Pub Date : 2024-01-01DOI: 10.22099/MBRC.2024.48583.1882
Hamid Behrouj, Mehran Erfani, Pooneh Mokarram
Cholesterol and the Wnt/β-catenin pathway have an effective role in the proliferation, survival, drug resistance, immune exhaustion, and metastasis of all types of cancer cells. Considering the role of LDLR and LRP6 proteins in cholesterol uptake by cells and activation of Wnt/β-catenin pathway, this study aims to examine the gene expression of LDLR and LRP6 in cell lines of breast cancer. Human breast cancer cell lines MCF7, MD468 and SKBR3 were cultured in suitable conditions and after extracting total RNA from them, real-Time PCR was used to measure the levels of gene expression for LDLR and LRP6. Our results showed that the expression of LDLR and LRP6 genes is significantly increased in MCF7 and MD468 cells compared to SKBR3 cells. These results suggest that LRP6 and LDLR can be considered as a therapeutic target in tumors that have a genetic profile similar to MCF7 and MD468 cells.
{"title":"Examining the expression of low-density lipoprotein receptor (<i>LDLR</i>) and low-density lipoprotein receptor-related protein 6 (<i>LRP6</i>) genes in breast cancer cell lines.","authors":"Hamid Behrouj, Mehran Erfani, Pooneh Mokarram","doi":"10.22099/MBRC.2024.48583.1882","DOIUrl":"https://doi.org/10.22099/MBRC.2024.48583.1882","url":null,"abstract":"<p><p>Cholesterol and the Wnt/β-catenin pathway have an effective role in the proliferation, survival, drug resistance, immune exhaustion, and metastasis of all types of cancer cells. Considering the role of LDLR and LRP6 proteins in cholesterol uptake by cells and activation of Wnt/β-catenin pathway, this study aims to examine the gene expression of <i>LDLR</i> and <i>LRP6</i> in cell lines of breast cancer. Human breast cancer cell lines MCF7, MD468 and SKBR3 were cultured in suitable conditions and after extracting total RNA from them, real-Time PCR was used to measure the levels of gene expression for <i>LDLR</i> and <i>LRP6</i>. Our results showed that the expression of <i>LDLR</i> and <i>LRP6</i> genes is significantly increased in MCF7 and MD468 cells compared to SKBR3 cells. These results suggest that <i>LRP6</i> and <i>LDL</i>R can be considered as a therapeutic target in tumors that have a genetic profile similar to MCF7 and MD468 cells.</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/PMC10946548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175674","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.2023.48223.1862
Ali Javanmard, Maryam Azimzadeh-Irani, Ghazal Tafazzoli, Ayla Esmaeilzadeh, Mohammad Shirinpoor-Kharf, Seyyed Mohammad Hasan Haghayeghi
Heterocephalus glaber, known as the Naked mole-rat, has an extraordinary immunity to Alzheimer's disease. The pathological hallmark of Alzheimer's disease is cerebral accumulations of plaques, consisting of self-aggregated amyloid beta peptides. Homo sapiens and H. glaber amyloid beta peptides are different in only one amino acid. Herein, computational structural analyses were carried out to determine whether plaque development in H. glaber is prevented by the replacement of His13 with Arg13 in the amyloid beta peptide. AlphaFold2 was used to predict the structure of the H. glaber amyloid beta peptide. HADDOCK and Hex were used to self-dock the peptides and dock ions on peptides, respectively. Illustrations were made by PyMol and ChimeraX. Using VMD, we calculated the radius of gyration. The phylogenetic analysis was conducted by Mega. The results showed an accurate structure with two alpha helices separated by a short coil for H. glaber. Self-docking of the two amyloid beta peptides demonstrated a globular conformation in the H. glaber dimer, implying the unlikeliness of amyloid beta peptides' self-aggregation to form fibrillar structures. This conformational state resulted in lower electrostatic energy compared to H. sapiens, contributing to H. glaber's lower tendency for fibril and, ultimately, plaque formation. Phylogenetic analysis confirmed that amyloid precursor protein is highly conserved in each taxon of rodentia and primata. This study provides insight into the connection between the structure of H. glaber amyloid beta and its plaque formation properties, showing that the Arg13 in H. glaber leads to fibril instability, and might prevent senile plaque accumulation.
