scholarly journals Balanced duplicated gene expression supports an autotetraploid ancestor of Salicaceae plants

2019 ◽  
Author(s):  
Yu-Hao Zhao ◽  
Jin-Peng Wang ◽  
Jia-Qing Yuan ◽  
Jing Li ◽  
Wei-Na Ge ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Function ◽  
Genome Duplication ◽  
Chromosome Doubling ◽  
Enrichment Analysis ◽  
Plant Groups ◽  
Pathway Annotation ◽  
Significant Difference ◽  
Similar Gene ◽  
Gene Expression Levels

Abstract Background Autopolyploids refer to the increase in the genome from the same species, usually produced by direct doubling of diploid chromosomes. The polyploid formed by chromosome doubling of the same species is called homologous polyploid. Results In order to further check whether the Salicaceae-common tetraploid is homologous or heterologous, with grape as the outer group, by performing gene collinearity analysis, we explored whether two sets of poplar chromosomes or chromosomal regions have balanced gene expression levels and similar gene function. Paired T-test showed that duplicated genes in colinearity were balanced in expression, which is expected if the tetraploid ancestor was homologous whole-genome duplication, or autopolyploidization. Moreover, KEGG enrichment analysis and pathway annotation showed that most of the differentially expressed genes were related to metabolism. A comparison of different groups of flowering plants suggests that autopolyploidization may not provide comparable biological and evolutionary vigor to establish large plant groups, as observed in poaceae and brassicaceae families. The present analysis contributes to understanding the biology and evolution of Salicacea plants and beyond. Conclusions There was no significant difference in gene expression and gene function between two sets of genomes of poplar.

scholarly journals Outcomes of GDPT (gemcitabine, cisplatin, prednisone, thalidomide) versus CHOP in newly diagnosed peripheral T-cell lymphoma patients

2020 ◽  
Vol 12 ◽  
pp. 175883592092382 ◽  
Author(s):  
Yuanyuan Sun ◽  
Ling Li ◽  
Xin Li ◽  
Lei Zhang ◽  
Xinhua Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Cell Lymphoma ◽  
T Cell Lymphoma ◽  
The Other ◽  
Newly Diagnosed ◽  
Peripheral T Cell Lymphoma ◽  
Angioimmunoblastic T Cell Lymphoma ◽  
Significant Difference ◽  
Gene Expression Levels

Aim: To compare the outcomes of GDPT [gemcitabine (G), cisplatin (D), prednisone (P), thalidomide (T)] versus CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) in treating newly diagnosed PTCL (peripheral T-cell lymphoma). Methods: An open-label prospective clinical trial with 153 newly diagnosed PTCL patients conducted between January 2010 and December 2018 was designed. Patients were randomly assigned to the GDPT (77 cases) and CHOP (76 cases) groups. Patients in each group were further divided into four subgroups: PTCL, not otherwise specified (PTCL-NOS); anaplastic large cell lymphoma (ALCL), angioimmunoblastic T cell lymphoma (AITL), and other types subgroup, in accordance with pathological patterns. Based on expression of RRM1, TOP2A, TUBB3, and ERCC1, patients were divided into groups with high and low gene expression levels. Clinical characteristics, side effects, efficacy, progression-free survival (PFS), and overall survival (OS) were compared. Results: There were no significant differences in the basic clinical features or side effects between the GDPT and CHOP groups. The overall response rate (ORR) of the GDPT group was better than that of the CHOP group (66.3% versus 50.0%, p = 0.042), as was the complete remission (CR) rate (42.9% versus 27.6%, p = 0.049). Patients in the GDPT group had a longer PFS and OS than the CHOP group. The 4-year PFS and OS rates in the GDPT group were both superior to those in the CHOP group (63.6% versus 53.0% for PFS, p = 0.035; 66.8% versus 53.6% for OS, p = 0.039). In the GDPT group, the difference in CR between the four subgroups was statistically significant ( p = 0.046). In the CHOP group, differences in both CR and ORR among the four subgroups were statistically significant ( p < 0.001 and p = 0.005, respectively). There were also statistically significant differences in CR between patients treated with CHOP and GDPT in the PTCL-NOS subgroup, AITL subgroup, and the other types subgroup ( p = 0.015; p = 0.003; p = 0.005, respectively). The data also showed a significant difference in OS among the four subgroups within the GDPT group ( p = 0.001). The OS of AITL was shorter than that of the other three subgroups. Four subgroups of CHOP showed a significant difference in PFS ( p = 0.019). There was no statistical association between responses and the gene expression levels of RRM1, ERCC1, TUBB3, and TOP2A. Conclusion: The GDPT group had better response rates and prolonged patient PFS and OS. As a promising new regimen, GDPT is expected to become the first-line therapy for PTCL. New agents should be applied to patients who do not achieve good responses with previous treatment, such as those diagnosed with angioimmunoblastic T cell lymphoma. Trial registration: This open randomized prospective clinical trial was registered at ClinicalTrials.gov (NCT01664975).

