Hepatotoxicity is a serious side effects of cyclophosphamide. Thus, the present research investigates the protective properties of sitagliptin against cyclophosphamide-induced hepatotoxicity. Fifty male rats were randomly divided into five groups. They were pre-treated with either sitagliptin or normal saline once a day for the first ten days of the study. To induce acute hepatotoxicity, cyclophosphamide (200 mg/kg, i.p) was injected only one time and 45 min after the last dose of sitagliptin. The rats were sacrificed on the 11th day, and their blood and liver were collected for biochemical, gene expression, and histopathological assessments. Our results showed that cyclophosphamide induced obvious liver toxicity as marked by an increase in serum levels of alanine transaminase and aspartate transaminase, reduced serum albumin and total protein levels, in addition to histopathological changes. The malondialdehyde, tumor necrosis factor-α, and interleukin-6 levels were also elevated and total antioxidant capacity declined in serum and hepatic homogenates. Sitagliptin magnificently attenuated the cylophosphamide-induced histological alterations, improved liver function tests, enhanced total antioxidant capacity, and decreased malondialdehyde, tumor necrosis factor-α, and interleukin-6 in the blood and hepatic tissues. These findings suggest that sitagliptin has hepatoprotective activity against cyclophosphamide toxicity, which may be due to its antioxidant and anti-inflammatory effects.
{"title":"The hepatoprotective effects of sitagliptin against cyclophosphamide-induced hepatotoxicity in rat.","authors":"Reza Maleki, Mohammad Foad Noorbakhsh, Nasrin Kazemipour, Maliheh Masoudian, Fatemeh Namazi, Saeed Nazifi","doi":"10.22099/mbrc.2024.49925.1964","DOIUrl":"10.22099/mbrc.2024.49925.1964","url":null,"abstract":"<p><p>Hepatotoxicity is a serious side effects of cyclophosphamide. Thus, the present research investigates the protective properties of sitagliptin against cyclophosphamide-induced hepatotoxicity. Fifty male rats were randomly divided into five groups. They were pre-treated with either sitagliptin or normal saline once a day for the first ten days of the study. To induce acute hepatotoxicity, cyclophosphamide (200 mg/kg, i.p) was injected only one time and 45 min after the last dose of sitagliptin. The rats were sacrificed on the 11th day, and their blood and liver were collected for biochemical, gene expression, and histopathological assessments. Our results showed that cyclophosphamide induced obvious liver toxicity as marked by an increase in serum levels of alanine transaminase and aspartate transaminase, reduced serum albumin and total protein levels, in addition to histopathological changes. The malondialdehyde, tumor necrosis factor-α, and interleukin-6 levels were also elevated and total antioxidant capacity declined in serum and hepatic homogenates. Sitagliptin magnificently attenuated the cylophosphamide-induced histological alterations, improved liver function tests, enhanced total antioxidant capacity, and decreased malondialdehyde, tumor necrosis factor-α, and interleukin-6 in the blood and hepatic tissues. These findings suggest that sitagliptin has hepatoprotective activity against cyclophosphamide toxicity, which may be due to its antioxidant and anti-inflammatory effects.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-01DOI: 10.22099/MBRC.2024.48801.1899
S A Smiline Girija
Epigenetic mechanisms attribute to the resistance and virulence of Acinetobacter baumannii sparking a renewed area of research. Unveiling the targets pertained to the epigenetic modulation in the bacterium would aid in the curbing its complications in various recalcitrant infections. This review thus throws light on the various epigenetic mechanisms exhibited by A. bauamnnii, urging the need to implement epigenetic based novel strategies in precision medicine.