{"title":"In-silico structural analysis of <i>Heterocephalus glaber</i> amyloid beta: an anti-Alzheimer's peptide.","authors":"Ali Javanmard, Maryam Azimzadeh-Irani, Ghazal Tafazzoli, Ayla Esmaeilzadeh, Mohammad Shirinpoor-Kharf, Seyyed Mohammad Hasan Haghayeghi","doi":"10.22099/mbrc.2023.48223.1862","DOIUrl":"10.22099/mbrc.2023.48223.1862","url":null,"abstract":"<p><p><i>Heterocephalus glaber</i>, known as the Naked mole-rat, has an extraordinary immunity to Alzheimer's disease. The pathological hallmark of Alzheimer's disease is cerebral accumulations of plaques, consisting of self-aggregated amyloid beta peptides. <i>Homo sapiens</i> and <i>H. glaber</i> amyloid beta peptides are different in only one amino acid. Herein, computational structural analyses were carried out to determine whether plaque development in <i>H. glaber</i> is prevented by the replacement of His13 with Arg13 in the amyloid beta peptide. AlphaFold2 was used to predict the structure of the <i>H. glaber</i> amyloid beta peptide. HADDOCK and Hex were used to self-dock the peptides and dock ions on peptides, respectively. Illustrations were made by PyMol and ChimeraX. Using VMD, we calculated the radius of gyration. The phylogenetic analysis was conducted by Mega. The results showed an accurate structure with two alpha helices separated by a short coil for <i>H. glaber</i>. Self-docking of the two amyloid beta peptides demonstrated a globular conformation in the <i>H. glaber</i> dimer, implying the unlikeliness of amyloid beta peptides' self-aggregation to form fibrillar structures. This conformational state resulted in lower electrostatic energy compared to <i>H. sapiens</i>, contributing to <i>H. glaber's</i> lower tendency for fibril and, ultimately, plaque formation. Phylogenetic analysis confirmed that amyloid precursor protein is highly conserved in each taxon of rodentia and primata. This study provides insight into the connection between the structure of <i>H. glaber</i> amyloid beta and its plaque formation properties, showing that the Arg13 in <i>H. glaber</i> leads to fibril instability, and might prevent senile plaque accumulation.</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/PMC10644309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139074629","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.2024.49649.1950
Nasrin Motazedian, Negar Azarpira, Kimia Falamarzi, Seyed Mohsen Dehghani, Maryam Ataollahi, Elaheh Esfandiari, Mahintaj Dara, Razieh Toobafard, Mehrab Sayadi, Seyed Ali Shekarforoush, Seyed Hossein Owji, Seyed Ali Malekhosseini
Biliary atresia (BA) is the primary cause of neonatal jaundice with various pathological mechanisms. Many BA patients may experience progressive liver dysfunction and eventually need a liver transplant. Therefore, identifying potential non-invasive biomarkers for BA is crucial. miR-122, the most abundant microRNA in the liver, plays significant roles in different liver diseases. This study aimed to assess miR-122 levels in BA patients. Eighteen patients with biliary atresia were selected at random from the Shiraz Pediatric Liver Cirrhosis Cohort Study (SPLCCS), along with 18 healthy controls. Blood samples were collected, and biochemical parameters (such as liver function tests) were measured. Quantitative reverse-transcription PCR (RT-PCR) was conducted on serum samples from both the case and control groups to analyze miR-122 levels. The study results indicated that serum miR-122 expression in BA patients was elevated compared to the control group, although it did not reach statistical significance. Additionally, no correlation was found between miR-122 expression and serum levels of liver enzymes or other laboratory findings in BA cases. miR-122 could be a potential target for diagnosing BA; however, further research with a larger population is necessary to determine if miR-122 could serve as a useful biomarker for diagnosing BA.
