Functional & Integrative Genomics最新文献

{"title":"Milletomics: a metabolomics centered integrated omics approach toward genetic progression","authors":"Saikat Mazumder,&nbsp;Debasmita Bhattacharya,&nbsp;Dibyajit Lahiri,&nbsp;Moupriya Nag","doi":"10.1007/s10142-024-01430-y","DOIUrl":"10.1007/s10142-024-01430-y","url":null,"abstract":"<div><p>Producing alternative staple foods like millet will be essential to feeding ten billion people by 2050. The increased demand for millet is driving researchers to improve its genetic variation. Millets include protein, dietary fiber, phenolic substances, and flavonoid components. Its climate resilience makes millet an appealing crop for agronomic sustainability. Integrative omics technologies could potentially identify and develop millets with desirable phenotypes that may have high agronomic value. Millets’ salinity and drought tolerance have been enhanced using transcriptomics. In foxtail, finger, and pearl millet, proteomics has discovered salt-tolerant protein, phytohormone-focused protein, and drought tolerance. Metabolomics studies have revealed that certain metabolic pathways including those involving lignin, flavonoids, phenylpropanoid, and lysophospholipids are critical for many processes, including seed germination, photosynthesis, energy metabolism, and the synthesis of bioactive chemicals necessary for drought tolerance. Metabolomics integration with other omics revealed metabolome engineering and trait-specific metabolite creation. Integrated metabolomics and ionomics are still in the development stage, but they could potentially assist in comprehending the pathway of ionomers to control nutrient levels and biofortify millet. Epigenomic analysis has shown alterations in DNA methylation patterns and chromatin structure in foxtail and pearl millets in response to abiotic stress. Whole-genome sequencing utilizing next-generation sequencing is the most proficient method for finding stress-induced phytoconstituent genes. New genome sequencing enables novel biotechnological interventions including genome-wide association, mutation-based research, and other omics approaches. Millets can breed more effectively by employing next-generation sequencing and genotyping by sequencing, which may mitigate climate change. Millet marker-assisted breeding has advanced with high-throughput markers and combined genotyping technologies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103191","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":"Bladder cancer: non-coding RNAs and exosomal non-coding RNAs","authors":"Jingang Zhao,&nbsp;Yangyang Ma,&nbsp;Xiaodong Zheng,&nbsp;Zhen Sun,&nbsp;Hongxiang Lin,&nbsp;Chuanjun Du,&nbsp;Jing Cao","doi":"10.1007/s10142-024-01433-9","DOIUrl":"10.1007/s10142-024-01433-9","url":null,"abstract":"<div><p>Bladder cancer (BCa) is a highly prevalent type of cancer worldwide, and it is responsible for numerous deaths and cases of disease. Due to the diverse nature of this disease, it is necessary to conduct significant research that delves deeper into the molecular aspects, to potentially discover novel diagnostic and therapeutic approaches. Lately, there has been a significant increase in the focus on non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), due to their growing recognition for their involvement in the progression and manifestation of BCa. The interest in exosomes has greatly grown due to their potential for transporting a diverse array of active substances, including proteins, nucleic acids, carbohydrates, and lipids. The combination of these components differs based on the specific cell and its condition. Research indicates that using exosomes could have considerable advantages in identifying and forecasting BCa, offering a less invasive alternative. The distinctive arrangement of the lipid bilayer membrane found in exosomes is what makes them particularly effective for administering treatments aimed at managing cancer. In this review, we have tried to summarize different ncRNAs that are involved in BCa pathogenesis. Moreover, we highlighted the role of exosomal ncRNAs in BCa.