{"title":"Hijacking the epigenetic mechanisms of <i>A. baumannii</i>.","authors":"S A Smiline Girija","doi":"10.22099/MBRC.2024.48801.1899","DOIUrl":"https://doi.org/10.22099/MBRC.2024.48801.1899","url":null,"abstract":"<p><p>Epigenetic mechanisms attribute to the resistance and virulence of <i>Acinetobacter baumannii</i> sparking a renewed area of research. Unveiling the targets pertained to the epigenetic modulation in the bacterium would aid in the curbing its complications in various recalcitrant infections. This review thus throws light on the various epigenetic mechanisms exhibited by <i>A. bauamnnii</i>, urging the need to implement epigenetic based novel strategies in precision medicine.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10946551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Preeclampsia (PE) is one of the serious complications of pregnancy and its exact etiology is unknown. Inflammasomes are multiportion complexes whose relation with PE has been described. Evidence showed the effect of NLRP3 inflammasome in PE pathogenesis. In the current study, we investigated the possible impacts of NLRP3 polymorphisms on PE. A total of 252 PE and 258 control pregnant women were selected for the study. The PCR-RFLP method was employed to genotype rs10754558 and rs4612666 polymorphisms. The RNAsnp and SpliceAid 2 software were used for in silico analysis. There was no relationship between NLRP3 polymorphisms and PE. In comparison to control women, the NLRP3 rs10754558 could increase the risk of severe PE in codominant and dominant models (OR=1.89, 95% CI=1.19-3.01, P=0.012, OR=1.95, 95% CI=1.24-3.06, P=0.0037, respectively). The findings of the in silico analysis revealed the effects of rs10754558 C to G and rs4612666 C to T substitutions on protein binding sites and rs10754558 C to G substitution on secondary RNA structure. These findings could confirm the finding those studies reported the impacts of these variants on various diseases. In conclusion, the NLRP3 rs10754558 variant was associated with an increased risk of EOPE and severe PE.
子痫前期(PE)是妊娠期严重并发症之一,其确切病因尚不清楚。炎症小体是一种多比例复合体,它与子痫前期的关系已被描述。有证据显示,NLRP3 炎症小体在 PE 发病机制中起作用。在本研究中,我们调查了 NLRP3 多态性对 PE 的可能影响。研究共选取了 252 名 PE 孕妇和 258 名对照组孕妇。采用 PCR-RFLP 方法对 rs10754558 和 rs4612666 多态性进行基因分型。采用 RNAsnp 和 SpliceAid 2 软件进行硅分析。NLRP3 多态性与 PE 之间没有关系。与对照组女性相比,NLRP3 rs10754558 可在显性和隐性模型中增加严重 PE 的风险(OR=1.89,95% CI=1.19-3.01,P=0.012;OR=1.95,95% CI=1.24-3.06,P=0.0037)。硅学分析结果显示,rs10754558 C 到 G 和 rs4612666 C 到 T 的置换对蛋白质结合位点有影响,而 rs10754558 C 到 G 的置换对二级 RNA 结构有影响。这些研究结果证实了这些变异对各种疾病的影响。总之,NLRP3 rs10754558变异与EOPE和重症PE风险增加有关。
{"title":"The effects of <i>NLRP3</i> rs10754558 and rs4612666 polymorphisms on preeclampsia susceptibility, onset, and severity: a case-control study and in silico analysis.","authors":"Mahnaz Rezaei, Marzieh Ghasemi, Mohsen Saravani, Rahele Ghasemian- Moghadam, Hossein Shahraki-Ghadimi, Mahtab Norouzi, Saeedeh Salimi","doi":"10.22099/mbrc.2024.49510.1936","DOIUrl":"10.22099/mbrc.2024.49510.1936","url":null,"abstract":"<p><p>Preeclampsia (PE) is one of the serious complications of pregnancy and its exact etiology is unknown. Inflammasomes are multiportion complexes whose relation with PE has been described. Evidence showed the effect of NLRP3 inflammasome in PE pathogenesis. In the current study, we investigated the possible impacts of <i>NLRP3</i> polymorphisms on PE. A total of 252 PE and 258 control pregnant women were selected for the study. The PCR-RFLP method was employed to genotype rs10754558 and rs4612666 polymorphisms. The RNAsnp and SpliceAid 2 software were used for in silico analysis. There was no relationship between <i>NLRP3</i> polymorphisms and PE. In comparison to control women, the <i>NLRP3</i> rs10754558 could increase the risk of severe PE in codominant and dominant models (OR=1.89, 95% CI=1.19-3.01, P=0.012, OR=1.95, 95% CI=1.24-3.06, P=0.0037, respectively). The findings of the in silico analysis revealed the effects of rs10754558 C to G and rs4612666 C to T substitutions on protein binding sites and rs10754558 C to G substitution on secondary RNA structure. These findings could confirm the finding those studies reported the impacts of these variants on various diseases. In conclusion, the <i>NLRP3</i> rs10754558 variant was associated with an increased risk of EOPE and severe PE.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11194025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141446620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-01DOI: 10.22099/mbrc.2024.49125.1989