scholarly journals Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation

2020 ◽  
Vol 21 (6) ◽  
pp. 1924 ◽  
Author(s):  
Limiao Jiang ◽  
Rengasamy Ramamoorthy ◽  
Srinivasan Ramachandran ◽  
Prakash P. Kumar
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Secondary Metabolism ◽  
Gene Mutation ◽  
Gene Function ◽  
Nucleotide Metabolism ◽  
Expression Levels ◽  
Rice Mutant ◽  
Choline Metabolism ◽  
Gene Expression Levels

Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the “Green Revolution”. Previously, we reported a novel semi-dwarf rice mutant (oscyp96b4) derived from the insertion of a single copy of Dissociator (Ds) transposon into the gene OsCYP96B4. However, the systems metabolic effect of the mutation is not well understood, which is important for understanding the gene function and developing new semi-dwarf mutants. Here, the metabolic phenotypes in the semi-dwarf mutant (M) and ectopic expression (ECE) rice line were compared to the wild-type (WT) rice, by using nuclear magnetic resonance (NMR) metabolomics and quantitative real-time polymerase chain reaction (qRT-PCR). Compared with WT, ECE of the OsCYP96B4 gene resulted in significant increase of γ-aminobutyrate (GABA), glutamine, and alanine, but significant decrease of glutamate, aromatic and branched-chain amino acids, and some other amino acids. The ECE caused significant increase of monosaccharides (glucose, fructose), but significant decrease of disaccharide (sucrose); induced significant changes of metabolites involved in choline metabolism (phosphocholine, ethanolamine) and nucleotide metabolism (adenosine, adenosine monophosphate, uridine). These metabolic profile alterations were accompanied with changes in the gene expression levels of some related enzymes, involved in GABA shunt, glutamate and glutamine metabolism, choline metabolism, sucrose metabolism, glycolysis/gluconeogenesis pathway, tricarboxylic acid (TCA) cycle, nucleotide metabolism, and shikimate-mediated secondary metabolism. The semi-dwarf mutant showed corresponding but less pronounced changes, especially in the gene expression levels. It indicates that OsCYP96B4 gene mutation in rice causes significant alteration in amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, and shikimate-mediated secondary metabolism. The present study will provide essential information for the OsCYP96B4 gene function analysis and may serve as valuable reference data for the development of new semi-dwarf mutants.

Outcomes of GDPT (gemcitabine, cisplatin, prednisone,thalidomide) versus CHOP in newly diagnosed peripheral T-cell lymphoma patients.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 8018-8018
Author(s):  
Ling Li ◽  
Yuanyuan Sun ◽  
Xin Li ◽  
Lei Zhang ◽  
Xinhua Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trial ◽  
T Cell ◽  
Cell Lymphoma ◽  
T Cell Lymphoma ◽  
The Other ◽  
Newly Diagnosed ◽  
Peripheral T Cell Lymphoma ◽  
Significant Difference ◽  
Gene Expression Levels