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103189","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":"Signaling molecules in the microenvironment of hepatocellular carcinoma","authors":"Wanjin Chen,&nbsp;Ming Tan,&nbsp;Hui Zhang,&nbsp;Tingting Gao,&nbsp;Jihua Ren,&nbsp;Shengtao Cheng,&nbsp;Juan Chen","doi":"10.1007/s10142-024-01427-7","DOIUrl":"10.1007/s10142-024-01427-7","url":null,"abstract":"<div><p>Hepatocellular carcinoma (HCC) is a major fatal cancer that is known for its high recurrence and metastasis. An increasing number of studies have shown that the tumor microenvironment is closely related to the metastasis and invasion of HCC. The HCC microenvironment is a complex integrated system composed of cellular components, the extracellular matrix (ECM), and signaling molecules such as chemokines, growth factors, and cytokines, which are generally regarded as crucial molecules that regulate a series of important processes, such as the migration and invasion of HCC cells. Considering the crucial role of signaling molecules, this review aims to elucidate the regulatory effects of chemokines, growth factors, and cytokines on HCC cells in their microenvironment to provide important references for clarifying the development of HCC and exploring effective therapeutic targets.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103193","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":"Application of single cell sequencing technology in ovarian cancer research (review)","authors":"Qiqolei Yuan,&nbsp;Nengyuan Lv,&nbsp;Qianying Chen,&nbsp;Siyi Shen,&nbsp;Yahui Wang,&nbsp;Jinyi Tong","doi":"10.1007/s10142-024-01432-w","DOIUrl":"10.1007/s10142-024-01432-w","url":null,"abstract":"<div><p>Ovarian cancer is a malignant tumor of ovary. It has the characteristics of difficult early diagnosis, poor late curative effect and high recurrence rate. It is the biggest disease that seriously threatens women’s health. Single cell sequencing technology refers to sequencing the genetic information carried by it at the single cell level to obtain the gene sequence, transcript, protein and epigenetic expression profile information of a certain cell type and conduct integrated analysis. It has unique advantages in the study of tumor occurrence and evolution, and can provide new methods for the study of ovarian cancer. This paper reviews the single cell sequencing technology and its application in ovarian cancer.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11358195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078801","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":"Infection by a multidrug-resistant Corynebacterium diphtheriae strain: prediction of virulence factors, CRISPR-Cas system analysis, and structural implications of mutations conferring rifampin resistance","authors":"Max Roberto Batista Araújo,&nbsp;Fernanda Diniz Prates,&nbsp;Juliana Nunes Ramos,&nbsp;Eduarda Guimarães Sousa,&nbsp;Sérgio Bokermann,&nbsp;Cláudio Tavares Sacchi,&nbsp;Ana Luiza de Mattos-Guaraldi,&nbsp;Karoline Rodrigues Campos,&nbsp;Mireille Ângela Bernardes Sousa,&nbsp;Verônica Viana Vieira,&nbsp;Marlon Benedito Nascimento Santos,&nbsp;Carlos Henrique Camargo,&nbsp;Lincoln de Oliveira Sant’Anna,&nbsp;Louisy Sanches dos Santos,&nbsp;Vasco Azevedo","doi":"10.1007/s10142-024-01434-8","DOIUrl":"10.1007/s10142-024-01434-8","url":null,"abstract":"<div><p>Cases of diphtheria, even in immunized individuals, are still reported in several parts of the world, including in Brazil. New outbreaks occur in Europe and other continents. In this context, studies on <i>Corynebacterium diphtheriae</i> infections are highly relevant, both for a better understanding of the pathogenesis of the disease and for controlling the circulation of clones and antimicrobial resistance genes. Here we present a case of cutaneous infection by multidrug-resistant <i>Corynebacterium diphtheriae</i> and provide its whole-genome sequencing. Genomic analysis revealed resistance genes, including <i>tet</i>(W), <i>sul</i>1, <i>cmx</i>, <i>rpo</i>B2, <i>rbp</i>A and mutation in <i>rpo</i>B. We performed phylogenetic analyzes and used the BRIG to compare the predicted resistance genes with those found in genomes from other significant isolates, including those associated with some outbreaks. Virulence factors such as <i>spa</i>D, <i>srt</i>BC, <i>spa</i>H, <i>srt</i>DE, surface-anchored pilus proteins (<i>sap</i>D), nonfimbrial adhesins (DIP0733, DIP1281, and DIP1621), <i>emb</i>C and <i>mpt</i>C (putatively involved in CdiLAM), <i>sig</i>A, <i>dtx</i>R and MdbA (putatively involved) in post-translational modification, were detected. We identified the CRISPR-Cas system in our isolate, which was classified as Type II-U based on the database and contains 15 spacers. This system functions as an adaptive immune mechanism. The strain was attributed to a new sequence type ST-928, and phylogenetic analysis confirmed that it was related to ST-634 of <i>C. diphtheriae</i> strains isolated in French Guiana and Brazil. In addition, since infections are not always reported, studies with the sequence data might be a way to complement and inform <i>C. diphtheriae</i> surveillance.