Shamimeh Validi, Iraj Saadat
Gastric cancer is one of the most prevalent malignancies in the world. Various factors play a role in the development of this disease as risk factors. One of these genes is the FOXP3, which is located on the short arm of the X chromosome (Xp11.23). The rs3761548 polymorphism in the promoter region of this gene increases cell proliferation. In the current study, the association between this genetic polymorphism and the risk of gastric cancer was investigated. This study included 147 patients (55 women, 92 men) with gastric cancer and 147 healthy individuals (53 women, 94 men). The PCR-RFLP method is used for genotyping. Statistical analysis showed that there was no significant association between this polymorphism and the risk of gastric cancer. However, the analysis of genotype, family history and smoking risk factors simultane-oussly revealed a significant relationship between simultaneous occurrence of two (OR=3.79, 95% CI=1.77-8.09, p=0.001) and three risk factors (OR=6.44, 95% CI=1.76-23.5, p=0.017) and the risk of gastric cancer.
{"title":"Association between rs3761548 polymorphism of <i>FOXP3</i> and the risk of gastric cancer: a case-control study.","authors":"Shamimeh Validi, Iraj Saadat","doi":"10.22099/mbrc.2024.49125.1989","DOIUrl":"10.22099/mbrc.2024.49125.1989","url":null,"abstract":"<p><p>Gastric cancer is one of the most prevalent malignancies in the world. Various factors play a role in the development of this disease as risk factors. One of these genes is the <i>FOXP3</i>, which is located on the short arm of the X chromosome (Xp11.23). The rs3761548 polymorphism in the promoter region of this gene increases cell proliferation. In the current study, the association between this genetic polymorphism and the risk of gastric cancer was investigated. This study included 147 patients (55 women, 92 men) with gastric cancer and 147 healthy individuals (53 women, 94 men). The PCR-RFLP method is used for genotyping. Statistical analysis showed that there was no significant association between this polymorphism and the risk of gastric cancer. However, the analysis of genotype, family history and smoking risk factors simultane-oussly revealed a significant relationship between simultaneous occurrence of two (OR=3.79, 95% CI=1.77-8.09, p=0.001) and three risk factors (OR=6.44, 95% CI=1.76-23.5, p=0.017) and the risk of gastric cancer.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-01DOI: 10.22099/mbrc.2024.49840.1954
Deepu Mathew, Ravisankar Valsalan, M Shijili
Multidrug and Toxic Compound Extrusion (MATE) proteins are responsible for the transport of a wide range of metabolites out of plant cells. This helps to protect the cells from toxins and other harmful compounds. MATE proteins also play a role in plant development, by regulating the transport of hormones and other signalling molecules. They transport a wide variety of substances, including organic acids, plant hormones, flavonoids, alkaloids, terpenes and other secondary metabolites. MATE proteins are thought to play similar roles in Coriander, in addition to stress responses. The MATE genes in the coriander genome have been identified and characterized. Detailed genome homology search and domain identification analysis have identified 91 MATE proteins in the genome assembly of coriander. A phylogenetic analysis of the identified proteins divided them into five major clades. The functions of the transporters in each cluster were predicted based on the clustering pattern of the functionally characterized proteins. The amino acid sequences, exon-intron structures and motif details of all the 91 proteins are identified and described. This is the first work on the MATE transporters in coriander and the results deliver clues for the molecular mechanisms behind the stress responses and secondary metabolite transport in coriander.