8018 Background: Peripheral T-cell lymphoma(PTCL) is highly heterogeneous invasive NHL.There is no consensus standard treatment for it now. So outcomes of GDPT versus CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) in treating newly diagnosed PTCL were compared. Methods: An open-label prospective clinical trial with 153 newly diagnosed PTCL patients conducted between January 2010 and December 2018 was designed. Patients were randomly assigned to the GDPT group (77 cases) and CHOP group (76 cases). Patients in each group were further divided into four subgroups: PTCL-NOS, ALCL, AITL, and an other types, in accordance with pathological patterns. Based on expression of RRM1, TOP2A, TUBB3 and ERCC1, patients were divided into groups with high and low gene expression levels. Clinical characteristics, side effects, efficacy, PFS and OS were compared. Results: There were no significant differences in the basic clinical features or side effects between the GDPT and CHOP groups. The ORR of the GDPT group was better than that of the CHOP group (66.3%vs. 50.0%, P= 0.042), as was the CR rate (42.9% vs. 27.6%, P= 0.049). Patients in the GDPT group had a longer PFS and OS than the CHOP group. The 4-year PFS and OS rates in the GDPT group were both superior to those in the CHOP group (63.6% vs. 53.0% for PFS, P= 0.035; 66.8% vs. 53.6% for OS, P= 0.039).In the GDPT group, the difference in CR between the four subgroups was statistically significant (P = 0.046).In the CHOP group, differences in both CR and ORR among the four subgroups were statistically significant ( P= < 0.001 and P= 0.005, respectively).There were also statistically significant differences in CR between patients treated with CHOP and GDPT in the PTCL-NOS subgroup, AITL subgroup, and the other types subgroup( P= 0.015; P= 0.003; P= 0.005, respectively).The data also showed a significant difference in OS among the four subgroups within the GDPT group ( P= 0.001).The OS of AITL was shorter than that of the other three subgroups. Four subgroups of CHOP showed a significant difference in PFS ( P= 0.019). There was no statistical association between responses and the gene expression levels of RRM1, ERCC1, TUBB3 and TOP2A. Conclusions: The GDPT group had better response rates and prolonged the patients’ PFS and OS. As a promising new regimen, GDPT is expected to become the first-line therapy for PTCL. New agents should be applied to patients who do not achieve good responses with previous treatment, such as those diagnosed with angioimmunoblastic T cell lymphoma. Clinical trial information: NCT01664975 .

scholarly journals Propranolol significantly reduced DNA polymerase β expression in patients with essential tremor

2021 ◽  
Vol 40 (3) ◽  
pp. 207-215
Author(s):  
Nefise Kandemir ◽  
Sercan Kenanoglu ◽  
Murat Gultekin ◽  
Nuriye Gokce ◽  
Hilal Akalin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Treatment Group ◽  
Dna Polymerase ◽  
Patient Group ◽  
Control Group ◽  
Expression Levels ◽  
Significant Difference ◽  
Propranolol Treatment ◽  
Pre Treatment ◽  
Gene Expression Levels

Background Essential tremor (ET) is the most common movement disorder. Propranolol is a first-line medication for ET. We aimed to evaluate the effect of propranolol on the expression of poly (ADP-ribose) polymerase 1 (PARP1) and DNA polymerase beta (POLB) genes, which are known to be related to neurodegenerative diseases, in patients with ET. MethodsThirty-five healthy volunteers and thirty-five patients followed up with essential tremors were included in a non-randomized control experimental study. Expressions of PARP1 and POLB genes were compared between the control group and the patient group. In addition, pre- and post-treatment gene expression levels and Fahn-Tolosa-Marin tremor scale values of the patient group were compared after 8 weeks of propranolol treatment. The Wilcoxon rank and Mann Whitney U tests were used to analyze the data. ResultsAt baseline, PARP1 expression was significantly lower in the ET group than in the control group. (p<0.001). POLB gene expression was significantly higher in the pre-treatment ET group than in the controls (p<0.05). There was no significant difference in PARP1 expression levels before and after 8 weeks of propranolol treatment. POLB gene expression was significantly higher in the pre-treatment group than in the post-treatment group (p<0.001). ConclusionPropranolol significantly decreased POLB gene expression but there was no significant difference in PARP1 gene expression levels in the patient group, after 8 weeks of propranolol treatment.

