Pub Date : 2024-10-16DOI: 10.1016/j.genrep.2024.102064
Faisel Ahmad , Mahrukh Hameed Zargar , Mohammad Lateef , Arshad Hussain , Tahir Mohuiddin Malla , Mohd Ashraf Ganie , Iqbal Qasim , Sajad Ul Islam Mir , Saima Wani , Nadia Khurshid
<div><h3>Background</h3><div>Micro-deletions in the Y chromosome are recognized as the causative factor for male infertility. The prevalence of Y chromosome micro-deletions exhibits variation among infertile males across different areas and races globally. The study of Y chromosome micro- deletions is crucial among genetic variables owing to their ability to transmit genetic defects to the progeny. Microdeletion of the azoospermia factor (AZF) region associated with the long arm of the Y chromosome (Yq) has three sub-regions (AZFa, AZFb, and AZFc) that play an important role in spermatogenesis. The genes associated with the AZF region of the Y chromosome are believed to play a crucial role in the process of spermatogenesis by performing several activities such as gene silencing, transcription, ubiquitination, and maintenance of microtubule networks. Due to the absence of epidemiological research on Y chromosome micro-deletions in ethnic infertile male population of Kashmir, our study sought to examine the Y chromosome micro-deletions among non-obstructive azospermic infertile men in Kashmir.</div></div><div><h3>Objective</h3><div>The research was aimed to establish the frequency and characteristics of micro-deletions in the AZF region of Y chromosome in infertile males of our population with non-obstructive Azoospermia and normal Karyotype.</div></div><div><h3>Methods</h3><div>A total of 120 subjects were included in the study. Samples from 60 male patients with fertility issues (non-obstructive azoospermia) and an equal number of samples from normal men having established fatherhood (biological fathers) were taken for the study. The average age in years of cases and controls were 32.80 and 34.88 respectively. A total of 26.66 % of cases and 13.33 % of controls were found to be consanguineous, 36.66 % of cases and 40 % of controls were urban while 63.33 % of cases and 60 % of controls were from rural population. Molecular analysis was performed by multiplex polymerase chain reactions (PCR) using sequence tagged sites (STS) from 3 different regions of AZF of Y chromosome. To assess the frequency of AZF micro-deletions, molecular analysis was performed by multiplex polymerase chain reactions (PCR) using sequence tagged sites (STS) from 3 different regions of the Y chromosome (sY84 and sY86 for AZFa region; sY127 and sY134 for AZFb; sY254 and sY255 for AZFc region).</div></div><div><h3>Results</h3><div>In the present study a total of 9 out of 60 cases (15 %) were found to have Y chromosome micro- deletions in AZF region of Yq arm. The most frequent micro deletions were observed in AZF<sub>b</sub> region, 8 out of 60 cases (13.33 %) from AZF<sub>b</sub> region were found to have deletions.5 out of 60 cases (8.33 %) were reported with deletions associated to AZFc region region and 6.66 % of cases were found to harbor deletions in both AZF<sub>b</sub> and AZF<sub>c</sub> region. However no deletion was reported in the AZFa region in all the studied cas
背景Y染色体微缺失被认为是男性不育症的致病因素。在全球不同地区和种族的不育男性中，Y 染色体微缺失的发生率存在差异。由于 Y 染色体微缺失能够将遗传缺陷传递给后代，因此对 Y 染色体微缺失的研究在遗传变异中至关重要。与 Y 染色体（Yq）长臂相关的无精子症因子（AZF）微缺失区有三个亚区（AZFa、AZFb 和 AZFc），它们在精子发生过程中发挥着重要作用。据信，与 Y 染色体 AZF 区相关的基因在精子发生过程中发挥着至关重要的作用，可进行基因沉默、转录、泛素化和维持微管网络等多种活动。由于缺乏对克什米尔不育男性人群中 Y 染色体微缺失的流行病学研究，我们的研究试图检测克什米尔非阻塞性无精子症不育男性中的 Y 染色体微缺失情况。研究旨在确定我国非梗阻性无精子症且核型正常的不育男性中 Y 染色体 AZF 区微缺失的频率和特征。研究从 60 名有生育问题的男性患者（非梗阻性无精子症）和同等数量的已为人父的正常男性（生父）中抽取样本。病例和对照组的平均年龄分别为 32.80 岁和 34.88 岁。共发现 26.66% 的病例和 13.33% 的对照组为近亲结婚，36.66% 的病例和 40% 的对照组为城市人口，而 63.33% 的病例和 60% 的对照组为农村人口。利用 Y 染色体 AZF 的 3 个不同区域的序列标记位点 (STS) 进行多重聚合酶链反应 (PCR) 进行分子分析。为评估AZF微缺失的频率，使用Y染色体3个不同区域的序列标记位点（STS）（AZFa区域为sY84和sY86；AZFb区域为sY127和sY134；AZFc区域为sY254和sY255）进行多重聚合酶链式反应（PCR）进行分子分析。在 60 个病例中，有 5 个病例（8.33%）被报告与 AZFc 区域的缺失有关，有 6.66% 的病例被发现在 AZFb 和 AZFc 区域均存在缺失。然而，在所有研究病例中，均未发现 AZFa 区的缺失。本研究首次报道了我国人群中不育男性的 Y 染色体微缺失发生率。本研究的结果表明，这些基因微缺失是导致男性不育的一个主要因素。本研究强调，基于多重 PCR 的筛查是排除 Y 染色体微缺失作为男性不育致病因素的可靠方法，并建议在计划任何生殖援助之前进行基因检测。
