Functional & Integrative Genomics最新文献

{"title":"Identification, charectrization and genetic transformation of lignin and pectin polysaccharides through CRISPR/Cas9 in Nicotiana tobacum","authors":"Rana Imtiaz Ahmed,&nbsp;Angyan Ren,&nbsp;Dalal Sulaiman Alshaya,&nbsp;Sajid Fiaz,&nbsp;Yingzhen Kong,&nbsp;Shoaib Liaqat,&nbsp;Naushad Ali,&nbsp;Muhammad Abu Bakar Saddique,&nbsp;Kotb A. Attia,&nbsp;Mahmood Ul Hassan Taga","doi":"10.1007/s10142-024-01472-2","DOIUrl":"10.1007/s10142-024-01472-2","url":null,"abstract":"<div><p>CRISPR/<i>Cas9</i> system has been successfully implemented in animals and plants is a second-generation genome editing tool. We are able to optimize a <i>Cas9</i> system to edited <i>Ntab06050</i> and <i>Ntab0857410</i> genes in HD and K326 tobacco cultivars respectively. The gene <i>Ntab06050</i> is related to lignin synthesis while the gene <i>Ntab0857410</i> belongs to pectin synthesis by utilizing <i>Agrobacterium</i>-mediated leaf disc method. We have constructed total eight different constructs for the lignin related gene family <i>CCoAMT</i>, out of which three constructs have been selected from <i>Ntab0184090</i>, two constructs from <i>Ntab0392460</i> while one construct from each <i>Ntab0540120</i>, <i>Ntab0857410</i> and <i>Ntab0135940</i> gene. To study the <i>Cas9</i> system in pectin related genes, total five constructs have been utilized under <i>Cas9</i> system and multiple target sites were selected by identifying PAM sequences. Out of which three constructs were targeted from <i>NtabGAE1</i>and <i>NtabGAE6</i> homologous while two were targeted from <i>NtabGAUT4</i> homologous. Where as, UDP-D-glucuronate 4-epimerase gene family is a Golgi localized, might have a role in the interconvertion of UDP-D-GlcA and UDP-D-GalA in pectin synthesis. We have succeeded in the mutation of pectin related <i>NtabGAUT4</i> and lignin related <i>NtabCCoAMT</i> genes with 6.2% and 9.4% mutation frequency.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reference-based genome assembly and comparative genomics of Calamus Brandisii Becc. for unveiling sex-specific genes for early gender detection","authors":"Muneera Parveen Abdul Bari,&nbsp;Suma Arun Dev,&nbsp;Sarath Paremmal,&nbsp;Sreekumar V. B,&nbsp;Modhumita Ghosh Dasgupta","doi":"10.1007/s10142-024-01468-y","DOIUrl":"10.1007/s10142-024-01468-y","url":null,"abstract":"<div><p><i>Calamus brandisii</i> Becc. is an endangered rattan species indigenous to the Western Ghats of India and used in the furniture and handicraft industries. However, its dioecious nature and longer flowering time pose challenges for conservation efforts. Developing markers for early gender detection in seedlings is crucial for maintaining viable populations for in-situ and <i>ex-situ</i> conservation. Currently, no sex chromosomes or gender-specific genes have been reported in the species. We report the first comprehensive comparative genomics study between the male and female genomes of <i>C. brandisii</i> to identify polymorphisms and potential genes for gender determination. Reference-based assembly was conducted and the male and female genomes were predicted to contain 43,810 and 50,493 protein-coding genes respectively. The haploid genome size was ∼691 Mb and ∼884 Mb for male and female genomes respectively. Comparative analysis revealed significant genetic variation between the two genomes including 619,776 SNPs, 73,659 InDels, 212,123 Structural variants (SVs) and 305 copy number variations (CNVs). A total of 5 male-specific and 11 female-specific genes linked to the sex determining region was predicted. The genomic variants identified between the two genomes could be used in development of markers for early gender identification in <i>C. brandisii</i> for restoration programs. The gender-specific genes identified in this study also provide new insights into the mechanisms of sex determination and differentiation in rattans.