O-152 Investigation of the relationship of sperm motility and Kisspeptin in subfertile men

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
A Kocaman ◽  
B Ayas
Keyword(s):  
Gene Expression ◽  
Intracellular Calcium ◽  
Sperm Motility ◽  
Laser Scanning ◽  
Calcium Release ◽  
Expression Levels ◽  
Significant Difference ◽  
Motility Parameters ◽  
Gene Expression Levels

Abstract Study question Does kisspeptin administration affect the motility parameters in sperm samples of subfertile cases? Summary answer Kisspeptin administration significantly increased gene expression levels related with sperm motility as well as intracellular calcium concentrations. What is known already Sperm motility problems are among the most important causes of male infertility. In recent years, a peptide named kisspeptin has been discovered that may have effects on sperm motility. Kisspeptin is known to trigger calcium release in hypothalamic neurons. In addition, kisspeptin administration increased sperm progressive motility in studies conducted on normozoospermic individuals. Furthermore, it is suggested that kisspeptin protein in seminal plasma is positively associated with semen quality. However, there is no evidence that how kisspeptin can affect sperm in men with infertility problems. Study design, size, duration This basic research study was an in vitro experimental approach involving the use of semen samples from an infertil cases between September to December in 2020. 40 men were included in both control and experimental groups. Participants/materials, setting, methods All analyses were performed on semen samples from 10 normozoospermic (NZ), 10 asthenozoospermic (AZ), 10 oligoasthenozoospermic (OAZ) and 10 oligoastenoteratozoospermic (OATZ) men, aging between (21-40) years. Basal serum and seminal kisspeptin levels were analyzed by ELISA. Sperm were divided into two groups. Kisspeptin-13 administered in vitro. KISS1, KISS1R, CATSPER1, AKAP4 gene expressions analyzed by qRT-PCR using 2−ΔΔCt algorithm. Intracellular calcium concentration was determined with floresence spectroflurometer and laser scanning confocal microscope. Main results and the role of chance The serum kisspeptin level of NZ was significantly higher than other groups (p &lt; 0.05). The semen kisspeptin level was significantly higher than OAZ and OATZ (p &lt; 0.05), but not in NZ (p &gt; 0.05). Also, KISS1 gene expression was higher in AZ compared to other groups (p &lt; 0.05). Biochemical and gene expression analysis of kisspeptin were consistent with each other. There was a significant increase in the expression of CATSPER1 gene in AZ compared to other groups (p &lt; 0.05). Also, AKAP4 gene expression was significantly higher in OATZ compared to other groups (p &lt; 0.05). No significant difference was documented for the expression of KISS1R (p &gt; 0.05). Intracellular calcium was significantly increased in AZ and NZ after kisspeptin administration. The intracellular calcium increase is consistent with increased CATSPER1 gene expression levels in AZ. Kisspeptin administration may have a significant effect on sperm motility parameters. Limitations, reasons for caution The biochemical and gene expression levels of KISS1 were consistent. However, gene expression was explored at the mRNA level for CATSPER1 and AKAP4. The protein expression analyses of these genes may confirm the results. Also, using kisspeptin antagonists may strength the results of intracellular calcium analysis. Wider implications of the findings Kisspeptin treatment for individuals diagnosed with asthenozoospermia may have therapeutic results. KISS1 quantitation may be a determining factor for the subfertility in routine semen analysis. Trial registration number OMU KAEK 2019/462

Optimizing the use of gene expression data to predict plant metabolic pathway memberships

2020 ◽  
Author(s):  
Peipei Wang ◽  
Bethany M. Moore ◽  
Sahra Uygun ◽  
Melissa D. Lehti-Shiu ◽  
Cornelius S. Barry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathway ◽  
Prediction Models ◽  
Error Rates ◽  
Training Data ◽  
Plant Metabolites ◽  
Pathway Annotation ◽  
Pathway Expression ◽  
Gene Expression Levels ◽  
Better Than

AbstractPlant metabolites produced via diverse pathways are important for plant survival, human nutrition and medicine. However, the pathway memberships of most plant enzyme genes are unknown. While co-expression is useful for assigning genes to pathways, expression correlation may exist only under specific spatiotemporal and conditional contexts. Utilizing >600 expression values and similarity data combinations from tomato, three strategies for predicting membership in 85 pathways were explored: naive prediction (identifying pathways with the most similarly expressed genes), unsupervised and supervised learning. Optimal predictions for different pathways require distinct data combinations that, in some cases, are indicative of biological processes relevant to pathway functions. Naive prediction produced higher error rates compared with machine learning methods. In 52 pathways, unsupervised learning performed better than a supervised approach, which may be due to the limited availability of training data. Furthermore, using gene-to-pathway expression similarities led to prediction models that outperformed those based simply on gene expression levels. Our study highlights the need to extensively explore expression-based features and prediction strategies to maximize the accuracy of metabolic pathway membership assignment. We anticipate that the prediction framework outlined here can be applied to other species and also be used to improve plant pathway annotation.