{"title":"Azoospermia factor gene microdeletions in infertile men with non-obstructive azoospermia and normal karyotype: First case-control study from Kashmir","authors":"Faisel Ahmad , Mahrukh Hameed Zargar , Mohammad Lateef , Arshad Hussain , Tahir Mohuiddin Malla , Mohd Ashraf Ganie , Iqbal Qasim , Sajad Ul Islam Mir , Saima Wani , Nadia Khurshid","doi":"10.1016/j.genrep.2024.102064","DOIUrl":"10.1016/j.genrep.2024.102064","url":null,"abstract":"<div><h3>Background</h3><div>Micro-deletions in the Y chromosome are recognized as the causative factor for male infertility. The prevalence of Y chromosome micro-deletions exhibits variation among infertile males across different areas and races globally. The study of Y chromosome micro- deletions is crucial among genetic variables owing to their ability to transmit genetic defects to the progeny. Microdeletion of the azoospermia factor (AZF) region associated with the long arm of the Y chromosome (Yq) has three sub-regions (AZFa, AZFb, and AZFc) that play an important role in spermatogenesis. The genes associated with the AZF region of the Y chromosome are believed to play a crucial role in the process of spermatogenesis by performing several activities such as gene silencing, transcription, ubiquitination, and maintenance of microtubule networks. Due to the absence of epidemiological research on Y chromosome micro-deletions in ethnic infertile male population of Kashmir, our study sought to examine the Y chromosome micro-deletions among non-obstructive azospermic infertile men in Kashmir.</div></div><div><h3>Objective</h3><div>The research was aimed to establish the frequency and characteristics of micro-deletions in the AZF region of Y chromosome in infertile males of our population with non-obstructive Azoospermia and normal Karyotype.</div></div><div><h3>Methods</h3><div>A total of 120 subjects were included in the study. Samples from 60 male patients with fertility issues (non-obstructive azoospermia) and an equal number of samples from normal men having established fatherhood (biological fathers) were taken for the study. The average age in years of cases and controls were 32.80 and 34.88 respectively. A total of 26.66 % of cases and 13.33 % of controls were found to be consanguineous, 36.66 % of cases and 40 % of controls were urban while 63.33 % of cases and 60 % of controls were from rural population. Molecular analysis was performed by multiplex polymerase chain reactions (PCR) using sequence tagged sites (STS) from 3 different regions of AZF of Y chromosome. To assess the frequency of AZF micro-deletions, molecular analysis was performed by multiplex polymerase chain reactions (PCR) using sequence tagged sites (STS) from 3 different regions of the Y chromosome (sY84 and sY86 for AZFa region; sY127 and sY134 for AZFb; sY254 and sY255 for AZFc region).</div></div><div><h3>Results</h3><div>In the present study a total of 9 out of 60 cases (15 %) were found to have Y chromosome micro- deletions in AZF region of Yq arm. The most frequent micro deletions were observed in AZF<sub>b</sub> region, 8 out of 60 cases (13.33 %) from AZF<sub>b</sub> region were found to have deletions.5 out of 60 cases (8.33 %) were reported with deletions associated to AZFc region region and 6.66 % of cases were found to harbor deletions in both AZF<sub>b</sub> and AZF<sub>c</sub> region. However no deletion was reported in the AZFa region in all the studied cas","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102064"},"PeriodicalIF":1.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142537372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-14DOI: 10.1016/j.genrep.2024.102057
Krishna Kumar Rai
The WD40 repeat-containing proteins are ancient proteins regulating various cellular and biological processes in eukaryotes. WD40 proteins are extensively studied in eukaryotes, and their genome-wide characterisation has revealed their hidden potential. On the contrary, in-depth taxonomic and functional description of WD40 proteins in prokaryotes, particularly in cyanobacteria, remains largely unexplored. In this study, we have comprehensively analysed cyanobacterial WD40 proteins and detailed comparisons among different cyanobacterial orders. About 7000 WD40 proteins were identified in all six cyanobacterial orders accounting for 22–43 % of all WD40s. While their abundance was less in Chroococcales, Pleurocapsales and, Stigonematales, the WD40s were profoundly present in Nostcales and Oscillatoriales, exhibiting multifarious functions such as cell signalling, transcription factors, catalytic enzymes and scaffold etc. Current systemic analysis showed that most WD40 proteins contain multiple WD40 domains, as indicated by their repeat numbers and average confidence scores. The observation also indicated that most WD40 proteins have complex hydrogen bond networks. Their taxonomic distribution and gene neighbourhood analysis revealed topical or newly repeated duplication events form most WD40s. Further, the studies confirmed that the recently formed WD40 proteins are highly repetitive with higher structural stability. Overall, the result of this study has described an assembly of cyanobacterial WD40 proteins and highlighting their evolution, distribution and probable functions.