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142411214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mechanism of MMP14-positive tumor-associated fibroblast subsets in inhibiting PD-1 immunotherapy for esophageal cancer through exosomal tsRNA-10522","authors":"Juzheng Wang,&nbsp;Chunlong Zheng,&nbsp;Jiayu Lu,&nbsp;Xinyao Xu,&nbsp;Guangyu Xiang,&nbsp;Jiahe Li,&nbsp;Jipeng Zhang,&nbsp;Xiaorong Mu,&nbsp;Qiang Lu","doi":"10.1007/s10142-024-01447-3","DOIUrl":"10.1007/s10142-024-01447-3","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear integration of MYB36 and APX-1 genes impart heat tolerance in wheat","authors":"Hina Firdous,&nbsp;Arfan Ali,&nbsp;Muhammad Mubashar Zafar,&nbsp;Faiz Ahmad Joyia,&nbsp;Muhammad Hamza,&nbsp;Abdul Razzaq,&nbsp;Muhammad Uzair,&nbsp;Sezai Ercisli,&nbsp;Waqas Shafqat Chattha,&nbsp;Mahmoud F. Seleiman,&nbsp;Naeem Khan,&nbsp;Xuefei Jiang","doi":"10.1007/s10142-024-01456-2","DOIUrl":"10.1007/s10142-024-01456-2","url":null,"abstract":"<div><p>Elevated temperatures during grain filling stage, exceeding the optimal range by 3–4 °C, not only results in a substantial yield reduction in wheat by 10–50% but activates disease and insect infestation. In this research, we introduced heat-tolerant <i>MYB36</i> and <i>APX-1</i> gene cassettes into wheat, employing an efficient <i>Agrobacterium</i> mediated transformation protocol, demonstrating higher transformation efficiency. The study encompassed the assembly of <i>MYB36</i> and <i>APX-1</i> gene cassettes, and confirmation of gene products in <i>Agrobacterium</i>, followed by the transformation of the <i>MYB36</i> and <i>APX-1</i> genes into wheat explants. We were able to select transgenic plant with various combinations. The transgenic plants with <i>APX-1</i> gene alone produced medium sized grain and spike whereas with both <i>APX-1</i> and <i>MYB36</i> genes expressed individually under <i>SPS</i> and <i>rd29a</i> promoter respectively showed good tolerance to heat at 32^oC at grain filling/milking stage and produced relatively bold grains. While non-transgenic plants grains were wrinkled with thin spike showing susceptibility to heat. This research contributes to the broader scientific understanding of plant stress responses and the combined effectiveness of <i>MYB36</i> and <i>APX-1</i> genes in crop improvement without disturbing normal nutritional values. The gene integration can serve as a valuable tool in breeding programs aimed at developing heat-tolerant wheat varieties. These findings also advance our comprehension of the functions of heat-induced genes and lay the foundation for selecting optimal candidates for in-depth functional studies of heat-responsive <i>MYB36</i> and <i>APX-1</i> genes in wheat.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ALDH2 alleviates inflammation and facilitates osteogenic differentiation of periodontal ligament stem cells in periodontitis by blocking ferroptosis via activating Nrf2","authors":"Jia Chen,&nbsp;Chen Hu,&nbsp;Xun Lu,&nbsp;Xiaoqin Yang,&nbsp;Meng Zhu,&nbsp;Xiaozhou Ma,&nbsp;Yiqiang Yang","doi":"10.1007/s10142-024-01465-1","DOIUrl":"10.1007/s10142-024-01465-1","url":null,"abstract":"<div><p>This paper elucidated the effects and mechanisms of aldehyde dehydrogenase 2 (ALDH2) on periodontitis. Rat model of periodontitis and periodontal ligament stem cell (PDLSC) model of periodontitis were constructed. PDLSC were transfected by ALDH2 overexpression vectors, and then treated by ML385 (Nrf2 inhibitor), ferrostatin-1 (ferroptosis inhibitor) and FIN56 (ferroptosis inducer), respectively. ALDH2, nuclear factor erythroid 2-related factor 2 (Nrf2) and glutathione peroxidase 4 (GPX4) proteins was evaluated by immunohistochemistry and Western blot. Ferroptosis-related factors, including Fe²⁺ and glutathione (GSH), were assessed by commercial