Transcriptional expression of survivin and its splice variants in cervical carcinomas

2007 ◽  
Vol 17 (5) ◽  
pp. 1092-1098 ◽  
Author(s):  
H. Futakuchi ◽  
M. Ueda ◽  
K. Kanda ◽  
K. Fujino ◽  
H. Yamaguchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Splice Variants ◽  
Transcriptional Expression ◽  
Tissue Samples ◽  
Expression Levels ◽  
Cervical Carcinomas ◽  
Significant Difference ◽  
Normal Controls ◽  
Gene Expression Levels

The objective of this study was to evaluate transcriptional expression of survivin and the two splice variants (survivin-2B and survivin-ΔEx3) in cervical carcinomas. The gene expression levels of survivin and its splice variants in 11 human cervical carcinoma cell lines and 20 malignant and 12 normal cervical tissue samples were analyzed using quantitative reverse transcription–polymerase chain reaction analysis. Gene expression levels of survivin and survivin-ΔEx3 in cell lines were higher than those in normal cervical tissues (P= 0.0193 and 0.0489). Transcript levels of survivin and survivin-ΔEx3 in carcinoma tissues were also higher than those in normal controls (P= 0.0016 and 0.0011). Gene expression levels of survivin and survivin-ΔEx3 in adenocarcinomas were statistically higher than those in squamous cell carcinomas (P= 0.0260 and 0.0487). There was no significant difference in survivin-2B gene expression between malignant and normal cervical samples or different histologic types. The ratios of survivin-2B/survivin and survivin-ΔEx3/survivin in carcinoma tissues were higher than those in normal controls (P= 0.0288 and 0.0081). Interestingly, the ratio of survivin-2B/survivin was increased in the patients with higher stages and with pelvic lymph node metastasis (P= 0.0205 and 0.0437), respectively. We conclude that survivin and its splice variants might be involved in the pathogenesis and development of cervical carcinomas.

scholarly journals DNA methylation in transposable elements disrupts the connection between three-dimensional chromatin organization and gene expression upon rice genome duplication.

2021 ◽  
Author(s):  
Zhenfei Sun ◽  
Yunlong Wang ◽  
Zhaojian Song ◽  
Hui Zhang ◽  
Min Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Genome Duplication ◽  
Rice Genome ◽  
Three Dimensional ◽  
Plant Evolution ◽  
Chromatin Organization ◽  
Regulatory Sequences ◽  
Chromosome Conformation ◽  
Significant Difference

Polyploidy serves as a major force in plant evolution and domestication of cultivated crops. However, the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene expression upon rice genome duplication is largely unknown. Here we compared the 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice by high-throughput chromosome conformation capture analysis, and found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor. Moreover, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domain (TAD) and loops uncouple from gene expression. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are not related to their expressions. Importantly, in contrast to that there was no significant difference of methylation levels in TEs in promoters of differentially expressed genes (DEGs) and non-DEGs between 2C and 4C rice, we found that the hypermethylated transposable elements across genes in compartment A/B switched regions and TAD boundaries suppress the expression of these genes. We propose that the rice genome doubling might modulate TE methylation which results in the disconnection between the alteration of 3D chromatin structure and gene expression.

scholarly journals Transcriptome-Wide Gene Expression in a Murine Model of Ventilator-Induced Lung Injury

2021 ◽  
Vol 2021 ◽  
pp. 1-23
Author(s):  
Zhao Li ◽  
Guoshao Zhu ◽  
Chen Zhou ◽  
Hui Wang ◽  
Le Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Injury ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Gene Set Enrichment Analysis ◽  
Hub Genes ◽  
Qrt Pcr ◽  
Ventilator Induced Lung Injury ◽  
Significant Difference ◽  
Tf Gene

