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.
Ali Javadmanesh; Mojtaba Tahmoorespour; Fahime Mohammadi
Abstract
The formation of muscle myofibrils as well as the growth and hypertrophy of the muscle are controlled by various genes. Also, bioinformatics tools could be used to integrate and analyze heterogeneous data sets. In this study, by integrating the data obtained by expression array and RNA-Seq, related to ...
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The formation of muscle myofibrils as well as the growth and hypertrophy of the muscle are controlled by various genes. Also, bioinformatics tools could be used to integrate and analyze heterogeneous data sets. In this study, by integrating the data obtained by expression array and RNA-Seq, related to the muscle tissue transcriptome of Texel sheep respectively before and after birth, the DEGs, gene network, GO and biological pathways has been investigated. The microarray expression profile was extracted from the GEO database, and the RNA-Seq expression profile was extracted from ArrayExpress database. DEGs were identified with limma and sva software packages in R environment and a gene network was drawn with STRING, an application in Cytoscape software. The clustering and gene ontology were done with CytoCluster and ClueGO applications. The results showed a significant difference between the juvenile and 70-days embryonic stages the expression of 103 genes, between the adult and juvenile stages the expression of 28 genes and between adult and 70-days embryonic stages the expression of 62 genes. By constructing the gene network between these DEGs, a total of 37 selected genes were identified. The results revealed the function of these genes in cell proliferation, protein synthesis, formation and organization of myofibrils, muscle contraction and lipid metabolism. By integrating the expression data, this study provided a general view of the differences in transcriptomes in the muscle tissue of sheep. Also, the selected genes such as BUB1, RFC2, KIAA0101, RAD51, CKS2 and UQCRB were identified for the first time being reported as effective genes for myogenesis.
Hani Firooz-zare; Alireza Safarzade; Elahe Talebi-Garakani
Abstract
New evidence indicates that exercise training as a stimulant of adipose tissue thermogenesis can play a positive role in preventing obesity.The purpose of research is to investigate the effect of eight weeks of progressive resistance training on the levels of proteins involved in the thermogenesis of ...
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New evidence indicates that exercise training as a stimulant of adipose tissue thermogenesis can play a positive role in preventing obesity.The purpose of research is to investigate the effect of eight weeks of progressive resistance training on the levels of proteins involved in the thermogenesis of visceral and subcutaneous adipose tissues in sucrose-fed rats. Method: Twenty- four male rats were divided into normal control, sucrose control, and progressive resistance training groups. The normal control group was fed only standard food and water. In addition to free access to water and standard food, the other two groups were fed a 10% sugar solution. The exercise program started after of nutritional intervention and continued for 8 weeks, 3 days a week. After 72 hours of the last training session and 4 hours of fasting, the rats were anesthetized and blood samples and visceral and subcutaneous adipose tissues were taken. Serum glucose and insulin level and insulin resistance index along with tissue levels of PGC-1α and UCP1 were measured. Results: The results showed that the consumption of sugar solution significantly increased serum glucose (P≥0.001) and insulin (P≥0.001) levels and HOMA-IR (P≥0.001) and decreased UCP1 levels in subcutaneous fat tissue (P≥0.03) compared to the control group. Also, progressive resistance training caused a significant decrease in insulin (P≥0.007), HOMA-IR (P≥0.025), increased UCP1 levels in visceral (P≥0.032) and subcutaneous (P≥0.005) adipose tissue compared to the sucrose control group. However, the levels of PGC1α in visceral and subcutaneous fat tissues did not show any significant changes. Conclusion: The results showed that progressive resistance training, in addition to improving insulin sensitivity, can play an effective role in the process of browning white adipose tissue by increasing the level of UCP1 in visceral and subcutaneous adipose tissue, and as a therapeutic method for improving insulin resistance and obesity.
Maryam M. Matin; Heydar Khadivi; Nasrin Sasani; Halimeh Hassanzadeh; Masoud Golestanipour; Ahmad Moloodi; Vahide Sadat Ebrahimi
Abstract
Bone graft substitutes are used in the field of bone tissue engineering, orthopedics, and dentistry to help bone repair. The sterility and apyrogenicity of the bone grafts before clinical use are considered as part of the regulatory requirements, however sterilization of biomaterials is challenging due ...