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078803","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":"Clinical trials and recent progress in HIV vaccine development","authors":"Akmal Zubair,&nbsp;Bushra Bibi,&nbsp;Faiza Habib,&nbsp;Arooba Sujan,&nbsp;Muhammad Ali","doi":"10.1007/s10142-024-01425-9","DOIUrl":"10.1007/s10142-024-01425-9","url":null,"abstract":"<div><p>The greatest obstacle for scientists is to develop an effective HIV vaccine. An effective vaccine represents the last hope for halting the unstoppable global spread of HIV and its catastrophic clinical consequences. Creating this vaccine has been challenging due to the virus’s extensive genetic variability and the unique role of cytotoxic T lymphocytes (CTL) in containing it. Innovative methods to stimulate CTL have demonstrated significant therapeutic advantages in nonhuman primate model systems, unlike traditional vaccination techniques that are not expected to provide safe and efficient protection against HIV. Human clinical trials are currently evaluating these vaccination strategies, which involve plasmid DNA and live recombinant vectors. This review article covers the existing vaccines and ongoing trial vaccines. It also explores the different approaches used in developing HIV vaccines, including their molecular mechanisms, target site effectiveness, and potential side effects.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078802","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":"Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species","authors":"Ali Tevfik Uncu,&nbsp;Aysenur Soyturk Patat,&nbsp;Ayse Ozgur Uncu","doi":"10.1007/s10142-024-01423-x","DOIUrl":"10.1007/s10142-024-01423-x","url":null,"abstract":"<div><p>Parsley is a commonly cultivated Apiaceae species of culinary and medicinal importance. Parsley has several recognized health benefits and the species has been utilized in traditional medicine since ancient times. Although parsley is among the most commonly cultivated members of Apiaceae, no systematic genomic research has been conducted on parsley. In the present work, parsley genome was sequenced using the long-read HiFi (high fidelity) sequencing technology and a draft contig assembly of 1.57 Gb that represents 80.9% of the estimated genome size was produced. The assembly was highly repeat-rich with a repetitive DNA content of 81%. The assembly was phased into a primary and alternate assembly in order to minimize redundant contigs. Scaffolds were constructed with the primary assembly contigs, which were used for the identification of AMP (antimicrobial peptide) genes. Characteristic AMP domains and 3D structures were used to detect and verify antimicrobial peptides. As a result, 23 genes (<i>PcAMP1-23</i>) representing defensin, snakin, thionin, lipid transfer protein and vicilin-like AMP classes were identified. Bioinformatic analyses for the characterization of peptide physicochemical properties indicated that parsley AMPs are extracellular peptides, therefore, plausibly exert their antimicrobial effects through the most commonly described AMP action mechanism of membrane attack. AMPs are attracting increasing attention since they display their fast antimicrobial effects in small doses on both plant and animal pathogens with a significantly reduced risk of resistance development. Therefore, identification and characterization of AMPs is important for their incorporation into plant disease management protocols as well as medicinal research for the treatment of multi-drug resistant infections.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071704","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":"Regulatory axis of circular RNA DTNB, microRNA-485-5p, and myeloid cell leukemia 1 attenuates inflammation and apoptosis in caerulein-treated AR42J cells","authors":"Xiao Tian,&nbsp;Yun Zhang,&nbsp;MiaoMiao Peng,&nbsp;YuXi Hou","doi":"10.1007/s10142-024-01411-1","DOIUrl":"10.1007/s10142-024-01411-1","url":null,"abstract":"<div><p>Acute pancreatitis (AP) is an inflammatory disease of the pancreas and the main cause of hospital admissions for gastrointestinal diseases. Here, the work studied the circular RNA DTNB/microRNA-485-5p/MCL1 axis in AP and hoped to unravel the related mechanism. Caerulein exposure replicated an AP model in AR42J cells, and caerulein-mediated expression of circDTNB, miR-485-5p, and MCL1 was recorded. After exposure, cells were intervened with transfection plasmids and tested for LDH release, apoptosis, and inflammation. To determine the interwork of circDTNB, miR-485-5p, and MCL1, prediction results and verification experiments were conducted. Caerulein exposure reduced circDTNB and MCL1, while elevated miR-485-5p levels in AR42J cells. Upregulating circDTNB protected AR42J cells from caerulein-induced LDH cytotoxicity, apoptosis, and inflammation, but circDTNB upregulation-induced protections could be muffled by inhibiting MCL1. On the contrary, downregulating circDTNB further damaged AR42J cells under caerulein exposure, however, this phenomenon could be partially rescued after silencing miR-485-5p. miR-485-5p was mechanistically verified to be a target of circDTNB to mediate MCL1. Overall, the circDTNB/miR-485-5p/MCL1 axis protects inflammatory response and apoptosis in caerulein-exposed AR42J cells, promisingly identifying circDTNB as a novel molecule for AP treatment.