{"title":"A comprehensive study of highly repetitive WD40 proteins in cyanobacteria","authors":"Krishna Kumar Rai","doi":"10.1016/j.genrep.2024.102057","DOIUrl":"10.1016/j.genrep.2024.102057","url":null,"abstract":"<div><div>The WD40 repeat-containing proteins are ancient proteins regulating various cellular and biological processes in eukaryotes. WD40 proteins are extensively studied in eukaryotes, and their genome-wide characterisation has revealed their hidden potential. On the contrary, in-depth taxonomic and functional description of WD40 proteins in prokaryotes, particularly in cyanobacteria, remains largely unexplored. In this study, we have comprehensively analysed cyanobacterial WD40 proteins and detailed comparisons among different cyanobacterial orders. About 7000 WD40 proteins were identified in all six cyanobacterial orders accounting for 22–43 % of all WD40s. While their abundance was less in Chroococcales, Pleurocapsales and, Stigonematales, the WD40s were profoundly present in Nostcales and Oscillatoriales, exhibiting multifarious functions such as cell signalling, transcription factors, catalytic enzymes and scaffold etc. Current systemic analysis showed that most WD40 proteins contain multiple WD40 domains, as indicated by their repeat numbers and average confidence scores. The observation also indicated that most WD40 proteins have complex hydrogen bond networks. Their taxonomic distribution and gene neighbourhood analysis revealed topical or newly repeated duplication events form most WD40s. Further, the studies confirmed that the recently formed WD40 proteins are highly repetitive with higher structural stability. Overall, the result of this study has described an assembly of cyanobacterial WD40 proteins and highlighting their evolution, distribution and probable functions.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102057"},"PeriodicalIF":1.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-11DOI: 10.1016/j.genrep.2024.102062
Jie Chen , Huiming Yuan , Jing Gao , Lu Liu , Adelino V.M. Canario
Somatostatin is a multifunctional hormone with several genes in teleost fishes. A zebrafish CRISPR/Cas9 knockout of the somatostatin 1.1 (sst1.1) with persistent hyperglycaemia and hyperlipidaemia displayed reduced fecundity when fed brine shrimp ad libitum. Here, we investigated the effect of feeding brine shrimp one to three times a day on fecundity and liver transcriptomics of the sst1.1 mutant compared to their wild-type siblings to unravel molecular pathways associated with the phenotype. We find that the sst1.1 deficient zebrafish had high mortality when fed at the highest rate and that in both genotypes, growth and fecundity were proportional to food intake. Although glucose and cholesterol decreased substantially at the lowest level of feeding, they were still higher in the mutant than in the wild-type zebrafish. Furthermore, sst1.1 deficiency had a small but significant effect on the hepatic expression of protein, carbohydrate, and fatty acid biosynthesis genes, contributing to the mutant's diabetic phenotype.
{"title":"Metabolic changes in response to food intake in somatostatin 1.1 deficient zebrafish","authors":"Jie Chen , Huiming Yuan , Jing Gao , Lu Liu , Adelino V.M. Canario","doi":"10.1016/j.genrep.2024.102062","DOIUrl":"10.1016/j.genrep.2024.102062","url":null,"abstract":"<div><div>Somatostatin is a multifunctional hormone with several genes in teleost fishes. A zebrafish CRISPR/Cas9 knockout of the <em>somatostatin 1.1</em> (<em>sst1.1</em>) with persistent hyperglycaemia and hyperlipidaemia displayed reduced fecundity when fed brine shrimp ad libitum. Here, we investigated the effect of feeding brine shrimp one to three times a day on fecundity and liver transcriptomics of the <em>sst1.1</em> mutant compared to their wild-type siblings to unravel molecular pathways associated with the phenotype. We find that the <em>sst1.1</em> deficient zebrafish had high mortality when fed at the highest rate and that in both genotypes, growth and fecundity were proportional to food intake. Although glucose and cholesterol decreased substantially at the lowest level of feeding, they were still higher in the mutant than in the wild-type zebrafish. Furthermore, <em>sst1.1</em> deficiency had a small but significant effect on the hepatic expression of protein, carbohydrate, and fatty acid biosynthesis genes, contributing to the mutant's diabetic phenotype.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102062"},"PeriodicalIF":1.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438001","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}
This study aimed to evaluate the association of CC Chemokine Receptor 5 (CCR5) G59029A and CC Chemokine Ligand 5 (CCL5) -28 C/G gene polymorphisms in patients with and without periodontitis.
Materials and methods
A total of 172 individuals were enrolled, divided into two groups: Group I (periodontally healthy, n = 86) and Group II (generalized chronic periodontitis, n = 86). Periodontal clinical parameters such as Periodontal Probing Depth (PPD), Clinical Attachment Loss (CAL), Plaque Index (PI), and Bleeding Index (BI) were recorded. Allele-specific PCR (AS-PCR) was used to identify polymorphic sites in the CCL5 and CCR5 genes.
Results
The heterozygous genotype CG and allele G was more prevalent in the Test group (p value = 0.001, 0.01) for CCL5 gene polymorphism. Similarly, the heterozygous genotype AG and allele G for CCR5 gene polymorphism was significantly higher in the Test group (p value = 0.002, 0.04).