胆道闭锁(BA)是导致新生儿黄疸的主要原因,其病理机制多种多样。许多胆道闭锁患者会出现进行性肝功能障碍,最终需要进行肝移植。miR-122是肝脏中含量最高的微RNA,在不同的肝脏疾病中发挥着重要作用。本研究旨在评估 BA 患者体内的 miR-122 水平。研究人员从设拉子小儿肝硬化队列研究(SPLCCS)中随机抽取了18名胆道闭锁患者和18名健康对照者。采集血样并测量生化指标(如肝功能检测)。研究人员对病例组和对照组的血清样本进行了定量反转录 PCR(RT-PCR),以分析 miR-122 的水平。研究结果表明,与对照组相比,BA 患者血清中的 miR-122 表达升高,但未达到统计学意义。然而,要确定 miR-122 能否作为诊断 BA 的有用生物标志物,还需要对更多人群进行进一步研究。
{"title":"Comparison of Mir122 expression in children with biliary atresia and healthy group.","authors":"Nasrin Motazedian, Negar Azarpira, Kimia Falamarzi, Seyed Mohsen Dehghani, Maryam Ataollahi, Elaheh Esfandiari, Mahintaj Dara, Razieh Toobafard, Mehrab Sayadi, Seyed Ali Shekarforoush, Seyed Hossein Owji, Seyed Ali Malekhosseini","doi":"10.22099/mbrc.2024.49649.1950","DOIUrl":"10.22099/mbrc.2024.49649.1950","url":null,"abstract":"<p><p>Biliary atresia (BA) is the primary cause of neonatal jaundice with various pathological mechanisms. Many BA patients may experience progressive liver dysfunction and eventually need a liver transplant. Therefore, identifying potential non-invasive biomarkers for BA is crucial. miR-122, the most abundant microRNA in the liver, plays significant roles in different liver diseases. This study aimed to assess miR-122 levels in BA patients. Eighteen patients with biliary atresia were selected at random from the Shiraz Pediatric Liver Cirrhosis Cohort Study (SPLCCS), along with 18 healthy controls. Blood samples were collected, and biochemical parameters (such as liver function tests) were measured. Quantitative reverse-transcription PCR (RT-PCR) was conducted on serum samples from both the case and control groups to analyze miR-122 levels. The study results indicated that serum miR-122 expression in BA patients was elevated compared to the control group, although it did not reach statistical significance. Additionally, no correlation was found between miR-122 expression and serum levels of liver enzymes or other laboratory findings in BA cases. miR-122 could be a potential target for diagnosing BA; however, further research with a larger population is necessary to determine if miR-122 could serve as a useful biomarker for diagnosing BA.</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/PMC11194029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141446616","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}
Sphingosine 1 phosphate (S1P) is involved in the pathogenesis of asthma by stimulation of the alpha-smooth muscle actin (SMA) expression and remodeling of fibroblasts. This study was designed to determine the effects of selected micro RNAs in regulation of S1P and related metabolic pathways in a human lung fibroblast cell line. The fibroblast cell line (CIRC-HLF, C580) was cultured and transfected with individual viral vectors carrying miR124, mi125b, mi133b or mi130a. After 48 hours, expression level of miRNAs and their target genes, sphingosine kinase 1(SPHK1), sphingosine 1-phosphate lyase 1 (SGPL1), sphingosine 1- phosphate receptor 1 (S1PR1) and sphingosine 1- phosphate receptor 2 (S1PR2) were determined. Expression of miRNA and mRNA determined by reverse transcriptionquantitative polymerase chain reaction (qPCR) showed that the expression level of the miRNAs was significantly higher in human lung fibroblasts following transfection compared to controls (vector backbone without miRNA). The expressions of miRNAs-targeted genes were significantly downregulated in transfected fibroblasts compared to control cells (p<0.05). Data show that miR 124, miR 125b, miR 133b and miR130a by targeting regulatory genes in S1P-pathway can down-regulate key factors such as SPHK1, SGPL1, S1PR1 and S1PR2 genes in lung fibroblasts. The results showed that S1P pathway and key factors are suppressed in lung fibroblasts expressing miR124, miR125b, miR130a or miR133b. It appears that suppression of any of the intermediate factors in S1P by miRNA can affect the regulation of the entire S1P pathway.
