Current Genomics最新文献

{"title":"Genes Selectively Expressed in Rat Organs","authors":"Dan Li, Xulian Wan, Yu Yun, Yongkun Li, Weigang Duan","doi":"10.2174/0113892029273121240401060228","DOIUrl":"https://doi.org/10.2174/0113892029273121240401060228","url":null,"abstract":"Background: Understanding organic functions at a molecular level is important for scientists to unveil the disease mechanism and to develop diagnostic or therapeutic methods. background: Understanding organic functions at a molecular level are important for scientists to unveil the mechanism of disease and to develop diagnostic or therapeutic methods. Aim: The present study tried to find genes selectively expressed in 11 rat organs, including the adrenal gland, brain, colon, duodenum, heart, ileum, kidney, liver, lung, spleen, and stomach. objective: Understanding organic functions at a molecular level are important for scientists to unveil the mechanism of disease and to develop diagnostic or therapeutic methods. The present study tried to find genes selectively expressed in 11 rat organs, including the adrenal gland, brain, colon, duodenum, heart, ileum, kidney, liver, lung, spleen, and stomach. Method: Three normal male Sprague-Dawley (SD) rats were anesthetized, their organs mentioned above were harvested, and RNA in the fresh organs was extracted. Purified RNA was reversely transcribed and sequenced using the Solexa high-throughput sequencing technique. The abundance of a gene was measured by the expected value of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM). Genes in organs with the highest expression level were sought out and compared with their median value in organs. If a gene in the highest expressed organ was significantly different (p < 0.05) from that in the medianly expressed organ, accompanied by q value < 0.05, and accounted for more than 70% of the total abundance, the gene was assumed as the selective gene in the organ. Results & Discussion: The Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) pathways were enriched by the highest expressed genes. Based on the criterion, 1,406 selective genes were screened out, 1,283 of which were described in the gene bank and 123 of which were waiting to be described. KEGG and GO pathways in the organs were partly confirmed by the known understandings and a good portion of the pathways needed further investigation. Conclusion: The novel selective genes and organic functional pathways are useful for scientists to unveil the mechanisms of the organs at the molecular level, and the selective genes’ products are candidate disease markers for organs.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"38 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574317","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":"Genomics in Diabetic Kidney Disease: A 2024 Update","authors":"Stefanos Roumeliotis, Maria Divani, Eleni Stamellou, Vassilios Liakopoulos","doi":"10.2174/0113892029300247240325080421","DOIUrl":"https://doi.org/10.2174/0113892029300247240325080421","url":null,"abstract":": Diabetic Kidney Disease (DKD) remains the leading cause of Chronic and End Stage Kidney Disease (ESKD) worldwide, with an increasing epidemiological burden. However, still, the disease awareness remains low, early diagnosis is difficult, and therapeutic management is ineffective. These might be attributed to the fact that DKD is a highly heterogeneous disease, with disparities and variability in clinical presentation and progression patterns. Besides environmental risk factors, genetic studies have emerged as a novel and promising tool in the field of DKD. Three decades ago, family studies first reported that inherited genetic factors might confer significant risk to DKD development and progression. During the past decade, genome-wide association studies (GWASs) screening the whole genome in large and multi-ethnic population-based cohorts identified genetic risk variants associated with traits defining DKD in both type 1 and 2 diabetes. Herein, we aim to summarize the existing data regarding the progress in the field of genomics in DKD, present how the revolution of GWAS expanded our understanding of pathophysiologic disease mechanisms and finally, suggest potential future directions.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"69 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574829","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":"Genomic and Metagenomic Insights into the Distribution of Nicotine-Degrading Enzymes in Human Microbiota","authors":"Ying Guan, Zhouhai Zhu, Qiyuan Peng, Meng Li, Xuan Li, Jia-Wei Yang, Yan-Hong Lu, Meng Wang, Bin-Bin Xie","doi":"10.2174/0113892029302230240319042208","DOIUrl":"https://doi.org/10.2174/0113892029302230240319042208","url":null,"abstract":"Introduction: Nicotine degradation is a new strategy to block nicotine-induced pathology. The potential of human microbiota to degrade nicotine has not been explored. Aims: This study aimed to uncover the genomic potentials of human microbiota to degrade nicotine. Method: To address this issue, we performed a systematic annotation of Nicotine-Degrading Enzymes (NDEs) from genomes and metagenomes of human microbiota. A total of 26,295 genomes and 1,596 metagenomes for human microbiota were downloaded from public databases and five types of NDEs were annotated with a custom pipeline. We found 959 NdhB, 785 NdhL, 987 NicX, three NicA1, and three NicA2 homologs. Results: Genomic classification revealed that six phylum-level taxa, including Proteobacteria, Firmicutes, Firmicutes_A, Bacteroidota, Actinobacteriota, and Chloroflexota, can produce NDEs, with Proteobacteria encoding all five types of NDEs studied. Analysis of NicX prevalence revealed differences among body sites. NicX homologs were found in gut and oral samples with a high prevalence but not found in lung samples. NicX was found in samples from both smokers and non-smokers, though the prevalence might be different.