Conclusion
The study found a significant association between CCL5 and CCR5 gene polymorphisms and periodontitis.
{"title":"CC chemokine receptor 5 and CC chemokine ligand 5 gene polymorphisms in patients with periodontitis - A case–control study","authors":"Ayshwarya Karthika Muralidharan, Sangeetha Subramanian, Prakash P.S.G., Devapriya Appukuttan, Jasmine Crena, Anitha C.M.","doi":"10.1016/j.genrep.2024.102061","DOIUrl":"10.1016/j.genrep.2024.102061","url":null,"abstract":"<div><h3>Aim</h3><div>This study aimed to evaluate the association of CC Chemokine Receptor 5 (CCR5) G59029A and CC Chemokine Ligand 5 (CCL5) -28 C/G gene polymorphisms in patients with and without periodontitis.</div></div><div><h3>Materials and methods</h3><div>A total of 172 individuals were enrolled, divided into two groups: Group I (periodontally healthy, n = 86) and Group II (generalized chronic periodontitis, n = 86). Periodontal clinical parameters such as Periodontal Probing Depth (PPD), Clinical Attachment Loss (CAL), Plaque Index (PI), and Bleeding Index (BI) were recorded. Allele-specific PCR (AS-PCR) was used to identify polymorphic sites in the CCL5 and CCR5 genes.</div></div><div><h3>Results</h3><div>The heterozygous genotype CG and allele G was more prevalent in the Test group (p value = 0.001, 0.01) for CCL5 gene polymorphism. Similarly, the heterozygous genotype AG and allele G for CCR5 gene polymorphism was significantly higher in the Test group (p value = 0.002, 0.04).</div></div><div><h3>Conclusion</h3><div>The study found a significant association between CCL5 and CCR5 gene polymorphisms and periodontitis.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102061"},"PeriodicalIF":1.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142425212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-10DOI: 10.1016/j.genrep.2024.102058
Elham Amiri , Hamid Reza Goli , Mehrdad Gholami , Zohre Bari , Arash Kazemi Veisari , Hafez Tirgar Fakheri , Jamshid Yazdani Charati , Maryam Salehiyan , Mohammad Ahanjan
Urease-positive bacteria other than Helicobacter pylori have been shown to be present in the mouth, stomach, intestines, urinary tract, and skin. The aim of this study was to evaluate the prevalence of non-H. pylori urease-positive bacteria in the gastric biopsies of patients with gastritis and the antibiotic resistance pattern of the isolates, along with the prevalence of ureA, ureB, and ureC genes. In this study, 165 biopsies were collected from the gastric antrum of patients with gastritis referred to hospitals by a gastroenterologist. After Rapid Urease Test, the samples were transferred to the microbiology laboratory using a Brain Heart Infusion broth transfer medium. Next, the non-H. pylori bacteria were identified by the standard microbiological methods. Also, the H. pylori-positive samples were detected using the pathological testing, stool antigen detection test, and enzyme linked sorbent assay. However, after the growth and purification of microorganisms, the urease test was carried out again. In the next step, the DNAs of all confirmed isolates were extracted and the presence of ureA, ureB, and ureC genes was evaluated using the specific primers by the PCR method. Among the 100 urease-positive biopsies, 77 samples were infected with H. pylori and 23 were non-H. pylori-positive. Staphylococcus epidermidis was the most prevalent non-H. pylori-positive bacteria in this study. The antibiotic resistance pattern of the bacteria showed that tetracycline and erythromycin were the least effective antibiotics against the gram-positive and -negative, respectively. However, the lowest resistance rate of gram-positive bacteria was detected against co-trimoxazole, while cefotaxime, chloramphenicol, and ceftriaxone were the most effective antibiotics against the gram-negative bacteria. In addition, the ureA gene was detected among 21.73 % of the non-H. pylori isolates, while 8.69 % and 43.47 % of them were ureB and ureC positive, respectively. This study showed a considerable significance of non-H. pylori urease-positive bacteria causing gastritis. It seems that the diagnosis of these organisms can be effective in treatment of patients with gastritis. Also, the ureC gene was predominant to produce the urease in these isolates.
