Gene Reports最新文献

{"title":"Genome mining approach reveals the CRISPR-Cas characteristics and diversity of targeting phages in Lactobacillus iners strains","authors":"Yousef Nami ,&nbsp;Behnaz Dehghanzad ,&nbsp;Mohaddeseh Rostampour ,&nbsp;Bahman Panahi","doi":"10.1016/j.genrep.2024.101968","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101968","url":null,"abstract":"<div><p>This study utilized a genomic approach to investigate CRISPR-Cas systems, focusing on <em>Lactobacillus iners</em> strains, which are crucial for bacterial defense against bacteriophage attacks. Genome sequences were analyzed to understand the diversity, occurrence, and evolution of these systems. Spacer sequences within CRISPR arrays were examined to identify targeted phages. The research explored the evolutionary paths of spaceromes within each CRISPR array subtype, considering acquisition and deletion events influenced by phage pressure. Results revealed that approximately 50 % of L. <em>iners</em> strains possess complete CRISPR-Cas systems, predominantly subtype II-A and I-E. Homology analysis indicated that subtype I-E systems target a wider range of foreign phages compared to subtype II-A systems. Overall, the findings underscore the varied components and structure of CRISPR-Cas systems in L. <em>iners</em> strains, highlighting their role as active immune defenses against phages and foreign DNA.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141543030","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}

{"title":"The roles of miR-383 as a diagnostic and prognostic biomarker in human cancers","authors":"Reza Panahizadeh ,&nbsp;Mohammadamin Vatankhah ,&nbsp;Pourya Gholizadeh ,&nbsp;Elnaz Faghfuri ,&nbsp;Yasamin Pahlavan ,&nbsp;Narges Soozangar ,&nbsp;Kazem Nejati-Koshki","doi":"10.1016/j.genrep.2024.101966","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101966","url":null,"abstract":"<div><p>Emerging evidence indicates that Long non-coding RNAs (LncRNAs) and microRNAs (miRNAs) play crucial roles in the biology of cancerous cells. MicroRNAs are small non-coding RNAs, which play essential roles in the different cellular processes of various cancers. The miR-383 was initially found as a tumor suppressor and prognostic marker in different human cancers. The regulation of miR-383 and its target gene expression could be helpful in the prevention of tumorigenesis, improving cancer prognosis, and enhancing 5-year survival of patients with cancer. Current study suggests that miR-383 expression is implicated in the pathogenesis and in predicting molecular progression, cellular proliferation, and patient prognosis in various carcinomas. The up-regulation of miR-383 can reduce the prognosis of the cancers. MiR-383 exerts its tumor-suppressive effects in vitro by targeting specific proteins and molecules, which regulate the signaling pathways of cancer cells. Therefore, we aimed to discuss the different functions of miR-383 in various cancers and highlight its role in the signaling pathways regulation, that are involved in cancers.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141606037","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}

{"title":"Thermophage triumph: Harnessing archaeal plasmids in the fight against tuberculosis","authors":"Kannan Kamala ,&nbsp;Pitchiah Sivaperumal","doi":"10.1016/j.genrep.2024.101967","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101967","url":null,"abstract":"","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141543029","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}

{"title":"Multiple cytokinin elevates indirect regeneration potential of indica rice mature embryo","authors":"Monoj Sutradhar ,&nbsp;Brijesh Kumar Singh ,&nbsp;Subhasis Samanta ,&nbsp;Md. Nasim Ali ,&nbsp;Nirmal Mandal","doi":"10.1016/j.genrep.2024.101965","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101965","url":null,"abstract":"<div><p>The concept of producing high quality mature seed derived callus competent to genetic transformation followed by efficient full plant regeneration is not unique in rice. But the process is lacking in terms of regeneration efficiency, genotype dependency especially in <em>indica</em> rice. Further, most of the research has only been focused on elite <em>indica</em> cultivars and popular local varieties are neglected. Our extensive literature study also revealed that among all the factors responsible for higher rice regeneration efficiency, the combination, concentration, and type plant growth regulators (PGRs) are mostly responsible for <em>indica</em> rice genotypes. Hence, the present study is focused on standardization of popular local <em>indica</em> rice cultivars for callus induction and regeneration by tweaking the PGRs in culture media, according to their amenability. The plant regeneration potential was assessed on both traditional organogenesis frequency and morphology-based scoring matrix. This revealed the best suitable PGR concentration-combination for efficient organogenesis and the genotype Khitish to be most responsive for indirect regeneration (78.68 ± 1.50 %). The highly polymorphic SSR marker based clonal fidelity test also validated the absence of somaclonal variation among the regenerated plants. This study would be helpful in improving the regeneration potential in local <em>indica</em> rice varieties and genetic transformation studies.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141543031","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}