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"305 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140202090","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":"Prediction of Deleterious Single Amino Acid Polymorphisms with a Consensus Holdout Sampler","authors":"Óscar Álvarez-Machancoses, Eshel Faraggi, Enrique deAndrés-Galiana, Juan Fernández-Martínez, Andrzej Kloczkowski","doi":"10.2174/0113892029236347240308054538","DOIUrl":"https://doi.org/10.2174/0113892029236347240308054538","url":null,"abstract":"Background: Single Amino Acid Polymorphisms (SAPs) or nonsynonymous Single Nucleotide Variants (nsSNVs) are the most common genetic variations. They result from missense mutations where a single base pair substitution changes the genetic code in such a way that the triplet of bases (codon) at a given position is coding a different amino acid. Since genetic mutations sometimes cause genetic diseases, it is important to comprehend and foresee which variations are harmful and which ones are neutral (not causing changes in the phenotype). This can be posed as a classification problem. Methods: Computational methods using machine intelligence are gradually replacing repetitive and exceedingly overpriced mutagenic tests. By and large, uneven quality, deficiencies, and irregularities of nsSNVs datasets debase the convenience of artificial intelligence-based methods. Subsequently, strong and more exact approaches are needed to address these problems. In the present work paper, we show a consensus classifier built on the holdout sampler, which appears strong and precise and outflanks all other popular methods. objective: Roughly a half of known disease-related mutations are due to non-synonymous variants [8-9], expressed as amino-acid mutations. Therefore, it is important to unravel the links between nonsynonymous Single Nucleotide Variants and associated diseases to discriminate between pathogenic and neutral substitutions. It has been found that these substitutions could be directly related to pathological effects such as Parkinson’s or Alzheimer’s diseases, or to the involvement in complex diseases, such as cancer development. Results: We produced 100 holdouts to test the structures and diverse classification variables of diverse classifiers during the training phase. The finest performing holdouts were chosen to develop a consensus classifier and tested using a k-fold (1 ≤ k ≤5) cross-validation method. We also examined which protein properties have the biggest impact on the precise prediction of the effects of nsSNVs. Conclusion: Our Consensus Holdout Sampler outflanks other popular algorithms, and gives excellent results, highly accurate with low standard deviation. The advantage of our method emerges from using a tree of holdouts, where diverse LM/AI-based programs are sampled in diverse ways.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140165510","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":"Testing the Significance of Ranked Gene Sets in Genome-Wide Transcriptome Profiling Data Using Weighted Rank Correlation Statistics","authors":"Min Yao, Hao He, Binyu Wang, Xinmiao Huang, Sunli Zheng, Jianwu Wang, Xuejun Gao, Tinghua Huang","doi":"10.2174/0113892029280470240306044159","DOIUrl":"https://doi.org/10.2174/0113892029280470240306044159","url":null,"abstract":"Objective: Ignoring the rank information during the enrichment analysis will lead to improper statistical inference. We address this issue by developing of new method to test the significance of ranked gene sets in genome-wide transcriptome profiling data. Methods: A method was proposed by first creating ranked gene sets and gene lists and then applying weighted Kendall's tau rank correlation statistics to the test. After introducing top-down weights to the genes in the gene set, a new software called \"Flaver\" was developed. Results: Theoretical properties of the proposed method were established, and its differences over the GSEA approach were demonstrated when analyzing the transcriptome profiling data across 55 human tissues and 176 human cell-lines. The results indicated that the TFs identified by our method have higher tendency to be differentially expressed across the tissues analyzed than its competitors. It significantly outperforms the well-known gene set enrichment analyzing tools, GOStats (9%) and GSEA (17%), in analyzing well-documented human RNA transcriptome datasets. Conclusions: The method is outstanding in detecting gene sets of which the gene ranks were correlated with the expression levels of the genes in the transcriptome data.