial BAX. Our results demonstrate that predisposition to BAX activation impairs tumor biology in HCC. Selective BAX inhibition or lack thereof delineates distinct subgroups of HCC patients with molecular features and differential response pattern to apoptotic stimuli and inhibition of DNA repair mechanisms.

scholarly journals Impairment of the Natriuretic Peptide System in Follitropin Receptor Knockout Mice and Reversal by Estradiol: Implications for Obesity-Associated Hypertension in Menopause

Endocrinology ◽  
2007 ◽  
Vol 149 (3) ◽  
pp. 1399-1406 ◽  
Author(s):  
Najara O. Belo ◽  
M. Ram Sairam ◽  
Adelina M. dos Reis
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Natriuretic Peptide ◽  
Cardiovascular Effects ◽  
Estradiol Treatment ◽  
Age Related ◽  
The Status ◽  
Peptide System ◽  
Natriuretic Peptide System

Estrogen is considered a major regulator of adipose tissue in females. Estrogen increases circulating levels of atrial natriuretic peptide (ANP), a hormone with renal and cardiovascular effects. The aim of this study was to determine the status of the natriuretic peptide system in female follitropin-receptor knockout (FORKO) mice that could be associated with obesity and hypertension observed in these mutants. Furthermore, estradiol treatment was used to reverse alterations observed. FORKO and wild-type (WT) mice received daily injections of estradiol for 4 d. On the fifth day, blood was collected for determination of plasma ANP levels, and selected tissues were collected for determination of ANP, natriuretic peptide receptor type-A (NPR-A) and type-C (NPR-C) gene expression by RT-PCR and binding of [125I]ANP by autoradiography. At 5 months of age, FORKO mice were heavier and had more adipose tissue than WT mice. FORKO mice had lower plasma ANP levels and atrial ANP gene expression and higher renal and adipocyte NPR-C gene expression than WT mice. Estradiol treatment reduced weight gain and increased atrial ANP synthesis as well as decreased ANP clearance NPR-C receptors, resulting in elevation of circulating ANP level. In conclusion, this study shows that FORKO females have an impaired natriuretic peptide system, which may contribute to the susceptibility of FORKO mice to developing age-related hypertension previously shown in these animals. This study establishes a relation between estrogen, adipose tissue, and ANP, which may have important implications in menopausal women.

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