{"title":"Revolutionizing genetic diagnostics: Innovative techniques for inherited disease detection","authors":"Shradha Devi Dwivedi,&nbsp;Sachin Dev Yadav,&nbsp;Divya Sahu,&nbsp;Deependra Singh,&nbsp;Manju Rawat Singh","doi":"10.1016/j.genrep.2024.101963","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101963","url":null,"abstract":"<div><p>Genetic inheritance refers to the process by which traits and characteristics are passed from one generation to the next through the transmission of genetic information. This information is stored in the form of DNA (deoxyribonucleic acid), which is organized into structures called genes. Genetic hereditary disorders can be broadly classified into four categories on the basis of mode of inheritance and location of genes or chromosomes, they are: x-linked dominant, x-linked recessive, autosomal dominant and autosomal recessive. A specific diagnostic method is necessary for the diagnosis of inherited disorders. For instance, ARMPCR (amplification refractory mutation system polymerase chain reaction) is used to identify sickle cell anaemia, Breast cancer by crisper technology, and HIV (human immunodeficiency virus) can be detected by sandwich ELISA (enzyme linked immunosorbent assay) test. Mutation on FMR1 alleles in Fragile-X syndrome can be determined by TP-PCR (Triplet Repeat Primed-Polymerase Chain Reaction). Alteration on FBN1 gene in Marfan syndrome can be identified by a FISH (fluorescence in situ hybridization) test. All these tests are highly specific in nature, which depend upon genomic sequences, temperature, blood count and many more. To get a deeper comprehension of hereditary problems, we have expanded on a numerous methods and diagnostic criteria in this study. This study discusses many techniques for quickly and precisely identifying genetically inherited disorders.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141606035","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}

{"title":"Detecting drug-resistant human cytomegalovirus mutations in liver transplant recipients: A study of the UL97 gene","authors":"Leila Jalilsani ,&nbsp;Ramin Yaghobi ,&nbsp;Bita Geramizadeh ,&nbsp;Afsoon Afshari ,&nbsp;Mohammad Hossein Karimi","doi":"10.1016/j.genrep.2024.101962","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101962","url":null,"abstract":"<div><p>Human cytomegalovirus (HCMV or HHV-5) is a member of the beta herpesvirus family and remains dormant for life after the initial infection. However, if conditions such as immunosuppression occur, the virus can become active again and lead to severe diseases. The incidence of disease in solid organ transplant (SOT) recipients is reduced by prophylactic use of ganciclovir (either intravenously or orally). This study aimed to determine the pattern of clinical mutations associated with the cytomegalovirus <em>UL97</em> gene after treatment with ganciclovir and the effect of these mutations on disease progression in liver transplant recipients infected with Iranian HCMV strains. Six HCMV-positive liver transplant recipients were enrolled, comprising 3 (50.0 %) males and 3 (50.0 %) females. Sequence analysis and mutation detection were performed using Finch software (version 1.4.0) and the NCBI Nucleotide Blast database, whereas phylogenetic analysis was performed using MEGA X (version 10.0.5). Mann-Whitney U nonparametric test, Chi-square test, Spearman's correlation coefficient analysis, were employed for statistical analysis. The results of the study showed that two samples from two patients had mutations in the <em>UL97</em> gene, and the viral load of the mutated samples decreased after administering antiviral medications. Furthermore, the phylogenetic tree demonstrated a close relationship between the Iranian HCMV strains and global reference sequences.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141482582","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}