{"title":"Drug resistance of urease-positive bacteria other than Helicobacter pylori and distribution of urease genes in patients with gastritis","authors":"Elham Amiri , Hamid Reza Goli , Mehrdad Gholami , Zohre Bari , Arash Kazemi Veisari , Hafez Tirgar Fakheri , Jamshid Yazdani Charati , Maryam Salehiyan , Mohammad Ahanjan","doi":"10.1016/j.genrep.2024.102058","DOIUrl":"10.1016/j.genrep.2024.102058","url":null,"abstract":"<div><div>Urease-positive bacteria other than <em>Helicobacter pylori</em> have been shown to be present in the mouth, stomach, intestines, urinary tract, and skin. The aim of this study was to evaluate the prevalence of non-<em>H. pylori</em> urease-positive bacteria in the gastric biopsies of patients with gastritis and the antibiotic resistance pattern of the isolates, along with the prevalence of <em>ureA</em>, <em>ureB</em>, and <em>ureC</em> genes. In this study, 165 biopsies were collected from the gastric antrum of patients with gastritis referred to hospitals by a gastroenterologist. After Rapid Urease Test, the samples were transferred to the microbiology laboratory using a Brain Heart Infusion broth transfer medium. Next, the non-<em>H. pylori</em> bacteria were identified by the standard microbiological methods. Also, the <em>H. pylori</em>-positive samples were detected using the pathological testing, stool antigen detection test, and enzyme linked sorbent assay. However, after the growth and purification of microorganisms, the urease test was carried out again. In the next step, the DNAs of all confirmed isolates were extracted and the presence of <em>ureA</em>, <em>ureB</em>, and <em>ureC</em> genes was evaluated using the specific primers by the PCR method. Among the 100 urease-positive biopsies, 77 samples were infected with <em>H. pylori</em> and 23 were non-<em>H. pylori</em>-positive. <em>Staphylococcus epidermidis</em> was the most prevalent non-<em>H. pylori</em>-positive bacteria in this study. The antibiotic resistance pattern of the bacteria showed that tetracycline and erythromycin were the least effective antibiotics against the gram-positive and -negative, respectively. However, the lowest resistance rate of gram-positive bacteria was detected against co-trimoxazole, while cefotaxime, chloramphenicol, and ceftriaxone were the most effective antibiotics against the gram-negative bacteria. In addition, the <em>ureA</em> gene was detected among 21.73 % of the non-<em>H. pylori</em> isolates, while 8.69 % and 43.47 % of them were <em>ureB</em> and <em>ureC</em> positive, respectively. This study showed a considerable significance of non-<em>H. pylori</em> urease-positive bacteria causing gastritis. It seems that the diagnosis of these organisms can be effective in treatment of patients with gastritis. Also, the <em>ureC</em> gene was predominant to produce the urease in these isolates.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102058"},"PeriodicalIF":1.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1016/j.genrep.2024.102060
Shravani A S , Priyanka R , Indumathi A N , Prabhakar Kamarthy , Venkatachalam Perumal , Venkateswarlu Raavi
Analysis of gene expression (e.g. Ferredoxin Reductase: FDXR) changes in the blood samples have shown potential as predictive markers of disease, prognosis for therapy as well as triage and dose estimation in radiation-exposed populations. Similarly, quantification of micronuclei (MN) formation has been presented as a rapid cytogenetic marker for those applications. It was cautioned that the reliable utilization of these markers for prediction of disease, therapy prognosis, and dose estimation depends upon the information on known variables that affect these markers. Literature suggests that advanced glycation end products/oxidative stress in diabetic conditions can alter the levels of DNA damage and gene expression, and impact the segregation of the exposed from unexposed during nuclear disasters. Therefore, we investigated the influence of Type 2 diabetes mellitus (T2DM) on baseline expression of the FDXR and frequency of MN. Peripheral blood samples were collected from healthy volunteers (HV) (n = 60; 43 males and 17 females) and T2DM patients (n = 60; 32 males and 28 females), and performed real-time quantification of FDXR gene expression and analysis of MN frequency using microscopy. The basal level of FDXR gene expression (2.55 folds) (p < 0.01) and the frequency of MN is significantly (p < 0.01) higher (4 folds) in T2DM patients when compared to HV. Further, subgroup analysis found that gender, alcohol, smoking, duration of T2DM, complications, and medications increased both the expression of the FDXR gene and frequency of MN in T2DM; nevertheless, the increase was not significant, except for gender (p < 0.05) and medication (p < 0.05) on the frequency of MN. Overall results indicate that the T2DM patients showed a higher basal level expression of the FDXR gene and MN frequency when compared to HV and suggest an altered metabolic condition in T2DM is a confounding factor that impacts the levels of those markers. The increased levels of these markers might need to be considered to monitor medical radiation exposures and reliable biodosimetry during large-scale radiological accidents.