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Bone graft substitutes are used in the field of bone tissue engineering, orthopedics, and dentistry to help bone repair. The sterility and apyrogenicity of the bone grafts before clinical use are considered as part of the regulatory requirements, however sterilization of biomaterials is challenging due to the physicochemical changes resulting from the localized increase in gamma dose during irradiation. The effects of gamma radiation dose on biological behaviors of synthetic bone grafts have not been extensively investigated. The purpose of the present study was to evaluate the effects of gamma radiation sterilization doses on OsvehOss synthetic bone grafts via chemical, mechanical and in vitro biological examinations.
Methods: XRD analysis and compression test were carried out to evaluate the chemical and mechanical changes of synthetic bone grafts induced by the highest gamma radiation dose applied in this study. Human osteosarcoma MG-63 cells were used to assay their osteogenic response while grown on a biphasic (60HA/40TCP) bone graft substitute. Cell attachment and proliferation were confirmed via scanning electron microscopy (SEM) on days 3, 7 and 14 of culture. Alkaline phosphatase (ALP) activity was determined to assess osteogenesis. Alizarin red S (ARS) staining was also used to identify calcium deposition in osteocytes developed after differentiation of MG-63 cells.
Results and Conclusion: Our results illustrated that gamma irradiation did not cause dose-dependent changes in chemical and mechanical properties of OsvehOss BCP bone grafts when the doses increased up to 50 kGy. Furthermore, OsvehOss BCP samples demonstrated high osteoconductivity in all irradiation treatment groups. ALP and ARS analyses also indicated that application of irradiation doses up to 50 kGy for sterilization of OsvehOss BCP grafts had no significant effects on osteogenesis and calcium deposition in osteoblast cells cultured on grafts. In conclusion, OsvehOss biomaterials can be sterilized safely for biomedical applications.
Fereshteh Jozaghkar; Abasalt Hosseinzadeh Colagar; Mohammadreza Hosseinzadeh; Faramarz Mehrnejad; Emadoddin Moudi
Abstract
Prostate neoplasm, 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 neoplasm, 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. In this study, the association of HNF1B-rs4794758 and LMTK2-rs7791463 polymorphisms with prostate cancer and benign prostatic hyperplasia was investigated 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.
Robabeh Golestani; Masoumeh Mehraban Sang Atash; Najme Gord Noshahri; Mohammad Zare Mehrjerdi; Yaser Yousefpoor
Abstract
The demand for bioethanol as a renewable energy source is rising. This study was screened high-ethanol-producing microorganisms found in grapes to reduce production costs and compete with other fuels. .
The grapes and their waste samples were collected from Iranian vineyards. Microorganisms were initially ...
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The demand for bioethanol as a renewable energy source is rising. This study was screened high-ethanol-producing microorganisms found in grapes to reduce production costs and compete with other fuels. .
The grapes and their waste samples were collected from Iranian vineyards. Microorganisms were initially screened by growing them in a glucose-enriched culture medium containing 10% ethanol to isolate ethanol-tolerant ones. The bioethanol-producing microorganisms were then qualitatively isolated during fermentation using high-throughput screening (HTS) based on CO2 production and changing bromothymol blue to green color. Promising strains were selected based on the amount of ethanol production by the CO2 flow meter. The selected strains were identified using 18S rRNA sequencing and PCR by the S. cerevisiae species-specific primers (ScHO). Finally, the growth of the most promising strain was optimized using the response surface methodology (RSM) in a shaking incubator.
A total of one hundred isolates were tested using HTS devices. Out of these, nine strains were quantitatively screened, and SCL-25 and SCL-62 were chosen to continue based on their high ethanol production rate. The ethanol production rate for SCL-25 was 12.86%, while SCL-62 was 14.35%. After molecular characterization, it was confirmed that SCL-25 was 100% similar to Saccharomyces cerevisiae, whereas SCL-62 was 99% similar to Saccharomyces cerevisiae. The PCR products amplified by ScHO showed a 400 bp band in agarose gel electrophoresis, confirming them as S. cerevisiae. Moreover, isolate SCL-62 showed ethanol production higher than the commercial strain. The RSM optimization results showed that the growth of the SCL-62 strain increased two times at 35 °C, pH 5.0, Brix degree 20, and agitation rate 200 rpm. Therefore, the SCL-62 strain has the potential to produce efficient and cost-effective bioethanol.
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.
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