{"title":"Molecular characterization of head and neck infection causing bacterial communities using 16S rRNA in eastern Indian population","authors":"","doi":"10.1016/j.genrep.2024.101959","DOIUrl":"10.1016/j.genrep.2024.101959","url":null,"abstract":"<div><p>Head and neck infections (HNI) are dangerous illnesses caused by a variety of bacterial species. The absence of enough surveillance as well as information regarding the bacteria prevalence in the infected area and the use of excessive antibiotics leads to multidrug-resistant (MDR) pathogens that cause serious health hazards. Thus, in the present study, a surveillance program was carried out in an eastern state of India, known as Odisha to decipher the pool of bacterial genus prevalence and their relationship with related species. The positive clinical specimens obtained through preliminary screening by Vitek 2 were further characterized by utilizing the 16S rRNA gene followed by population genetic and phylogenetic analysis. The investigation resulted four bacterial species, such as <em>Staphylococcus aureus</em>, <em>Klebsiella pneumoniae</em>, <em>Acinetobacter baumannii</em>, and <em>Pseudomonas aeruginosa</em>. According to population genetic factors, the haplotype (Hd) and nucleotide diversity (π) ranged from 0.558 to 0.828 and 0.03236 to 0.28428. The phylogeny analysis revealed that the present isolates were closely related to Chinese isolates. The prevalence of these pathogens within the eastern part of India and its transboundary potential revealed through phylogenetic analysis need further in-depth research to obtain a better therapeutic approach.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141638084","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}

{"title":"Evaluation of the diagnostic role of circulating miR-16, miR-10b, and miR-21 expression in patients with nonalcoholic fatty liver disease","authors":"Fatemeh Amani ,&nbsp;Amirhossein Sahebkar ,&nbsp;Seyed Hamid Aghaee-Bakhtiari ,&nbsp;Mohammadreza Farzanehfar ,&nbsp;Saeedeh Askarian ,&nbsp;Reza Kazemi Oskuee","doi":"10.1016/j.genrep.2024.101964","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101964","url":null,"abstract":"<div><p>Non-alcoholic fatty liver disease (NAFLD) is a growing global health concern and is characterized by fat accumulation in the liver in the absence of significant alcohol consumption. However, current diagnostic tools, including liver biopsy and imaging techniques, have limitations in terms of accessibility, invasiveness, and sensitivity. Recently, microRNAs (miRNAs) have emerged as non-invasive biomarkers for the diagnosis of NAFLD. In this study, we investigated the expression of three microRNAs (miR-16, miR-10b, and miR-21) in patients with NAFLD across different disease stages compared with healthy subjects. First, miRNAs were extracted from serum samples collected from 34 healthy controls and 38 patients with NAFLD, including 20 with grade 1 and 18 with grade 2 of the disease. Subsequently, cDNA was synthesized from RNA, and miR-21, miR-16, and miR-10b expression was measured using RT-qPCR. The results revealed the downregulation of miR-16 in the early and advanced stages of NAFLD. The serum expression of miR-21 (<em>p</em> &lt; 0 0.01) and miR-10b (<em>p</em> &lt; 0.05) increased in the total NAFLD samples compared with the control group. Moreover, miR-10b expression was significantly higher in patients with stage 2 of NAFLD than in those with stage1 of NAFLD (p &lt; 0.05), suggesting its potential as a biomarker to distinguish between the different grades of the disease. Our results revealed the clinical value of these miRNAs as non-invasive, sensitive, and stage-specific biomarkers for NAFLD. These findings suggest that the assessment of miR-16, miR-21, and miR-10b expression levels could serve as a potentially useful tool for the diagnosis of NAFLD presence and severity.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141596669","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}