{"title":"Genome-wide mining and characterization of MATE transporters in Coriandrum sativum L.","authors":"Deepu Mathew, Ravisankar Valsalan, M Shijili","doi":"10.22099/mbrc.2024.49840.1954","DOIUrl":"10.22099/mbrc.2024.49840.1954","url":null,"abstract":"<p><p>Multidrug and Toxic Compound Extrusion (MATE) proteins are responsible for the transport of a wide range of metabolites out of plant cells. This helps to protect the cells from toxins and other harmful compounds. MATE proteins also play a role in plant development, by regulating the transport of hormones and other signalling molecules. They transport a wide variety of substances, including organic acids, plant hormones, flavonoids, alkaloids, terpenes and other secondary metabolites. MATE proteins are thought to play similar roles in Coriander, in addition to stress responses. The MATE genes in the coriander genome have been identified and characterized. Detailed genome homology search and domain identification analysis have identified 91 MATE proteins in the genome assembly of coriander. A phylogenetic analysis of the identified proteins divided them into five major clades. The functions of the transporters in each cluster were predicted based on the clustering pattern of the functionally characterized proteins. The amino acid sequences, exon-intron structures and motif details of all the 91 proteins are identified and described. This is the first work on the MATE transporters in coriander and the results deliver clues for the molecular mechanisms behind the stress responses and secondary metabolite transport in coriander.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11194028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141446618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To investigate the effects of thymidylate synthase (TS) 3'UTR genotype on promotor methylation of tumor-related genes in 22 patients with sporadic colorectal cancer (CRC) from southern Iran. We evaluated the correlations of TS 3'UTR genotype with promoter methylation of hTERT, hMLH1, MSH2, MMP2, CDH1, p14, p16, and p21 genes in CRC patients. The polymorphism of TS 3'UTR was evaluated through mutagenically specific PCR. The genes promoter methylation was determined using methylation-specific PCR. For 10 patients, the gene expression profile of epigenetic regulating enzymes, histone deacetylases (HDACs) and DNA methyltransferases(DNMTs), was also examined in both tumor and normal adjacent tissues by quantitative real time PCR. There was a significant association between the hMLH1 methylation and age of patients (P= 0.039) and also between MSH2 methylation and tumor site (P= 0.036). There was insignificant association between gene-specific methylation and TS 3'UTR genotype. However, all polymorphic genotypes of TS were associated with higher methylation of hMLH1 and CDH1 and lower methylation of MSH2. The -6bp/+6bp (heterozygous mutant) and [-6bp/+6bp, +6bp/+6bp] (homozygous mutant) genotypes resulted in higher methylation of p16, and -6bp/+6bp and [-6bp/+6bp, +6bp/+6bp] genotypes were correlated with lower methylation of MMP2. The overexpression of epigenetic enzymes, HDACs and DNMTs, was also demonstrated. There was no association between DNMTs transcript levels and gene-specific hypermethylation. The polymorphic TS genotypes, especially -6bp/+6bp, could affect methylation frequencies of studied genes. Moreover, promoter methylation status was not dependent on DNMTs gene expression. Large sample size studies may contribute to validate these findings.
{"title":"The effects of thymidylate synthase 3'UTR genotype on methylation of tumor-specific genes promoter in 22 colorectal cancer patients from southern Iran.","authors":"Maryam Niknam, Fakhraddin Naghibalhossaini, Mozhdeh Zamani, Seyed Vahid Hosseini, Pooneh Mokarram","doi":"10.22099/mbrc.2023.48009.1850","DOIUrl":"https://doi.org/10.22099/mbrc.2023.48009.1850","url":null,"abstract":"<p><p>To investigate the effects of <i>thymidylate synthase (TS)</i> 3'UTR genotype on promotor methylation of tumor-related genes in 22 patients with sporadic colorectal cancer (CRC) from southern Iran. We evaluated the correlations of <i>TS</i> 3'UTR genotype with promoter methylation of <i>hTERT, hMLH1, MSH2, MMP2, CDH1, p14, p16,</i> and <i>p21</i> genes in CRC patients. The polymorphism of <i>TS</i> 3'UTR was evaluated through mutagenically specific PCR. The genes promoter methylation was determined using methylation-specific PCR. For 10 patients, the gene expression profile of epigenetic regulating enzymes, <i>histone deacetylases (HDACs)</i> and <i>DNA methyltransferases</i> <i>(DNMTs),</i> was also examined in both tumor and normal adjacent tissues by quantitative real time PCR. There was a significant association between the <i>hMLH1</i> methylation and age of patients (<i>P</i>= 0.039) and also between <i>MSH2</i> methylation