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003308","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":"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/s10142-024-01422-y","DOIUrl":"10.1007/s10142-024-01422-y","url":null,"abstract":"<div><p>Rice root system plays a crucial role in plant adaptation under adverse conditions, particularly drought stress. However, the regulatory gene networks that govern rice root development during stress exposure remain largely unexplored. In this study, we applied a QTL sequencing method to identify QTL/gene controlling the crown root development under Jasmonic acid simulation using the Bulk-segregant analysis. Two rice cultivars with contrasting phenotypes from the Vietnamese traditional rice collection were used as parent pairs for crossing. The single-seed descent method was employed to generate an F2 population of progenies. This F2/3 population was further segregated based on root count under JA stress. Pooled DNA from the two extreme groups in this population was sequenced, and SNP indexes across all loci in these pools were calculated. We detected a significant genomic region on chromosome 10, spanned from 20.39–20.50 Mb, where two rice <i>RLKs</i> were located, <i>OsPUB54</i> and <i>OsPUB58</i>. Receptor-like kinases (RLKs) are pivotal in regulating various aspects of root development in plants, and the U-box E3 ubiquitination ligase class was generally known for its degradation of some protein complexes. Notably, <i>OsPUB54</i> was strongly induced by JA treatment, suggesting its involvement in the degradation of the Aux/IAA protein complex, thereby influencing crown root initiation. Besides, the Eukaryotic translation initiation of factor 3 subunit L (eIF3l) and the Mitogen-activated protein kinase kinase kinase 37 (MAPKKK 37) proteins identified from SNPs with high score index which suggests their significant roles in the translation initiation process and cellular signaling pathways, respectively. This information suggests several clues of how these candidates are involved in modifying the rice root system under stress conditions.\u0000</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003307","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":"A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis","authors":"Kasmika Borah,&nbsp;Himanish Shekhar Das,&nbsp;Soumita Seth,&nbsp;Koushik Mallick,&nbsp;Zubair Rahaman,&nbsp;Saurav Mallik","doi":"10.1007/s10142-024-01415-x","DOIUrl":"10.1007/s10142-024-01415-x","url":null,"abstract":"<div><p>Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results. Feature selection and feature extraction are two pivotal techniques employed to address these challenges by reducing the dimensionality of the data, thereby enhancing model performance, interpretability, and computational efficiency. Feature selection and feature extraction can be categorized into statistical and machine learning methods. The present study conducts a comprehensive and comparative review of various statistical, machine learning, and deep learning-based feature selection and extraction techniques specifically tailored for NGS and microarray data interpretation of humankind. A thorough literature search was performed to gather information on these techniques, focusing on array-based and NGS data analysis. Various techniques, including deep learning architectures, machine learning algorithms, and statistical methods, have been explored for microarray, bulk RNA-Seq, and single-cell, single-cell RNA-Seq (scRNA-Seq) technology-based datasets surveyed here. The study provides an overview of these techniques, highlighting their applications, advantages, and limitations in the context of high-dimensional NGS data. This review provides better insights for readers to apply feature selection and feature extraction techniques to enhance the performance of predictive models, uncover underlying biological patterns, and gain deeper insights into massive and complex NGS and microarray data.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999118","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}