{"title":"FDXR gene expression and micronucleus frequency in Type 2 diabetes mellitus patients and their importance in case of radiation exposures","authors":"Shravani A S , Priyanka R , Indumathi A N , Prabhakar Kamarthy , Venkatachalam Perumal , Venkateswarlu Raavi","doi":"10.1016/j.genrep.2024.102060","DOIUrl":"10.1016/j.genrep.2024.102060","url":null,"abstract":"<div><div>Analysis of gene expression (e.g. Ferredoxin Reductase: <em>FDXR</em>) changes in the blood samples have shown potential as predictive markers of disease, prognosis for therapy as well as triage and dose estimation in radiation-exposed populations. Similarly, quantification of micronuclei (MN) formation has been presented as a rapid cytogenetic marker for those applications. It was cautioned that the reliable utilization of these markers for prediction of disease, therapy prognosis, and dose estimation depends upon the information on known variables that affect these markers. Literature suggests that advanced glycation end products/oxidative stress in diabetic conditions can alter the levels of DNA damage and gene expression, and impact the segregation of the exposed from unexposed during nuclear disasters. Therefore, we investigated the influence of Type 2 diabetes mellitus (T2DM) on baseline expression of the <em>FDXR</em> and frequency of MN. Peripheral blood samples were collected from healthy volunteers (HV) (<em>n</em> = 60; 43 males and 17 females) and T2DM patients (n = 60; 32 males and 28 females), and performed real-time quantification of <em>FDXR</em> gene expression and analysis of MN frequency using microscopy. The basal level of <em>FDXR</em> gene expression (2.55 folds) (<em>p</em> < 0.01) and the frequency of MN is significantly (<em>p</em> < 0.01) higher (4 folds) in T2DM patients when compared to HV. Further, subgroup analysis found that gender, alcohol, smoking, duration of T2DM, complications, and medications increased both the expression of the <em>FDXR</em> gene and frequency of MN in T2DM; nevertheless, the increase was not significant, except for gender (<em>p</em> < 0.05) and medication (<em>p</em> < 0.05) on the frequency of MN. Overall results indicate that the T2DM patients showed a higher basal level expression of <em>the FDXR</em> gene and MN frequency when compared to HV and suggest an altered metabolic condition in T2DM is a confounding factor that impacts the levels of those markers. The increased levels of these markers might need to be considered to monitor medical radiation exposures and reliable biodosimetry during large-scale radiological accidents.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102060"},"PeriodicalIF":1.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142425213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1016/j.genrep.2024.102059
Juan Tan , Yiyun Xu , Yan Wang , Huiming Cui , Wenrong Wang , Ting Yin , Jianxin Tan , Zhengfeng Xu
Background
Femur length is one of the important indicators for evaluating fetal growth and development. Short femur is a common prenatal ultrasound finding. This study aimed to investigate the genetic etiology of fetal short femur using trio-based whole exome sequencing (WES), so as to provide evidence for prenatal diagnosis and evaluate the application of trio-WES in prenatal diagnosis of fetal short femur.
Methods
We retrospectively analyzed the clinical phenotype and WES results of eight fetuses with short femur diagnosed by prenatal ultrasound. The results of WES were validated by Sanger sequencing. The pathogenicity of the mutations was evaluated. Minigene assay was performed to investigate the effects of intronic mutation on mRNA splicing. The pregnancy outcome was followed up.
Results
A total of seven mutations were detected in eight short femur fetuses. Among them, COL2A1 (p.Gly1107Glu), GNAS (p.Lys739Glu) and FGFR3 (c.1075 + 95C > G) were novel mutations that had not been reported. Minigene assay showed that c.1075 + 95C > G in FGFR3 partially retained a 90 bp sequence in intron 8.
Conclusions
The results of this study enriched the mutant spectrums of COL2A1, GNAS and FGFR3 genes, and demonstrated the value of trio-WES in prenatal diagnosis of fetuses with short femur.
{"title":"Identification of mutations using whole exome sequencing in eight fetuses presenting with short femur","authors":"Juan Tan , Yiyun Xu , Yan Wang , Huiming Cui , Wenrong Wang , Ting Yin , Jianxin Tan , Zhengfeng Xu","doi":"10.1016/j.genrep.2024.102059","DOIUrl":"10.1016/j.genrep.2024.102059","url":null,"abstract":"<div><h3>Background</h3><div>Femur length is one of the important indicators for evaluating fetal growth and development. Short femur is a common prenatal ultrasound finding. This study aimed to investigate the genetic etiology of fetal short femur using trio-based whole exome sequencing (WES), so as to provide evidence for prenatal diagnosis and evaluate the application of trio-WES in prenatal diagnosis of fetal short femur.</div></div><div><h3>Methods</h3><div>We retrospectively analyzed the clinical phenotype and WES results of eight fetuses with short femur diagnosed by prenatal ultrasound. The results of WES were validated by Sanger sequencing. The pathogenicity of the mutations was evaluated. Minigene assay was performed to investigate the effects of intronic mutation on mRNA splicing. The pregnancy outcome was followed up.</div></div><div><h3>Results</h3><div>A total of seven mutations were detected in eight short femur fetuses. Among them, <em>COL2A1</em> (p.Gly1107Glu), <em>GNAS</em> (p.Lys739Glu) and <em>FGFR3</em> (c.1075 + 95C > G) were novel mutations that had not been reported. Minigene assay showed that c.1075 + 95C > G in FGFR3 partially retained a 90 bp sequence in intron 8.</div></div><div><h3>Conclusions</h3><div>The results of this study enriched the mutant spectrums of COL2A1, <em>GNAS</em> and <em>FGFR3</em> genes, and demonstrated the value of trio-WES in prenatal diagnosis of fetuses with short femur.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102059"},"PeriodicalIF":1.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142425209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-06DOI: 10.1016/j.genrep.2024.102056
Doha El-Sayed Ellakwa , Seham Mohamed Saied El Nakeeb , Sawsan Ahmed Abd El Mohsen
Worldwide, liver fibrosis (LF) causes complications and has an elevated death rate. The prevalence of mesenchymal stem cell therapy (MSC) is a result of the lack of liver donors. In recent years, the study of stem cell therapy has advanced into a promising and cutting-edge field of study. The purpose of this study is to assess the possible value of in vitro preconditioning of bone marrow-derived mesenchymal stem cells (BMSCs) with sodium hydrogen sulfide (NaHS), which aims to encourage rats to benefit from stem cell therapy with carbon tetrachloride-induced liver fibrosis. Materials and Methods: Fifty male albino rats (6 weeks old & 120–150 g) were divided equally into 5 groups (10 rats each); the 1st group served as a negative control, the 2nd group was a positive control, in which rats received 2 mL/kg CCl4 (1:1 corn oil) twice a week for five weeks, and the remaining three groups received, in addition to CCL4, a NaHS solution (10 μmol/kg) every 2 days for 6 weeks, one dose of BMSCs (3 × 106 cells per rat) intravenously, and a single dose of BMSCs (3 × 106 cells per rat) in culture with 200 μmol/L NaHS for 24 h. Quantitative gene expression of transforming growth factor-beta (TGF-β), Smad, collagen, α-SMA, MAPK, β-catenin, GSK-3B, and CBS was carried out using real-time polymerase chain reaction; whereas the serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and albumin were estimated using colorimetric analysis. Also, the relative expression of MAPK, β-catenin, and GSK-3B by Western blot was done. Histopathological analysis was used to gauge the progression of LF. Results: The liver fibrosis group exhibited significantly increased serum ALT and AST levels, along with decreased serum albumin levels, compared to controls. Additionally, compared to controls, there was a rise in the gene expression of TGF-β, Smad, collagen, α-SMA, MAPK, β-catenin, and GSK-3B, while the gene expression of CBS is decreased. The biochemical parameters indicated above were greatly improved by BMSCs pretreated with H2S, and the liver sections produced from this group demonstrated a notable improvement in histopathology. Conclusion: The study investigated and demonstrated how NaHS affected the efficacy of BMSC therapy in rats with CCl4-induced liver fibrosis.