and tumor site (<i>P</i>= 0.036). There was insignificant association between gene-specific methylation and <i>TS</i> 3'UTR genotype. However, all polymorphic genotypes of <i>TS</i> were associated with higher methylation of <i>hMLH1</i> and <i>CDH1</i> and lower methylation of <i>MSH2</i>. The -6bp/+6bp (heterozygous mutant) and [-6bp/+6bp, +6bp/+6bp] (homozygous mutant) genotypes resulted in higher methylation of <i>p16</i>, and -6bp/+6bp and [-6bp/+6bp, +6bp/+6bp] genotypes were correlated with lower methylation of <i>MMP2</i>. The overexpression of epigenetic enzymes, <i>HDACs</i> and <i>DNMTs,</i> was also demonstrated. There was no association between DNMTs transcript levels and gene-specific hypermethylation. The polymorphic TS genotypes, especially -6bp/+6bp, could affect methylation frequencies of studied genes. Moreover, promoter methylation status was not dependent on <i>DNMTs</i> gene expression. Large sample size studies may contribute to validate these findings.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10946552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The use of a combination of three-drug regimen has improved HIV-1 infected patients' life span and quality; however the emergence of drug-resistant strains remains a main problem. Reverse transcriptase inhibitors (RTIs) consist of a main part of highly active anti-retroviral therapy (HAART) regimen. The present study aimed to investigate resistant mutations to RTI drugs in both treatment naïve and under treatment HIV patients in Mashhad city, north-eastern Iran. RNA was extracted from sera of 22 treatment naïve and 22 under treatment patients. The mean age of under treated and treatment naive groups were 38.5±6.7 and 40.8±7.9 respectively. cDNA was synthesized and amplified with Nested PCR assay targeting specific sequences of RT gene. The PCR products were sent for sequencing. Bidirectional sequencing results were analysed using HIV drug resistance database supplied by Stanford University (HIV Drug Resistance Database, https://hivdb.stanford.edu). Among under treatment patients 10 out of 22 (45%) had at least one high-level resistance mutation which was higher than high level resistance mutation rate among treatment naive cases (P<0.01). Detected resistance mutations were as follows: K101E, K103N, K103E, V106M, V108I, E138A, V179T, Y181C, M184V, Y188L, Y188H, Y188F, G190A, L210W, T215F, T215Y, K219Q, and P225H. A high level of resistance mutations to RT inhibitors was observed that causes drug resistance especially against lamivudine (3TC). Such mutations should be considered as probable responsible for therapeutic failure. Serial surveillance studies of circulating drug resistance mutations are recommended.
{"title":"A survey of resistance mutations to reverse transcriptase inhibitors (RTIs) among HIV-1 patients in northeast of Iran.","authors":"Zahra Mazaheri, Sahar Tahaghoghi-Hajghorbani, Kazem Baesi, Kiarash Ghazvini, Saeid Amel-Jamehdar, Masoud Youssefi","doi":"10.22099/mbrc.2024.48729.1895","DOIUrl":"10.22099/mbrc.2024.48729.1895","url":null,"abstract":"<p><p>The use of a combination of three-drug regimen has improved HIV-1 infected patients' life span and quality; however the emergence of drug-resistant strains remains a main problem. Reverse transcriptase inhibitors (RTIs) consist of a main part of highly active anti-retroviral therapy (HAART) regimen. The present study aimed to investigate resistant mutations to RTI drugs in both treatment naïve and under treatment HIV patients in Mashhad city, north-eastern Iran. RNA was extracted from sera of 22 treatment naïve and 22 under treatment patients. The mean age of under treated and treatment naive groups were 38.5±6.7 and 40.8±7.9 respectively. cDNA was synthesized and amplified with Nested PCR assay targeting specific sequences of RT gene. The PCR products were sent for sequencing. Bidirectional sequencing results were analysed using HIV drug resistance database supplied by Stanford University (HIV Drug Resistance Database, https://hivdb.stanford.edu). Among under treatment patients 10 out of 22 (45%) had at least one high-level resistance mutation which was higher than high level resistance mutation rate among treatment naive cases (P<0.01). Detected resistance mutations were as follows: K101E, K103N, K103E, V106M, V108I, E138A, V179T, Y181C, M184V, Y188L, Y188H, Y188F, G190A, L210W, T215F, T215Y, K219Q, and P225H. A high level of resistance mutations to RT inhibitors was observed that causes drug resistance especially against lamivudine (3TC). Such mutations should be considered as probable responsible for therapeutic failure. Serial surveillance studies of circulating drug resistance mutations are recommended.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11194027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141446614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.22099/mbrc.2023.47756.1845