{"title":"Down-regulation of key regulatory factors in sphingosine-1-phosphate (S1P) pathway in human lung fibroblasts transfected with selected microRNAs.","authors":"Abdolamir Allameh, Mostafa Atashbasteh, Esmaeil Mortaz, Bahareh Naeeni, Majid Jafari-Khorchani","doi":"10.22099/mbrc.2024.49810.1951","DOIUrl":"10.22099/mbrc.2024.49810.1951","url":null,"abstract":"<p><p>Sphingosine 1 phosphate (S1P) is involved in the pathogenesis of asthma by stimulation of the alpha-smooth muscle actin (SMA) expression and remodeling of fibroblasts. This study was designed to determine the effects of selected micro RNAs in regulation of S1P and related metabolic pathways in a human lung fibroblast cell line. The fibroblast cell line (CIRC-HLF, C580) was cultured and transfected with individual viral vectors carrying miR124, mi125b, mi133b or mi130a. After 48 hours, expression level of miRNAs and their target genes, sphingosine kinase 1(SPHK1), sphingosine 1-phosphate lyase 1 (SGPL1), sphingosine 1- phosphate receptor 1 (S1PR1) and sphingosine 1- phosphate receptor 2 (S1PR2) were determined. Expression of miRNA and mRNA determined by reverse transcriptionquantitative polymerase chain reaction (qPCR) showed that the expression level of the miRNAs was significantly higher in human lung fibroblasts following transfection compared to controls (vector backbone without miRNA). The expressions of miRNAs-targeted genes were significantly downregulated in transfected fibroblasts compared to control cells (p<0.05). Data show that miR 124, miR 125b, miR 133b and miR130a by targeting regulatory genes in S1P-pathway can down-regulate key factors such as SPHK1, SGPL1, S1PR1 and S1PR2 genes in lung fibroblasts. The results showed that S1P pathway and key factors are suppressed in lung fibroblasts expressing miR124, miR125b, miR130a or miR133b. It appears that suppression of any of the intermediate factors in S1P by miRNA can affect the regulation of the entire S1P pathway.</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/PMC11416850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308170","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.2023.47247.1825
Smitha Soman, Siya Ram
tRNAs act as adaptors during protein synthesis and are chemically modified post-transcriptionally for their structural stability as well as accuracy of the translation. Hypomodifications of tRNAs are known to cause various human diseases, including cancer. Studies in bacteria and yeasts showed that levels of tRNA modifications vary under different stress conditions, enabling the organism to modulate gene expression for survival. Isopentelylation of the base 37 (i6A37) in the anticodon stem-loop by tRNA isopentenyltransferase (MiaA) is well-conserved modification present in prokaryotes and eukaryotes. i6A37 modification increases both the speed and fidelity of translation. A homozygous p.Arg323Gln mutation in the tRNA binding region of tRNA isopentenyltransferase reduced i6A37 levels in humans, affecting mitochondrial translation and thereby causing neurodevelopmental disorder. In this study, we mutated the Arg residue at the conserved position to Gln in Mycobacterium tuberculosis (M. tb) MiaA and analyzed the i6A modification activity of the enzyme on its target tRNAs. We found that p.Arg274Gln mutant MiaA could not modify the target tRNAs, tRNALeuCAA, tRNAPheGAA, and tRNASerCGA from M. tb, confirming the role of Arg residue in tRNA binding.