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"2012 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140147457","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":"Effect of Calebin-A on Critical Genes Related to NAFLD: A Protein-Protein Interaction Network and Molecular Docking Study","authors":"Ali Mahmoudi, Mohammad Mahdi Hajihasani, Muhammed Majeed, Tannaz Jamialahmadi, Amirhossein Sahebkar","doi":"10.2174/0113892029280454240214072212","DOIUrl":"https://doi.org/10.2174/0113892029280454240214072212","url":null,"abstract":"Background:: Calebin-A is a minor phytoconstituent of turmeric known for its activity against inflammation, oxidative stress, cancerous, and metabolic disorders like Non-alcoholic fatty liver disease(NAFLD). Based on bioinformatic tools, the present study explored the intersection of possible targets that interacted with Calebin-A and the essential genes involved in NAFLD. Subsequently, the details of the interaction of critical proteins with Calebin-A were investigated using the molecular docking technique. Methods:: We first probed the intersection of genes/ proteins between NAFLD and Calebin-A through online databases. Besides, we performed an enrichment analysis using the ClueGO plugin to investigate signaling pathways and gene ontology. Next, we evaluate the possible interaction of Calebin-A with significant hub proteins involved in NAFLD through a molecular docking study. Results:: We identified 87 intersection genes Calebin-A targets associated with NAFLD. PPI network analysis introduced 10 hub genes (TP53, TNF, STAT3, HSP90AA1, PTGS2, HDAC6, ABCB1, CCT2, NR1I2, and GUSB). In KEGG enrichment, most were associated with Sphingolipid, vascular endothelial growth factor A (VEGFA), C-type lectin receptor, and mitogen-activated protein kinase (MAPK) signaling pathways. The biological processes described in 87 intersection genes are mostly concerned with regulating the apoptotic process, cytokine production, and intracellular signal transduction. Molecular docking results also directed that Calebin-A had a high affinity to bind hub proteins linked to NAFLD. Conclusion:: Here, we showed that Calebin-A, through its effect on several critical genes/ proteins and pathways, might repress the progression of NAFLD.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"11 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140004337","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":"Preface 25 Years of Current Genomics.","authors":"Fabio Coppedè","doi":"10.2174/138920292501240205235837","DOIUrl":"10.2174/138920292501240205235837","url":null,"abstract":"","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"25 1","pages":"1"},"PeriodicalIF":1.8,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10964086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305146","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":"DHFS-ECM: Design of a Dual Heuristic Feature Selection-based Ensemble Classification Model for the Identification of Bamboo Species from Genomic Sequences","authors":"Aditi R. Durge, Deepti D. Shrimankar","doi":"10.2174/0113892029268176240125055419","DOIUrl":"https://doi.org/10.2174/0113892029268176240125055419","url":null,"abstract":"Problem: Analyzing genomic sequences plays a crucial role in understanding biological diversity and classifying Bamboo species. Existing methods for genomic sequence analysis suffer from limitations such as complexity, low accuracy, and the need for constant reconfiguration in response to evolving genomic datasets. Aim: This study addresses these limitations by introducing a novel Dual Heuristic Feature Selection- based Ensemble Classification Model (DHFS-ECM) for the precise identification of Bamboo species from genomic sequences. Methods: The proposed DHFS-ECM method employs a Genetic Algorithm to perform dual heuristic feature selection. This process maximizes inter-class variance, leading to the selection of informative N-gram feature sets. Subsequently, intra-class variance levels are used to create optimal training and validation sets, ensuring comprehensive coverage of class-specific features. The selected features are then processed through an ensemble classification layer, combining multiple stratification models for species-specific categorization. Results: Comparative analysis with state-of-the-art methods demonstrate that DHFS-ECM achieves remarkable improvements in accuracy (9.5%), precision (5.9%), recall (8.5%), and AUC performance (4.5%). Importantly, the model maintains its performance even with an increased number of species classes due to the continuous learning facilitated by the Dual Heuristic Genetic Algorithm Model. Conclusion: DHFS-ECM offers several key advantages, including efficient feature extraction, reduced model complexity, enhanced interpretability, and increased robustness and accuracy through the ensemble classification layer. These attributes make DHFS-ECM a promising tool for real-time clinical applications and a valuable contribution to the field of genomic sequence analysis.