{"title":"The impact of hydrogen sulfide on mesenchymal stem cells in rats suffering from liver fibrosis via suppression of TGF-β signaling","authors":"Doha El-Sayed Ellakwa , Seham Mohamed Saied El Nakeeb , Sawsan Ahmed Abd El Mohsen","doi":"10.1016/j.genrep.2024.102056","DOIUrl":"10.1016/j.genrep.2024.102056","url":null,"abstract":"<div><div>Worldwide, liver fibrosis (LF) causes complications and has an elevated death rate. The prevalence of mesenchymal stem cell therapy (MSC) is a result of the lack of liver donors. In recent years, the study of stem cell therapy has advanced into a promising and cutting-edge field of study. The purpose of this study is to assess the possible value of in vitro preconditioning of bone marrow-derived mesenchymal stem cells (BMSCs) with sodium hydrogen sulfide (NaHS), which aims to encourage rats to benefit from stem cell therapy with carbon tetrachloride-induced liver fibrosis. Materials and Methods: Fifty male albino rats (6 weeks old & 120–150 g) were divided equally into 5 groups (10 rats each); the 1st group served as a negative control, the 2nd group was a positive control, in which rats received 2 mL/kg CCl4 (1:1 corn oil) twice a week for five weeks, and the remaining three groups received, in addition to CCL4, a NaHS solution (10 μmol/kg) every 2 days for 6 weeks, one dose of BMSCs (3 × 10<sup>6</sup> cells per rat) intravenously, and a single dose of BMSCs (3 × 10<sup>6</sup> cells per rat) in culture with 200 μmol/L NaHS for 24 h. Quantitative gene expression of transforming growth factor-beta (TGF-β), Smad, collagen, α-SMA, MAPK, β-catenin, GSK-3B, and CBS was carried out using real-time polymerase chain reaction; whereas the serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and albumin were estimated using colorimetric analysis. Also, the relative expression of MAPK, β-catenin, and GSK-3B by Western blot was done. Histopathological analysis was used to gauge the progression of LF. Results: The liver fibrosis group exhibited significantly increased serum ALT and AST levels, along with decreased serum albumin levels, compared to controls. Additionally, compared to controls, there was a rise in the gene expression of TGF-β, Smad, collagen, α-SMA, MAPK, β-catenin, and GSK-3B, while the gene expression of CBS is decreased. The biochemical parameters indicated above were greatly improved by BMSCs pretreated with H2S, and the liver sections produced from this group demonstrated a notable improvement in histopathology. Conclusion: The study investigated and demonstrated how NaHS affected the efficacy of BMSC therapy in rats with CCl4-induced liver fibrosis.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102056"},"PeriodicalIF":1.0,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142425210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-05DOI: 10.1016/j.genrep.2024.102052
Joefred Mbogho Abogo , Cédric Sima Obiang , Herman Begouabe , Rick Léonid Ngoua Meye Misso , Juliette Ornely Orango Bourdette , Guy Roger Ndong Atome , Louis Clément Obame Engonga , Joseph Privat Ondo
Nowadays, a variety of infectious and non-infectious disorders are treated with various plants. This paper seeks to provide a framework for assessing and tracking the management of bacterial infections using immunological indicators of inflammation (cytokines). Thus, it demonstrates the production of inflammatory markers, the regulation of these markers by various plant extracts, the elimination of the various bacteria causing bacterial infections by these plant extracts, and, of course, a current report on the consequences of bacterial infections and their resistance to antibiotics. It has been demonstrated that plant extracts have a variety of immunomodulatory effects in vivo in addition to having antibacterial efficacy against multiple bacterial strains. The potential efficacy of medicinal plant extracts in controlling immune system gene expression makes them a vital tool for the diagnosis, management, and prevention of bacterial infections. The beliefs provided in this study need further investigation and refinement using modern scientific and technological methods.