{"title":"Arginine to glutamine mutation in the substrate binding region impaired the isopentenyl activity of <i>Mycobacterium tuberculosis</i> MiaA.","authors":"Smitha Soman, Siya Ram","doi":"10.22099/mbrc.2023.47247.1825","DOIUrl":"10.22099/mbrc.2023.47247.1825","url":null,"abstract":"<p><p>tRNAs act as adaptors during protein synthesis and are chemically modified post-transcriptionally for their structural stability as well as accuracy of the translation. Hypomodifications of tRNAs are known to cause various human diseases, including cancer. Studies in bacteria and yeasts showed that levels of tRNA modifications vary under different stress conditions, enabling the organism to modulate gene expression for survival. Isopentelylation of the base 37 (i<sup>6</sup>A37) in the anticodon stem-loop by tRNA isopentenyltransferase (MiaA) is well-conserved modification present in prokaryotes and eukaryotes. i<sup>6</sup>A37 modification increases both the speed and fidelity of translation. A homozygous p.Arg323Gln mutation in the tRNA binding region of tRNA isopentenyltransferase reduced i<sup>6</sup>A37 levels in humans, affecting mitochondrial translation and thereby causing neurodevelopmental disorder. In this study, we mutated the Arg residue at the conserved position to Gln in <i>Mycobacterium tuberculosis</i> (M. tb) MiaA and analyzed the i6A modification activity of the enzyme on its target tRNAs. We found that p.Arg274Gln mutant MiaA could not modify the target tRNAs, tRNA<sup>Leu</sup>CAA, tRNA<sup>Phe</sup>GAA, and tRNA<sup>Ser</sup>CGA from M. tb, confirming the role of Arg residue in tRNA binding.</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/PMC10644310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139074627","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}
Autophagy is a cellular process that plays a major role in the fate of tumor cells. Understanding the role of autophagy in cancer therapy is a major challenge, particularly for breast cancer as the sole top cause of mortality among women. In this study, we evaluated the gene expression of mTOR and Beclin1 and the levels of p62 protein, in breast tumors and compared them to a control condition. To explore the role of autophagy in breast cancer, we acquired tumor biopsies from 41 new cases of breast cancer patients. We extracted total RNA from each biopsy and used real-time PCR to quantify Beclin1 and mTOR-specific RNA expression. In addition, we evaluated the expression of the p62 protein in paraffin-embedded tumor tissue using the immunohistochemistry technique. The data revealed an upregulation of Beclin1 and a downregulation of mTOR in tumor tissues compared to the control condition. The correlation between p62 expression and Beclin1/mTOR showed a negative and positive correlation, respectively, confirming autophagy activation in the tumor tissues. However, there was no correlation between autophagy markers and tumor size, grade and stage. The findings revealed that autophagy activation was found in breast tumor tissues, suggesting that autophagy can be a target for breast cancer therapy.