{"title":"Comparative expression profile of selected genes in Venturia inaequalis Cooke (Wint.) infecting apple fruits and leaves","authors":"Suhani Bhagta ,&nbsp;Sundaresha Siddappa ,&nbsp;Vinay Bhardwaj ,&nbsp;Anil Kant","doi":"10.1016/j.genrep.2024.101961","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101961","url":null,"abstract":"<div><p>Scab is a noxious fungal disease of apples (<em>Malus domestica</em> Borkh) in all apple producing regions caused by a host-specific phytopathogen <em>Venturia inaequalis</em> Cooke (Wint.). Its symptoms include black or brown lesions on leaves as well as on fruits, and causes fruit deformation. In this study, <em>V. inaequalis</em> was isolated from infected fruit samples and expression level of selected pathogenesis related genes in scab infected fruits and leaves was studied. The isolated fungus formed a brown coloured mat-like colony having septate mycelium and produced acute ovoid shaped conidia. Molecular characterization of the fungus was done by amplification and sequencing of internal transcribed spacer (<em>ITS</em>) and Cytochrome (<em>CYP51A1</em>) regions of the isolate. The Sanger sequencing of amplicons and sequence analysis using BLAST tool of the NCBI against GenBank database confirmed that the obtained sequence of <em>ITS</em> and <em>CYP51A1</em> regions had 99.6 % and 98 % sequence identity with the reference <em>V. inaequalis</em>, respectively. The isolated strain of <em>V. inaequalis</em> was submitted in the fungal repository of Microbial Type Culture Collection (MTCC), India. The phylogenetic analysis of <em>ITS</em> region of the isolate revealed that the isolated strain of <em>V. inaequalis</em> was more closely related to <em>Fusicladium eriobotryae</em> compared to other <em>Venturia</em> species. The expression levels of pathogenesis related genes viz. <em>CIN1</em>, <em>CE5</em> and <em>VICE16</em> were higher in infected leaves as compared to infected fruits. Whereas expression of <em>VICE12</em> and <em>GH28</em> were higher in infected fruits compared to infected leaves. <em>VICE4</em> gene showed equal level of expression during infection in both fruits and leaves, which was also maximum as compared to the control treatment. The transcript analysis of aforementioned genes of <em>V. inaequalis</em> gives the insights of the pathogen's expression profile during pathogenesis in fruits and leaves. This expression analysis can form a basis selecting pathogenesis related genes as targets for developing dsRNA expressing constructs with an aim to reduce RNAi mediated silencing of specific genes, in a futuristic biotechnological based solution to deal with apple scab disease.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141482583","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}

{"title":"Association of ORMDL3 single nucleotide polymorphic variants with bronchial asthma in Pathan population","authors":"Waqas Safir ,&nbsp;Saba Altaf ,&nbsp;Peerzada Fawad Ullah Jan ,&nbsp;Nodia Shujaat ,&nbsp;Fahim Ullah Khan ,&nbsp;Atia Rehman ,&nbsp;Samra Kousar ,&nbsp;Muhammad Usman Ghani ,&nbsp;Muhammad Farooq Sabar ,&nbsp;Mariam Shahid","doi":"10.1016/j.genrep.2024.101958","DOIUrl":"https://doi.org/10.1016/j.genrep.2024.101958","url":null,"abstract":"<div><h3>Background</h3><p>Single nucleotide polymorphic variants of chromosome 17q21 potential candidate genes have been found to associate with asthma predisposition in many ethnically diverse populations. Identifying the potential SNPs, that are associated with asthma in a certain population, may lead to early diagnosis of genetic predisposition, thus reducing the treatment cost by timely management. This research work was planned to study the association of SNPs residing on chromosome 17q21, with asthma, in the Pathan population of Pakistan.</p></div><div><h3>Methods</h3><p>Sixty- two physician-diagnosed bronchial asthma cases and one hundred, age and gender-matched, control subjects of the Pathan ethnic group were enrolled for this study. Five SNPs from 17q21 were analyzed for their association with asthma by the Single Base Extension method using capillary-based electrophoresis. Allelic, dominant and recessive genotypic association analyses were done by PLINK and SHEsis plus version beta software, followed by Haploview v4.1 analysis of relevant haplotypes.</p></div><div><h3>Results</h3><p>Out of five studied SNPs, rs8076131 was significantly associated with bronchial asthma whereas rs9894164 tended to show a marginal association. Haplotype ‘TATT’ seemed to be a marginal risk factor associated with bronchial asthma in the studied population.</p></div><div><h3>Conclusion</h3><p>rs8076131 may be used as a predictive indicator of Bronchial Asthma development in risk allele carriers of Pathan ethnicity.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141444204","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}