Background. Mechanical ventilation could lead to ventilator-induced lung injury (VILI), but its underlying pathogenesis remains largely unknown. In this study, we aimed to determine the genes which were highly correlated with VILI as well as their expressions and interactions by analyzing the differentially expressed genes (DEGs) between the VILI samples and controls. Methods. GSE11434 was downloaded from the gene expression omnibus (GEO) database, and DEGs were identified with GEO2R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using DAVID. Next, we used the STRING tool to construct protein-protein interaction (PPI) network of the DEGs. Then, the hub genes and related modules were identified with the Cytoscape plugins: cytoHubba and MCODE. qRT-PCR was further used to validate the results in the GSE11434 dataset. We also applied gene set enrichment analysis (GSEA) to discern the gene sets that had a significant difference between the VILI group and the control. Hub genes were also subjected to analyses by CyTargetLinker and NetworkAnalyst to predict associated miRNAs and transcription factors (TFs). Besides, we used CIBERSORT to detect the contributions of different types of immune cells in lung tissues of mice in the VILI group. By using DrugBank, small molecular compounds that could potentially interact with hub genes were identified. Results. A total of 141 DEGs between the VILI group and the control were identified in GSE11434. Then, seven hub genes were identified and were validated by using qRT-PCR. Those seven hub genes were largely enriched in TLR and JAK-STAT signaling pathways. GSEA showed that VILI-associated genes were also enriched in NOD, antigen presentation, and chemokine pathways. We predicted the miRNAs and TFs associated with hub genes and constructed miRNA-TF-gene regulatory network. An analysis with CIBERSORT showed that the proportion of M0 macrophages and activated mast cells was higher in the VILI group than in the control. Small molecules, like nadroparin and siltuximab, could act as potential drugs for VILI. Conclusion. In sum, a number of hub genes associated with VILI were identified and could provide novel insights into the pathogenesis of VILI and potential targets for its treatment.

scholarly journals Robust Biofilm-Forming Ionizing Radiation Resistant Bacillus subtilis isolated from Ramsar-Iran, Emphasis on Molecular Genetic profiling Analysis

2020 ◽  
Author(s):  
dhuha saeed ali ◽  
reza vazifehmand(Former Corresponding Author) ◽  
Yaya Rukayadi ◽  
Son Radu ◽  
Mirsasan Mirpour ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Ionizing Radiation ◽  
Biofilm Formation ◽  
Genetic Variations ◽  
Negative Control ◽  
Expression Levels ◽  
Significant Difference ◽  
Radiation Resistant ◽  
Gene Expression Levels

Abstract Background The production of structurally complex multicellular communities or biofilms is a mode of growth that is believed to require and involves a differential gene expression as compared to their planktonic counterpart. There is a poor knowledge of biofilm formation and its molecular signaling function in a radiation resistance bacteria. Therefore, the aim of the present study was to investigate the genetic variations and gene expression levels of some critical genes involved in the biofilm formation and matrix production in an ionizing-radiation-resistant B. subtilis (RAM-04) isolated from Abe-Siah hot spring, Ramsar- Iran. Bacillus subtilis DSM-10 a non-ionizing-radiation-resistant and standard strain model considered as a negative control. Results Quantification of biofilms performed using crystal violet assay and Scanning Electron Microscopy that the results presented a significant difference of a high level of the biofilm formation in terms of quantity and structure by Bacillus subtilis (RAM-04) as compared to Bacillus subtilis DSM-10. At the Molecular level, a total of 13 genes including ( tapA ) yqxM-sipW-tasA (operon), sinR , sinI , ccpA , epsA-O , spoOB , spoOA , slrA , slrR , ymcA and abrB were selected to study the genetic variations and gene expression levels using direct sequencing method and quantitative PCR technique. Primary analysis revealed genetic variations in ( tapA ) yqxM-sipW-tasA (operon), sinR , sinI , epsA-O , and slrR in B. subtilis (RAM-04) as compared to the negative control. The result of gene expression revealed a significant difference between test and control bacteria. ( tapA ) yqxM-sipW-tasA operon was significantly over expressed ( p = 0.000 with expression folding of 13, 11, 8 respectively) and the expression level of ccpA and slrR were significantly down ( p = 0.000 with expression folding of 0.2 and 0.3 respectively). Conclusions These results support the hypothesis that the induction of biofilm formation is performed by ( tapA ) yqxM-sipW-tasA operon signaling pathway, which in turn indicate that this operon has a positive role in biofilm formation in ionizing-radiation-resistant B. subtilis (RAM-04) under natural radiation environment.

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