Mohammad Nasrabadi; Faezeh Berenjkar; Maryam Hashemabadi; Mahdi Askari; Gholamreza Hashemitabar
Abstract
Escherichia coli is reported as the most common organism in humams and animals and introduced as a critical priority bacterium due to antibiotic resistance according to World Health Organization. The multi drug resistant (MDR) and Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli stains have ...
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Escherichia coli is reported as the most common organism in humams and animals and introduced as a critical priority bacterium due to antibiotic resistance according to World Health Organization. The multi drug resistant (MDR) and Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli stains have become a global health challenge worldwide since the related infections are difficult to treat. Poultry has been considered as an important reservoir of E. coli, can play an important role in transmitting these strains to humans. The objective of this study was to determine the prevalence of ESBL-producing and MDR E. coli isolated from poultry and their association with different phylogroups. The current study was conducted on a collection of 100 E. coli isolates from colibacillosis in poultry. Antimicrobial susceptibility testing, ESBL production, the prevalence of ESBL-mediated genes (blaTEM, blaSHV, blaOXA, and blaCTX-M) were assessed and phylogenetic groups were analyzed using the Clermont 2013 and 2019 updated methods. The highest resistance was against tetracycline (88%), trimethoprim/sulfamethoxazole (86%), and chloramphenicol (70%). Also, the frequency of ESBL-production and MDR was (41%) and (70%), respectively. The blaTEM was the most prevalent gene among isolates with a frequency of 48%. Phylogroup analysis assigned E. coli isolates to B1 (23%), D (22%), A (10%), G (11%), F (8%), B2 (5%), and C (4%). Applying antimicrobial stewardship is critical because the circulation of ESBL-producing E. coli and MDR isolates threatens medicine and veterinary. In addition, our results revealed the noticeable prevalence of the novel phylogroup G in poultry for the first time in Iran.
Fereshteh Jozaghkar; Abasalt Hosseinzadeh Colagar; Mohammadreza Hosseinzadeh; Faramarz Mehrnejad; Emadoddin Moudi
Abstract
Prostate neoplasms, such as prostate cancer and benign prostatic hyperplasia, are complex and heterogeneous diseases that are caused by environmental, metabolic, and genetic factors. Various reports showed the relationship of several genes, including the HNF1B and LMTK2 genes, in the occurrence of prostate ...
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Prostate neoplasms, such as prostate cancer and benign prostatic hyperplasia, are complex and heterogeneous diseases that are caused by environmental, metabolic, and genetic factors. Various reports showed the relationship of several genes, including the HNF1B and LMTK2 genes, in the occurrence of prostate cancer. This study investigated the association of HNF1B-rs4794758 and LMTK2-rs7791463 polymorphisms with prostate cancer and benign prostatic hyperplasia in a case-control study, followed by bioinformatics analysis. For this purpose, blood samples were collected from 70 healthy men, 58 men with benign prostatic hyperplasia (positive digital rectal examination or DRE and PSA levels below 4 ng/mL), and 70 men with prostate cancer (positive DRE, PSA levels above 4 ng/mL, and diagnoses confirmed by pathological findings). These men were referred to Shahid Beheshti Hospital in Babol. After genomic DNA extraction, the genotype was determined using PCR-RFLP. A genotypic and allelic analysis revealed that the rs4794758 polymorphism with AA genotype (OR: 4.808, 95%CI: 1.260-18.348, P= 0.022) had a significant difference between the prostate cancer group and the benign prostatic hyperplasia group compared to the control group. Allele A of this polymorphism was also significantly associated with prostate cancer (OR: 1.705, 95%CI: 1.055-2.755, P= 0.030). However, there was no correlation between different genotypes of the rs7791463 polymorphism with prostate cancer and benign prostatic hyperplasia. Bioinformatics analysis by some online servers and software showed that the rs4794758 polymorphism possibly changes the hnRNA splicing pattern. So, this polymorphism could probably provide a locus for the TBP transcription factor. In addition, the rs7791463 polymorphism potentially alters the hnRNA splicing pattern and changes the reading frame. Based on the data, HNF1B-rs4794758 polymorphism is associated with prostate cancer susceptibility, which can be considered a molecular risk factor in future studies.
Seyed Morteza Babamir; Shima amirsadri; Shahyar Arab
Abstract
The protein’s motifs (called super secondary structures) are dense three-dimensional structures of proteins consisting of a number of secondary structures in a specific geometric arrangement. The prediction of motifs is a matter of concern and has been studied. The previous studies dealt with the motif ...