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"134 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139951511","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":"Expression Profiling of EMT Transcriptional Regulators ZEB1 and ZEB2 in Different Histopathological Grades of Oral Squamous Cell Carcinoma Patients","authors":"Neha Baqai, Rafat Amin, Tehseen Fatima, Zeba Ahmed, Nousheen Faiz","doi":"10.2174/0113892029284920240212091903","DOIUrl":"https://doi.org/10.2174/0113892029284920240212091903","url":null,"abstract":"Background: Pakistan has a high burden of oral cancers, with a prevalence rate of around 9%. Oral Squamous Cell Carcinoma (OSCC) accounts for about 90% of oral cancer cases. Epithelial to Mesenchymal Transition (EMT) gets highly stimulated in tumor cells by adopting subsequent malignant features of highly invasive cancer populations. Zinc Finger E-Box binding factors, ZEB1 and ZEB2, are regulatory proteins that promote EMT by suppressing the adherent ability of cells transforming into highly motile cancerous cells. The present study aimed to analyze the expression of EMT regulators, ZEB1 and ZEB2, and their association with the clinicopathological features in different grades of OSCC patients. Methods: Tissue samples were collected for both case and control groups from the recruited study participants. Cancer tissues (cases) were collected from the confirmed OSCC patients, and healthy tissues (controls) were collected from third-molar dental extraction patients. The study participants were recruited with informed consent and brief demographic and clinical characteristics. The case group was further segregated with respect to the histological cancer grading system into well-differentiated (WD), moderately differentiated (MD), and poorly differentiated (PD) squamous cell carcinoma (SCC) groups. RNA was extracted from the tissue samples for expression profiling of ZEB1 and ZEB2 genes through quantitative real-time PCR (qRT-PCR) Results: All of the recruited participants had a mean age of 46.55 ± 11.7 (years), with most of them belonging to Urdu speaking ethnic group and were married. The BMI (kg/m2 ) of the healthy participants was in the normal range (18-22 kg/m2 ). However, BMI was found to be reduced with the proliferation in the pathological state of cancer. The oral hygiene of patients was better than the healthy participants, possibly due to the strict oral hygiene practice concerns of consultants. Every recruited OSCC patient had one or multiple addiction habits for more than a year. Patients reported health frailty (46.6%), unhealed mouth sores (40%), swallowing difficulties and white/reddish marks (80%), and restricted mouth opening (64.4%). Furthermore, 82.2% of the recruited patients observed symptoms within 1-12 months, and buccal mucosa was the most exposed tumor site among 55.6% of the patients. Expression profiling of EMT regulators showed gradual over-expressions of ZEB1 (8, 20, and 42 folds) and ZEB2 (4, 10, and 18 folds) in respective histological cancer grades. Conclusion: High expressions of ZEBs have been significantly associated with cancer progression and poor health. However, no association was found between OSCC with other clinicopathological features when compared to healthy controls","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"87 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139751828","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":"COVID-19: Recent Insight in Genomic Feature, Pathogenesis, Immunological Biomarkers, Treatment Options and Clinical Updates on SARS-CoV-2","authors":"Rohitas Deshmukh, Ranjit K Harwansh, Akash Garg, Sakshi Mishra, Rutvi Agrawal, Rajendra Jangde","doi":"10.2174/0113892029291098240129113500","DOIUrl":"https://doi.org/10.2174/0113892029291098240129113500","url":null,"abstract":": SARS-CoV-2 is a highly contagious and transmissible viral infection that first emerged in 2019 and since then has sparked an epidemic of severe respiratory problems identified as “coronavirus disease 2019” (COVID-19) that causes a hazard to human life and safety. The virus developed mainly from bats. The current epidemic has presented a significant warning to life across the world by showing mutation. There are different tests available for testing Coronavirus, and RTPCR is the best, giving more accurate results, but it is also time-consuming. There are different options available for treating n-CoV-19, which include medications such as Remdesivir, corticosteroids, plasma therapy, Dexamethasone therapy, etc. The development of vaccines such as BNT126b2, ChAdOX1, mRNA-1273 and BBIBP-CorV has provided great relief in dealing with the virus as they decreased the mortality rate. BNT126b2 and ChAdOX1 are two n-CoV vaccines found to be most effective in controlling the spread of infection. In the future, nanotechnology-based vaccines and immune engineering techniques can be helpful for further research on Coronavirus and treatment of this deadly virus. The existing knowledge about the existence of SARS-- CoV-2, along with its variants, is summarized in this review. This review, based on recently published findings, presents the core genetics of COVID-19, including heritable characteristics, pathogenesis, immunological biomarkers, treatment options and clinical updates on the virus, along with patents.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"49 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139751750","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}