kits. Pro-inflammatory factors (interleukin-6 [IL-6] and tumor necrosis factor-α [TNF-α]) and osteogenic differentiation-related proteins (osteocalcin [OCN] and runt-related transcription factor 2 [RUNX2]) were scrutinized by commercial kits and Western blot. In both periodontal tissues of periodontitis rats and PDLSC model of periodontitis, down-regulated ALDH2, Nrf2, GPX4 and GSH, but elevated Fe²⁺ level was discovered. ALDH2 overexpression in PDLSC resulted in an increase in Nrf2 expression. In PDLSC model of periodontitis, ALDH2 increased GPX4 and GSH levels, decreased Fe²⁺, IL-6 and TNF-α levels, and elevated OCN and RUNX2 expression. However, these effects of ALDH2 were counteracted by ML385. Additionally, the suppression of ALDH2 on IL-6 and TNF-α levels and promotion of it on OCN and RUNX2 expression in PDLSC model of periodontitis was further intensified by ferrostatin-1, but reversed by FIN56. ALDH2 may alleviate inflammation and facilitate osteogenic differentiation of PDLSC in periodontitis by hindering ferroptosis via activating Nrf2, suggesting it to be a promising candidate for treating periodontitis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"KRAS mutations detection methodology: from RFLP to CRISPR/Cas based methods","authors":"Firouzeh Morshedzadeh,&nbsp;Mohammad Reza Abbaszadegan,&nbsp;Maryam Peymani,&nbsp;Sina Mozaffari-Jovin","doi":"10.1007/s10142-024-01421-z","DOIUrl":"10.1007/s10142-024-01421-z","url":null,"abstract":"<div><p>In personalized cancer medicine, the identification of <i>KRAS</i> mutations is essential for making treatment decisions and improving patient outcomes. This work presents a comprehensive review of the current approaches for detection of <i>KRAS</i> mutations in different cancers. We highlight the value of fast and reliable <i>KRAS</i> mutations discovery and the effectiveness of molecular testing for selecting individuals who might benefit from targeted therapy. We provide an overview of various methods and tools available for detecting <i>KRAS</i> mutations, such as digital droplet PCR, next-generation sequencing (NGS), and polymerase chain reaction (PCR). We also address the difficulties and limitations in the identification of <i>KRAS</i> mutations, namely tumor heterogeneity and the emergence of resistance mechanisms. This article aims to guide clinicians in <i>KRAS</i> mutation identification.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation","authors":"Justin L. Blaize,&nbsp;Jada Lauren N. Garzon,&nbsp;Niall G. Howlett","doi":"10.1007/s10142-024-01453-5","DOIUrl":"10.1007/s10142-024-01453-5","url":null,"abstract":"<div><p>Fanconi anemia (FA) is a rare genetic disease characterized by congenital abnormalities and increased risk for bone marrow failure and cancer. Central nervous system defects, including acute and irreversible loss of neurological function and white matter lesions with calcifications, have become increasingly recognized among FA patients, and are collectively referred to as Fanconi Anemia Neurological Syndrome or FANS. The molecular etiology of FANS is poorly understood. In this study, we have used a functional integrative genomics approach to further define the function of the FANCD2 protein and FA pathway. Combined analysis of new and existing FANCD2 ChIP-seq datasets demonstrates that FANCD2 binds nonrandomly throughout the genome with binding enriched at transcription start sites and in broad regions spanning protein-coding gene bodies. FANCD2 demonstrates a strong preference for large neural genes involved in neuronal differentiation, synapse function, and cell adhesion, with many of these genes implicated in neurodevelopmental and neuropsychiatric disorders. Furthermore, FANCD2 binds to regions of the genome that replicate late, undergo mitotic DNA synthesis (MiDAS) under conditions of replication stress, and are hotspots for copy number variation. Our analysis describes an important targeted role for FANCD2 and the FA pathway in the maintenance of large neural gene stability.