{"title":"Evaluation of <i>Beclin1</i> and <i>mTOR</i> genes and p62 protein expression in breast tumor tissues of Iranian patients.","authors":"Maryam Adelipour, Mahshid Naghashpour, Mohammad Reza Roshanazadeh, Hadi Chenaneh, Asma Mohammadi, Pegah Pourangi, Seyed Rouhollah Miri, Atefeh Zahedi, Mahmood Haghighatnezhad, Sahar Golabi","doi":"10.22099/mbrc.2023.47597.1837","DOIUrl":"10.22099/mbrc.2023.47597.1837","url":null,"abstract":"<p><p>Autophagy is a cellular process that plays a major role in the fate of tumor cells. Understanding the role of autophagy in cancer therapy is a major challenge, particularly for breast cancer as the sole top cause of mortality among women. In this study, we evaluated the gene expression of <i>mTOR</i> and <i>Beclin1</i> and the levels of p62 protein, in breast tumors and compared them to a control condition. To explore the role of autophagy in breast cancer, we acquired tumor biopsies from 41 new cases of breast cancer patients. We extracted total RNA from each biopsy and used real-time PCR to quantify <i>Beclin1</i> and <i>mTOR</i>-specific RNA expression. In addition, we evaluated the expression of the p62 protein in paraffin-embedded tumor tissue using the immunohistochemistry technique. The data revealed an upregulation of <i>Beclin1</i> and a downregulation of <i>mTOR</i> in tumor tissues compared to the control condition. The correlation between p62 expression and <i>Beclin1</i>/<i>mTOR</i> showed a negative and positive correlation, respectively, confirming autophagy activation in the tumor tissues. However, there was no correlation between autophagy markers and tumor size, grade and stage. The findings revealed that autophagy activation was found in breast tumor tissues, suggesting that autophagy can be a target for breast cancer therapy.</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/PMC10644314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139074628","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.2023.48386.1872
Mostafa Saadat
{"title":"The importance of examining the Hardy-Weinberg Equilibrium in genetic association studies.","authors":"Mostafa Saadat","doi":"10.22099/mbrc.2023.48386.1872","DOIUrl":"10.22099/mbrc.2023.48386.1872","url":null,"abstract":"","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/PMC10644312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139074631","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.2024.48723.1894
Maria E B P Mota, Patrik D Mathews, Tiago Milanin, Omar Mertins, Fernando Paiva, Carina E Oliveira, Luiz E R Tavares
Herein, a detailed molecular phylogeny analysis was developed to determine the phylogenetic position of a new freshwater histozoic myxosporean cnidarian, Henneguya markiana sp. nov. from the world's largest tropical wetland area, Pantanal, Brazil. The new species is described using an integrative taxonomy approach including morphology, biological traits and molecular data. Phylogenetic analysis inferred by Maximum Likehood method showed the new Henneguya species in a well-supported clade of myxosporean gill parasites of South American characids fishes. In this same clade, the new Henneguya described appeared in a sub-clade clustering with H. lacustris and H. chydadea. Nevertheless, the sequences of the new species and H. lacustris and H.chydadea have a large genetic divergence of 10.4% (148 nucleotides-nt) and 10.5% (147 nt) respectively. To the best of our knowledge, this is the first report of a cnidarian myxosporean species parasitizing a fish from Stevardiinae from South America. In the light of the differences observed from the integrative taxonomy, we are confident that this isolate is a new species of Henneguya, increasing the knowledge of diversity of this enigmatic group of cnidarians.
本文通过详细的分子系统发育分析,确定了来自世界上最大的热带湿地--巴西潘塔纳尔--的一种新的淡水组织胞器动物 Henneguya markiana sp.该新物种的描述采用了综合分类方法,包括形态学、生物学特征和分子数据。通过最大似然法推断的系统进化分析表明,Henneguya 新种属于南美洲颊鱼类肌孢子虫鳃寄生虫中一个支持良好的支系。在同一支系中,新描述的 Henneguya 与 H. lacustris 和 H. chydadea 一起出现在一个亚支系中。然而,新种与 H. lacustris 和 H. chydadea 的序列在遗传学上存在较大差异,分别为 10.4%(148 个核苷酸-nt)和 10.5%(147 个 nt)。据我们所知,这是首次报道南美洲的一种刺胞动物肌孢子虫物种寄生在 Stevardiinae 的鱼类上。根据综合分类法观察到的差异,我们确信该分离物是 Henneguya 的一个新物种,从而增加了对这一神秘的刺胞动物群多样性的了解。