Nour Samman, Hassan Mohabatkar, Parisa Rabiei
Phospholipases, as important lipolytic enzymes, have diverse industrial applications. Regarding the stability of extremophilic archaea's proteins in harsh conditions, analyses of unusual features of their proteins are significantly important for their utilization. This research was accomplished to in silico study of archaeal phospholipases' properties and to develop a pioneering method for distinguishing these enzymes from other archaeal enzymes via machine learning algorithms and Chou's pseudo-amino acid composition concept. The non-redundant sequences of archaeal phospholipases were collected. BioSeq-Analysis sever was used with Support Vector Machine (SVM), Random Forests (RF), Covariance Discrimination (CD), and Optimized Evidence-Theoretic K-nearest Neighbor (OET-KNN) as powerful machine learnings algorithms. Also, different Chou's pseudo-amino acid composition modes were performed and then, 5-fold cross-validation was applied to the sequences. Based on our results, the OET-KNN predictor, with 96% accuracy, yields the best performance in SC-PseAAC mode by 5-fold cross-validation. This predictor also achieved very high values of specificity (95%), sensitivity (96%), Matthews's correlation coefficient (0.92), and accuracy (96%). The present investigation yielded a robust anticipatory model for the archaeal phospholipase prediction utilizing the tenets PseAAC and OET-KNN machine learning algorithm.
{"title":"Using several pseudo amino acid composition types and different machine learning algorithms to classify and predict archaeal phospholipases.","authors":"Nour Samman, Hassan Mohabatkar, Parisa Rabiei","doi":"10.22099/mbrc.2023.47756.1845","DOIUrl":"https://doi.org/10.22099/mbrc.2023.47756.1845","url":null,"abstract":"<p><p>Phospholipases, as important lipolytic enzymes, have diverse industrial applications. Regarding the stability of extremophilic archaea's proteins in harsh conditions, analyses of unusual features of their proteins are significantly important for their utilization. This research was accomplished to <i>in silico</i> study of archaeal phospholipases' properties and to develop a pioneering method for distinguishing these enzymes from other archaeal enzymes via machine learning algorithms and Chou's pseudo-amino acid composition concept. The non-redundant sequences of archaeal phospholipases were collected. BioSeq-Analysis sever was used with Support Vector Machine (SVM), Random Forests (RF), Covariance Discrimination (CD), and Optimized Evidence-Theoretic K-nearest Neighbor (OET-KNN) as powerful machine learnings algorithms. Also, different Chou's pseudo-amino acid composition modes were performed and then, 5-fold cross-validation was applied to the sequences. Based on our results, the OET-KNN predictor, with 96% accuracy, yields the best performance in SC-PseAAC mode by 5-fold cross-validation. This predictor also achieved very high values of specificity (95%), sensitivity (96%), Matthews's correlation coefficient (0.92), and accuracy (96%). The present investigation yielded a robust anticipatory model for the archaeal phospholipase prediction utilizing the tenets PseAAC and OET-KNN machine learning algorithm.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10387176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9922446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Extracting high-yield, high-quality DNA from plant samples is challenging due to the presence of the cell wall, pigments, and some secondary metabolites. The main CTAB method, two of its modified protocols (beta-mercaptoethanol or ammonium acetate were eliminated), the modified Murray and Thompson method, and the Gene All kit were statistically compared based on the quantity and quality of the total DNA (tDNA) extracted from fresh and dried leaves of three medicinal herbs P. harmala, T. ramosissima, and P. reptans. The suitability of the tDNAs for molecular studies was evaluated by polymerase chain reaction (PCR) of the fragments of the internal transcribed spacer (ITS) in nuclear DNA and the trnL-F region in chloroplast DNA. Some significant differences were found between the tDNAs extracted by five extraction methods. With the exception of P. harmala, where the PCR of both the ITS fragments and the trnL-F region worked successfully in all DNA samples, but only the ITS fragments, not the chloroplast trnL-F region, were amplified in the DNA samples of T. ramosissima and P. reptans. The chloroplast trnL-F region was amplified only in DNA samples extracted from fresh and dried leaves of the three studied herbs using the commercial kit. Gene All kit, the main CTAB method, and its modified protocols were the less time-consuming protocols that yielded DNA suitable for downstream PCR vis-a-vis the modified Murray and Thompson method.