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The protein’s motifs (called super secondary structures) are dense three-dimensional structures of proteins consisting of a number of secondary structures in a specific geometric arrangement. The prediction of motifs is a matter of concern and has been studied. The previous studies dealt with the motif prediction based on the polypeptide chain; however, the prediction of motifs based on the secondary structures leads to more accurate prediction. This study aims to address such a prediction. First, a number of secondary structures are constructed and then, based on the energy level and using a metaheuristic (evolutionary) algorithm called Imperialist Competitive Algorithm) (ICA) the protein’s motifs are predicted. The advantage of our approach over existing approaches is that secondary structural data as input of our algorithm leads to a more accurate prediction that is closer to the real protein third than previous algorithms. We applied our method to predict super secondaries of enzyme β−LACTAMASE whose specification was obtained from the PDB file in Yasara. This enzyme is produced by bacteria and provides multi-resistance to antibiotics β−LACTAMA. Then we evaluated our prediction using Root-Mean-Square Deviation (RMSD). It shows the average distance between the two proteins structurally having the same alignment. Having determined the structural alignment of the two proteins, we determined the similarity of their 3D structures using RMSD. If RMSD between two structures is less than 2, it denotes they are very similar. Accordingly, we used RMSD to show how much similarity exists between the motif obtained by our proposed algorithm for β−LACTAMASE and its native structure.
Ali Javadmanesh; Atefe Paknafs; Marjan Azghandi
Abstract
Rotavirus infections impose a significant global health burden, particularly affecting infants and young children and causing severe gastroenteritis . To combat this viral pathogen , there is a growing interest in exploring the therapeutic potential of lactoferrins derived from different farm animal ...
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Rotavirus infections impose a significant global health burden, particularly affecting infants and young children and causing severe gastroenteritis . To combat this viral pathogen , there is a growing interest in exploring the therapeutic potential of lactoferrins derived from different farm animal milk as antiviral agents. This study employed molecular simulation techniques to investigate the intricate binding mechanisms between different animal milk lactoferrins and rotavirus, providing insights into their molecular interactions . These animals were including cow , sheep , camel , goat , horse , buffalo in addition to human . Molecular dynamics simulation techniques were employed using Gromacs software to simulate the interaction between animal milk lactoferrins and rotavirus. Precise computational models and simulations were conducted to investigate the binding mechanisms and identify critical amino acid residues involved.Our findings indicate that cow lactoferrin exhibits superior interaction with rotavirus compared to other lactoferrin sources . We identified specific binding sites and crucial amino acid residues responsible for these interactions . These results provide insights into the molecular determinants governing the binding affinity and specificity of lactoferrins towards rotavirus. This study offers valuable insights for the design of targeted antiviral strategies against rotavirus infections . Animal milk lactoferrins , particularly cow lactoferrin , demonstrated a promising potential as an antiviral agent against retroviruses. These findings enhanced our understanding of the molecular mechanisms underlying lactoferrin - mediated antiviral activity, paving the way for future experimental and clinical investigations in this field and supporting the development of efficient antiviral therapeutics against rotavirus.
Ali Javadmanesh; Mitra Riasi
Abstract
TGF-β group member myostatin (MSTN) inhibits the growth and differentiation of skeletal muscle. It is unknown that how total inhibition of MSTN restricts the hyperproliferation of muscle cells, though. This study aimed to determine the differentially expressed genes and biological pathways associated ...
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TGF-β group member myostatin (MSTN) inhibits the growth and differentiation of skeletal muscle. It is unknown that how total inhibition of MSTN restricts the hyperproliferation of muscle cells, though. This study aimed to determine the differentially expressed genes and biological pathways associated with myostatin in mouse C2C12 myogenic cells and skeletal muscle tissue utilizing high throughput mRNA expression data. In both tissue and cell line, two experimental groups were compared including wild-type vs. MSTN-Knockout. Transcriptome data were extracted from GEO and analyzed using the LIMMA package in R environment, and GEO2R. Significant differentially expressed genes were considered as False discovery rate < 0.05 with log fold change > |0.5|. Lastly, the possible biological pathways were examined with KEGG database and the protein-protein interaction (PPI) network was created using Cytoscape software. To find key genes in the PPI network, a topological analysis was conducted using the Network analyzer tool in Cytoscape software. The total number of differentially expressed genes was 14549 for C2C12 cell line and 45267 for mouse skeletal muscle tissue; among them 235 and 1425 transcripts were significant. The comparison between these two DEG lists showed that 49 genes were common between myogenic C2C12 cell and skeletal muscle tissue. Additionally, three biological pathways between the C2C12 cell line and the skeletal muscle tissue were in common and they were associated to the decrease of MSTN gene expression including: hypertrophic cardiomyopathy, Axon guidance, and dilated cardiomyopathy. These pathways were all related to muscle tissue. Despite the large number of DEGs, only 49 were in common in tissue and cell line; this could indicate that comparing a tissue with its relevant cell line at transcriptome level might not be precise enough to draw a solid conclusion. This is due to the nature of cell heterogeneity of most tissues including skeletal muscle.