{"title":"Phylogenetic position inferred on SSU rDNA sequence gene and description of a new parasitic cnidarian (Endocnidozoa: Myxobolidae) infecting <i>Markiana nigripinnis</i> (Teleostei: Stevardiinae) from a small marginal lake floodplain, Brazil.","authors":"Maria E B P Mota, Patrik D Mathews, Tiago Milanin, Omar Mertins, Fernando Paiva, Carina E Oliveira, Luiz E R Tavares","doi":"10.22099/MBRC.2024.48723.1894","DOIUrl":"https://doi.org/10.22099/MBRC.2024.48723.1894","url":null,"abstract":"<p><p>Herein, a detailed molecular phylogeny analysis was developed to determine the phylogenetic position of a new freshwater histozoic myxosporean cnidarian, <i>Henneguya markiana</i> sp. nov. from the world's largest tropical wetland area, Pantanal, Brazil. The new species is described using an integrative taxonomy approach including morphology, biological traits and molecular data. Phylogenetic analysis inferred by Maximum Likehood method showed the new <i>Henneguya</i> species in a well-supported clade of myxosporean gill parasites of South American characids fishes. In this same clade, the new <i>Henneguya</i> described appeared in a sub-clade clustering with <i>H. lacustris</i> and <i>H. chydadea</i>. Nevertheless, the sequences of the new species and <i>H. lacustris</i> and <i>H.</i> <i>chydadea</i> have a large genetic divergence of 10.4% (148 nucleotides-nt) and 10.5% (147 nt) respectively. To the best of our knowledge, this is the first report of a cnidarian myxosporean species parasitizing a fish from Stevardiinae from South America. In the light of the differences observed from the integrative taxonomy, we are confident that this isolate is a new species of <i>Henneguya</i>, increasing the knowledge of diversity of this enigmatic group of cnidarians.</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/PMC10946550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175676","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}
Maple syrup urine disease (MSUD) represents an infrequent metabolic disease precipitated by an insufficiency of the enzymatic complex known as branched-chain alpha-keto acid dehydrogenase. MSUD can be classified as classic (severe), intermediate, or intermittent based on the severity of the condition. The disease is associated with mutations in several genes, including BCKDHA, BCKDHB, DBT, and DLD. This study aimed to investigate the genetic landscape of MSUD in Iranian patients and explore the clinical implications of identified gene variants. A comprehensive analysis was conducted using various molecular techniques and bioinformatics tools to predict protein stability, pathogenicity, amino acid conservation, and secondary/tertiary structure. The in silico analysis highlighted high-risk pathogenic variants and provided insights into their potential impact on protein structure and function. Furthermore, the predicted 3D structures of wild-type and mutant proteins elucidated structural differences. Protein-protein interaction analysis shed light on the network of interactions involving MSUD-related proteins. The Iranome database uncovered a potential pathogenic variant (c.554C>T) in the Persian population. This research contributes to a better understanding of MSUD genetics in the Iranian population and outlines potential avenues for further clinical investigations. The findings have implications for genetic testing, prognosis, and genetic counseling in affected families.
{"title":"A comprehensive in silico analysis of mutation spectrum of maple syrup urine disease (MSUD) genes in Iranian population.","authors":"Nahid Rezaie, Saeedeh Sadat Ghazanfari, Teymoor Khosravi, Fatemeh Vaghefi, Morteza Oladnabi","doi":"10.22099/mbrc.2024.49847.1958","DOIUrl":"10.22099/mbrc.2024.49847.1958","url":null,"abstract":"<p><p>Maple syrup urine disease (MSUD) represents an infrequent metabolic disease precipitated by an insufficiency of the enzymatic complex known as branched-chain alpha-keto acid dehydrogenase. MSUD can be classified as classic (severe), intermediate, or intermittent based on the severity of the condition. The disease is associated with mutations in several genes, including <i>BCKDHA</i>, <i>BCKDHB</i>, <i>DBT</i>, and <i>DLD</i>. This study aimed to investigate the genetic landscape of MSUD in Iranian patients and explore the clinical implications of identified gene variants. A comprehensive analysis was conducted using various molecular techniques and bioinformatics tools to predict protein stability, pathogenicity, amino acid