{"title":"Evaluation of the efficacy of medicinal plants based on immunological biomarkers in the treatment of bacterial infections: Current status and future directions","authors":"Joefred Mbogho Abogo , Cédric Sima Obiang , Herman Begouabe , Rick Léonid Ngoua Meye Misso , Juliette Ornely Orango Bourdette , Guy Roger Ndong Atome , Louis Clément Obame Engonga , Joseph Privat Ondo","doi":"10.1016/j.genrep.2024.102052","DOIUrl":"10.1016/j.genrep.2024.102052","url":null,"abstract":"<div><div>Nowadays, a variety of infectious and non-infectious disorders are treated with various plants. This paper seeks to provide a framework for assessing and tracking the management of bacterial infections using immunological indicators of inflammation (cytokines). Thus, it demonstrates the production of inflammatory markers, the regulation of these markers by various plant extracts, the elimination of the various bacteria causing bacterial infections by these plant extracts, and, of course, a current report on the consequences of bacterial infections and their resistance to antibiotics. It has been demonstrated that plant extracts have a variety of immunomodulatory effects <em>in vivo</em> in addition to having antibacterial efficacy against multiple bacterial strains. The potential efficacy of medicinal plant extracts in controlling immune system gene expression makes them a vital tool for the diagnosis, management, and prevention of bacterial infections. The beliefs provided in this study need further investigation and refinement using modern scientific and technological methods.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102052"},"PeriodicalIF":1.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142425214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study aimed to identify carriers of Spinal Muscular Atrophy (SMA) among 10,630 pregnant women in Guangdong Province and provide prenatal diagnoses for high-risk fetuses from carrier couples. The goal was to prevent the birth of children affected by SMA. We evaluated the effectiveness of quantitative PCR (qPCR) and multiplex ligation-dependent probe amplification (MLPA) in detecting deletions in the SMN1 gene, with MLPA as the reference standard.
Methods
Fluorescent qPCR was used for initial SMA carrier screening, followed by confirmatory testing with MLPA for all detected carriers.
Results
Of the 10,630 women screened, 219 were identified as carriers (2.06 % detection rate). This included 17 cases of heterozygous deletion of exon 7 (E7), 145 cases with deletions of both E7 and exon 8 (E8), and 57 cases of E8 deletion alone. The carrier rate for E7 heterozygous deletion was established at 1.5 %. Prenatal diagnosis for seven carrier couples revealed five fetuses as carriers and one affected by SMA. The diagnostic concordance between qPCR and MLPA was 100 %.
Conclusion
The combined use of qPCR and MLPA is vital in identifying SMA carriers, allowing for early diagnosis and informed reproductive decisions. The high sensitivity and specificity of qPCR, matching MLPA, demonstrate its value in clinical settings for SMA screening and prenatal diagnosis. Our findings emphasize the critical importance of selecting precise diagnostic methods to enhance clinical outcomes in genetic screening programs.
{"title":"Clinical significance of Spinal Muscular Atrophy carrier detection in Guangdong Province, China: Insights from quantitative polymerase chain reaction and multiplex ligation-dependent probe amplification analysis","authors":"Chenxia Xu , Jianming Peng , Xuewei Wu , Shengping Xiao , Sheng Zhang , Miaoyuan Li","doi":"10.1016/j.genrep.2024.102055","DOIUrl":"10.1016/j.genrep.2024.102055","url":null,"abstract":"<div><h3>Objective</h3><div>This study aimed to identify carriers of Spinal Muscular Atrophy (SMA) among 10,630 pregnant women in Guangdong Province and provide prenatal diagnoses for high-risk fetuses from carrier couples. The goal was to prevent the birth of children affected by SMA. We evaluated the effectiveness of quantitative PCR (qPCR) and multiplex ligation-dependent probe amplification (MLPA) in detecting deletions in the SMN1 gene, with MLPA as the reference standard.</div></div><div><h3>Methods</h3><div>Fluorescent qPCR was used for initial SMA carrier screening, followed by confirmatory testing with MLPA for all detected carriers.</div></div><div><h3>Results</h3><div>Of the 10,630 women screened, 219 were identified as carriers (2.06 % detection rate). This included 17 cases of heterozygous deletion of exon 7 (E7), 145 cases with deletions of both E7 and exon 8 (E8), and 57 cases of E8 deletion alone. The carrier rate for E7 heterozygous deletion was established at 1.5 %. Prenatal diagnosis for seven carrier couples revealed five fetuses as carriers and one affected by SMA. The diagnostic concordance between qPCR and MLPA was 100 %.</div></div><div><h3>Conclusion</h3><div>The combined use of qPCR and MLPA is vital in identifying SMA carriers, allowing for early diagnosis and informed reproductive decisions. The high sensitivity and specificity of qPCR, matching MLPA, demonstrate its value in clinical settings for SMA screening and prenatal diagnosis. Our findings emphasize the critical importance of selecting precise diagnostic methods to enhance clinical outcomes in genetic screening programs.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102055"},"PeriodicalIF":1.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142425211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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