{"title":"Comparison of five DNA extraction methods in three medicinal plants: <i>Peganum harmala</i> L., <i>Tamarix ramosissima</i> Ledeb., and <i>Potentilla reptans</i> L.","authors":"Zahra Salehi, Atefe Amirahmadi, Arezou Rezaei, Parisa Farrokh, Javad Ghasemian","doi":"10.22099/mbrc.2023.45131.1798","DOIUrl":"https://doi.org/10.22099/mbrc.2023.45131.1798","url":null,"abstract":"<p><p>Extracting high-yield, high-quality DNA from plant samples is challenging due to the presence of the cell wall, pigments, and some secondary metabolites. The main CTAB method, two of its modified protocols (beta-mercaptoethanol or ammonium acetate were eliminated), the modified Murray and Thompson method, and the Gene All kit were statistically compared based on the quantity and quality of the total DNA (tDNA) extracted from fresh and dried leaves of three medicinal herbs <i>P. harmala</i>, <i>T. ramosissima</i>, and <i>P. reptans</i>. The suitability of the tDNAs for molecular studies was evaluated by polymerase chain reaction (PCR) of the fragments of the internal transcribed spacer (ITS) in nuclear DNA and the <i>trn</i>L-F region in chloroplast DNA. Some significant differences were found between the tDNAs extracted by five extraction methods. With the exception of <i>P. harmala</i>, where the PCR of both the ITS fragments and the <i>trn</i>L-F region worked successfully in all DNA samples, but only the ITS fragments, not the chloroplast <i>trn</i>L-F region, were amplified in the DNA samples of <i>T. ramosissima</i> and <i>P. reptans</i>. The chloroplast <i>trn</i>L-F region was amplified only in DNA samples extracted from fresh and dried leaves of the three studied herbs using the commercial kit. Gene All kit, the main CTAB method, and its modified protocols were the less time-consuming protocols that yielded DNA suitable for downstream PCR vis-a-vis the modified Murray and Thompson method.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10186858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9845450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.22099/mbrc.2023.47706.1842
Atena Eslami-Farouji, Ahmad Reza Khosravi, Mahdi Gholami, Sasan Mohsenzadeh
Circumscribing species boundries is necessary in systematic plant biology. Even a mistake in delimiting taxa may lead to incorrect scientific interpretations. Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji is an endemic Iranian species with a narrow geographic distribution, and is genetically close to D. aucheri. The present study provided a phylogenetic review, time divergence, and planar network of both species to unravel the distinct position of both species along with the prediction of any conflicting or ambiguous signals. Regarding this purpose, here we represent that phylogenetic trees may fail to show reliable results toward the distinct position of genetically close species.
{"title":"A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, <i>Draba rimarum</i> (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and <i>Draba aucheri</i> Boiss. (Brassicaceae) as a case study.","authors":"Atena Eslami-Farouji, Ahmad Reza Khosravi, Mahdi Gholami, Sasan Mohsenzadeh","doi":"10.22099/mbrc.2023.47706.1842","DOIUrl":"10.22099/mbrc.2023.47706.1842","url":null,"abstract":"<p><p>Circumscribing species boundries is necessary in systematic plant biology. Even a mistake in delimiting taxa may lead to incorrect scientific interpretations. <i>Draba rimarum</i> (Rech.f.) A.R. Khosravi & A. Eslami-Farouji is an endemic Iranian species with a narrow geographic distribution, and is genetically close to <i>D. aucheri</i>. The present study provided a phylogenetic review, time divergence, and planar network of both species to unravel the distinct position of both species along with the prediction of any conflicting or ambiguous signals. Regarding this purpose, here we represent that phylogenetic trees may fail to show reliable results toward the distinct position of genetically close species.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10599596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54230204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}