conservation, and secondary/tertiary structure. The in silico analysis highlighted high-risk pathogenic variants and provided insights into their potential impact on protein structure and function. Furthermore, the predicted 3D structures of wild-type and mutant proteins elucidated structural differences. Protein-protein interaction analysis shed light on the network of interactions involving MSUD-related proteins. The Iranome database uncovered a potential pathogenic variant (c.554C>T) in the Persian population. This research contributes to a better understanding of MSUD genetics in the Iranian population and outlines potential avenues for further clinical investigations. The findings have implications for genetic testing, prognosis, and genetic counseling in affected families.</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/PMC11416852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308167","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}
L-asparaginase is a commercial enzyme with a wide variety of applications. Asparaginase is known as an anti-cancer agent that is effective for the treatment of certain lymphomas and leukemias by growth inhibition of human cancer cells. Additionally, asparaginase is used in the food industry in a pretreatment process to decrease the accumulation of carcinogenic acrylamide. In this paper, different aspects of bacterial and fungal asparaginases such as mass, hydrophobicity and hydrophilicity of pseudo amino acid composition (PseAAC), physicochem-ical properties, and structural motifs were studied, and ROC curve statistical analysis was used for the comparison. The results showed that none of the physicochemical properties of fungal and bacterial asparaginase could not be differed, except molecular weight and sequence length. MEME Suite analysis demonstrated that there was a motif that was specific for bacterial asparaginases. However, analysis based on the concept of PseACC indicated a differentiation line between fungal and bacterial asparaginases. In conclusion, although there was not any specific demonstration to separate the bacterial and fungal asparaginases in the case of physicochemical properties, PseAAC analysis can be an appropriate and usable method to differentiate between them.
L- 天冬酰胺酶是一种用途广泛的商用酶。众所周知,天冬酰胺酶是一种抗癌剂,通过抑制人类癌细胞的生长,可有效治疗某些淋巴瘤和白血病。此外,天冬酰胺酶还被用于食品工业的预处理过程,以减少致癌物质丙烯酰胺的积累。本文研究了细菌和真菌天冬酰胺酶的不同方面,如质量、假氨基酸组成(PseAAC)的疏水性和亲水性、理化性质和结构基团,并采用 ROC 曲线统计分析进行比较。结果表明,除分子量和序列长度外,真菌和细菌天冬酰胺酶的理化性质均无差异。MEME Suite 分析表明,细菌天冬酰胺酶有一个特异的主题。不过,基于 PseACC 概念的分析表明,真菌和细菌天冬酰胺酶之间存在着一条分界线。总之,虽然在理化性质方面没有任何具体的证据可以区分细菌和真菌天冬酰胺酶,但 PseAAC 分析可以作为区分它们的一种适当和可用的方法。
{"title":"In-silico comparison of fungal and bacterial asparaginase enzymes.","authors":"Negar Tafvizi, Mandana Behbahani, Hassan Mohabatkar","doi":"10.22099/mbrc.2024.50123.1981","DOIUrl":"10.22099/mbrc.2024.50123.1981","url":null,"abstract":"<p><p>L-asparaginase is a commercial enzyme with a wide variety of applications. Asparaginase is known as an anti-cancer agent that is effective for the treatment of certain lymphomas and leukemias by growth inhibition of human cancer cells. Additionally, asparaginase is used in the food industry in a pretreatment process to decrease the accumulation of carcinogenic acrylamide. In this paper, different aspects of bacterial and fungal asparaginases such as mass, hydrophobicity and hydrophilicity of pseudo amino acid composition (PseAAC), physicochem-ical properties, and structural motifs were studied, and ROC curve statistical analysis was used for the comparison. The results showed that none of the physicochemical properties of fungal and bacterial asparaginase could not be differed, except molecular weight and sequence length. MEME Suite analysis demonstrated that there was a motif that was specific for bacterial asparaginases. However, analysis based on the concept of PseACC indicated a differentiation line between fungal and bacterial asparaginases. In conclusion, although there was not any specific demonstration to separate the bacterial and fungal asparaginases in the case of physicochemical properties, PseAAC analysis can be an appropriate and usable method to differentiate between them.</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/PMC11416853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309718","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}