Fariba Mahmoudi; Khadijeh Haghighat; Homayoun Khazali
Abstract
Abstract
Stress is one of the most prevalent types of mental illnesses. Chrysin is a phytochemical compound with anti-stress effects. However, molecular mechanisms of its anxiolytic effects have not been studied. The present study aimed to investigate the gene expression of hypothalamic phoenixin and ...
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Abstract
Stress is one of the most prevalent types of mental illnesses. Chrysin is a phytochemical compound with anti-stress effects. However, molecular mechanisms of its anxiolytic effects have not been studied. The present study aimed to investigate the gene expression of hypothalamic phoenixin and nesfatin-1 in a rat model of acute stress treated with chrysin. In the study, twenty male Wistar rats weighing 200 ± 10 g were split up into four groups (n=5). For the third cerebral ventricle injection, cannulation was done in the skull. After one week of recovery, the rats were subjected to two hours of acute restraint stress. The control and stress groups received saline. Also, two stressed groups were given 20 or 40 µg of chrysin via the third cerebral ventricle, respectively. Hypothalamic samples were removed. Then, RNA was extracted. In the next step, cDNA was synthesized. Finally, relative gene expression was assessed by a real-time polymerase chain reaction (PCR). The results showed that, the mRNA levels of nesfatin-1 significant increase in the stressed rats in comparison to the control group. The mRNA level of nesfatin-1 in the chrysin-treated group was significantly reduced compared to the stressed group. Furthermore, the stressed rats showed a significant decrease in mRNA levels of phoenixin in comparison to the control group. There was no significantly increase in the mRNA level of phoenixin between the stressed group and the group receiving chrysin. In conclusion, down- regulation of the hypothalamic nesfatin may be involved in the mediating anti-anxiety effects of chrysin.
Ali Javadmanesh; Amir Rashid Lamir; Mitra Riasi; مهرداد موحد نسب; نازیلا دردمه; Elnaz Karbaschian; Kasra Kayyami; Helia Khayyami
Abstract
The growth and development of skeletal muscle tissue is largely regulated by myostatin during the tissue development in embryos. This tissue may overgrow if there is a deficiency in myostatin expression. Gene expression may be regulated in a particular way by oligonucleotide antisense molecules. It has ...
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The growth and development of skeletal muscle tissue is largely regulated by myostatin during the tissue development in embryos. This tissue may overgrow if there is a deficiency in myostatin expression. Gene expression may be regulated in a particular way by oligonucleotide antisense molecules. It has been demonstrated that a new DNA-based oligonucleotide can down-regulate myostatin expression in a rat model. The purpose of this work was to evaluate the impact of a DNAi-based myostatin inhibitor on the vesceral fat and leg muscle weights of Wistar rats undergoing strength training. Three groups of male rats, with an average weight of 203g ± 10.5, were chosen at four weeks of age. These cohorts comprised: 1) DNAi group had resistance training in addition to receiving 10 mg/kg of rat body weight of DNAi. 2) Resistance exercise and saline injection group Group for injection of saline. Then, weight measurements for the carcass, heart, liver, left kidney, right kidney, spleen, visceral fat, twin muscles, soleus muscle, and left leg were made for each group. Histological assessment on soleus muscle section was performed. One-way ANOVA was then used to examine the results and means were compared using Tukey’s test. As the data show, the proposed molecule did not significantly contribute to an increase in body weight, in contrast to previous assumptions. Nonetheless, the twin muscle's relative and absolute weights increased significantly with and visceral fat decreased with DNAi injection (P<0.05). Although weekly body weight increase and the final weights were not affected by DNAi injection, it could be explained by loosing fat tissue during experiment. This molecule is promising in increasing muscle tissue grow however further prolonged experiments and evaluating myostatin gene expression is recommended in future experiments.