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study","authors":"Suhas K. Kadam,&nbsp;Jin-Suk Youn,&nbsp;Asif S. Tamboli,&nbsp;JiYoung Yang,&nbsp;Jae Hong Pak,&nbsp;Yeon-Sik Choo","doi":"10.1007/s10142-024-01464-2","DOIUrl":"10.1007/s10142-024-01464-2","url":null,"abstract":"<div><p>The Asteraceae family, particularly the <i>Artemisia</i> genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of <i>Artemisia littoricola</i> sourced from Dokdo Island, employing comparative analyses across six diverse <i>Artemisia</i> species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of <i>A. littoricola</i> spans 150,985 bp, consistent with other <i>Artemisia</i> species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while <i>clp</i>P and <i>ycf</i>3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position <i>A. littoricola</i> within subgenus <i>Dracunculus</i>, indicating a close relationship with <i>A. scoparia</i> and <i>A. desertorum</i>. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding <i>Artemisia</i> diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of <i>Artemisia’s</i> intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning in oncological pharmacogenomics: advancing personalized chemotherapy","authors":"Cigir Biray Avci,&nbsp;Bakiye Goker Bagca,&nbsp;Behrouz Shademan,&nbsp;Leila Sabour Takanlou,&nbsp;Maryam Sabour Takanlou,&nbsp;Alireza Nourazarian","doi":"10.1007/s10142-024-01462-4","DOIUrl":"10.1007/s10142-024-01462-4","url":null,"abstract":"<div><p>This review analyzes the application of machine learning (ML) in oncological pharmacogenomics, focusing on customizing chemotherapy treatments. It explores how ML can analyze extensive genomic, proteomic, and other omics datasets to identify genetic patterns associated with drug responses. This, in turn, facilitates personalized therapies that are more effective and have fewer side effects. Recent studies have emphasized ML’s revolutionary role of ML in personalized oncology treatment by identifying genetic variability and understanding cancer pharmacodynamics. Integrating ML with electronic health records and clinical data shows promise in refining chemotherapy recommendations by considering the complex influencing factors. Although standard chemotherapy depends on population-based doses and treatment regimens, customized techniques use genetic information to tailor treatments for specific patients, potentially enhancing efficacy and reducing adverse effects.However, challenges, such as model interpretability, data quality, transparency, ethical issues related to data privacy, and health disparities, remain. Machine learning has been used to transform oncological pharmacogenomics by enabling personalized chemotherapy treatments. This review highlights ML’s potential of ML to enhance treatment effectiveness and minimize side effects through detailed genetic analysis. It also addresses ongoing challenges including improved model interpretability, data quality, and ethical considerations. The review concludes by emphasizing the importance of rigorous clinical trials and interdisciplinary collaboration in the ethical implementation of ML-driven personalized medicine, paving the way for improved outcomes in cancer patients and marking a new frontier in cancer treatment.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: QTL-seq identifies genomic region associated with the crown root development under Jasmonic acid response","authors":"Tam Thi Thanh Tran,&nbsp;Liem Huu Minh Le,&nbsp;Trang Thi Nguyen,&nbsp;Thanh Chi Nguyen,&nbsp;Trang Thi Huyen Hoang,&nbsp;Phat Tien Do,&nbsp;Huong Thi Mai To","doi":"10.1007/s10142-024-01461-5","DOIUrl":"10.1007/s10142-024-01461-5","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}