Molecular Biology Research Communications最新文献

{"title":"In silico analysis for SARS-CoV-2 detection in the context of genetic variability of the Algerian omicron variant.","authors":"Chahinez Amira Dahmani, Asmaa Azzoune, Abdallah Boudjema","doi":"10.22099/mbrc.2024.50192.1985","DOIUrl":"10.22099/mbrc.2024.50192.1985","url":null,"abstract":"<p><p>The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations have raised concerns regarding its potential for increased transmissibility and immune escape. In this study, we test the compatibility of the different primers and probes available in different commercial kits sold internationally with all the sequences of SARS-CoV-2 analyzed in Algeria until March 2023. The Algerian SARS-CoV-2 Omicron variant sequences were aligned with the Muscle tool using Genious software. We also used primers and probes sequences of seven international RT-qPCR kits; CDC China, Charite Germany, HKU Hong Kong, NIH Thailand, NIID Japan, CDC US, and Pasteur Institute. We used the primer check v2.0 developed by VIROSCIENCE LAB, To identify the different mutations located at the level of primers and probes about the Algerian sequences of SARS-CoV2. Statistical tests were carried out by calculating the <math> <msup> <mrow><mrow><mi>x</mi></mrow> </mrow> <mrow><mrow><mn>2</mn></mrow> </mrow> </msup> </math> test. We found regarding the Forward primer sequences that the two Thailand and Japan kits are less specific to the Algerian version of the SARS-CoV-2 Omicron variant genome compared to the other kits (<i>p</i>=10^-6). Furthermore, regarding the Reverse primers and fluorescent Probes, the three kits; Thailand, Japan, and CDC US; are less effective (<i>p</i>=10^-6). Regarding all primers and probes, this work allowed us to conclude that the four RT-qPCR kits: CDC China, Charite Germany, NHD Hong Kong, and Pasteur Institute seem to be more specific for the Algerian omicron genome detection and therefore for diagnosis of COVID-19 in Algeria.</p>","PeriodicalId":19025,"journal":{"name":"Molecular Biology Research Communications","volume":"13 4","pages":"223-234"},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308171","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}

{"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":"13 4","pages":"247-252"},"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}

{"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":"13 3","pages":"165-173"},"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}

{"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":"13 2","pages":"51-53"},"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}

{"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":"13 3","pages":"155-164"},"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}

{"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":"13 2","pages":"89-102"},"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}

{"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":"13 3","pages":"117-125"},"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}

{"title":"Using several pseudo amino acid composition types and different machine learning algorithms to classify and predict archaeal phospholipases.","authors":"Nour Samman,&nbsp;Hassan Mohabatkar,&nbsp;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":"12 3","pages":"117-126"},"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}

{"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,&nbsp;Atefe Amirahmadi,&nbsp;Arezou Rezaei,&nbsp;Parisa Farrokh,&nbsp;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":"12 1","pages":"1-16"},"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}

{"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,&nbsp;Ahmad Reza Khosravi,&nbsp;Mahdi Gholami,&nbsp;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":"12 4","pages":"155-163"},"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}