Displaying publications 21 - 40 of 367 in total

Abstract:
Sort:
  1. Metabolomics and its role in understanding cellular responses in plants
    Bhalla R, Narasimhan K, Swarup S
    Plant Cell Rep, 2005 Dec;24(10):562-71.
    PMID: 16220342
    A natural shift is taking place in the approaches being adopted by plant scientists in response to the accessibility of systems-based technology platforms. Metabolomics is one such field, which involves a comprehensive non-biased analysis of metabolites in a given cell at a specific time. This review briefly introduces the emerging field and a range of analytical techniques that are most useful in metabolomics when combined with computational approaches in data analyses. Using cases from Arabidopsis and other selected plant systems, this review highlights how information can be integrated from metabolomics and other functional genomics platforms to obtain a global picture of plant cellular responses. We discuss how metabolomics is enabling large-scale and parallel interrogation of cell states under different stages of development and defined environmental conditions to uncover novel interactions among various pathways. Finally, we discuss selected applications of metabolomics.
    Matched MeSH terms: Gene Expression Profiling/methods; Gene Expression Profiling/trends*
  2. Fulltext Reference gene validation for gene expression normalization in canine osteosarcoma: a geNorm algorithm approach
    Selvarajah GT, Bonestroo FAS, Timmermans Sprang EPM, Kirpensteijn J, Mol JA
    BMC Vet Res, 2017 Nov 25;13(1):354.
    PMID: 29178874 DOI: 10.1186/s12917-017-1281-3
    BACKGROUND: Quantitative PCR (qPCR) is a common method for quantifying mRNA expression. Given the heterogeneity present in tumor tissues, it is crucial to normalize target mRNA expression data using appropriate reference genes that are stably expressed under a variety of pathological and experimental conditions. No studies have validated specific reference genes in canine osteosarcoma (OS). Previous gene expression studies involving canine OS have used one or two reference genes to normalize gene expression. This study aimed to validate a panel of reference genes commonly used for normalization of canine OS gene expression data using the geNorm algorithm. qPCR analysis of nine canine reference genes was performed on 40 snap-frozen primary OS tumors and seven cell lines.

    RESULTS: Tumors with a variety of clinical and pathological characteristics were selected. Gene expression stability and the optimal number of reference genes for gene expression normalization were calculated. RPS5 and HNRNPH were highly stable among OS cell lines, while RPS5 and RPS19 were the best combination for primary tumors. Pairwise variation analysis recommended four and two reference genes for optimal normalization of the expression data of canine OS tumors and cell lines, respectively.

    CONCLUSIONS: Appropriate combinations of reference genes are recommended to normalize mRNA levels in canine OS tumors and cell lines to facilitate standardized and reliable quantification of target gene expression, which is essential for investigating key genes involved in canine OS metastasis and for comparative biomarker discovery.

    Matched MeSH terms: Gene Expression Profiling/methods; Gene Expression Profiling/veterinary*
  3. Fulltext mRNA profile provides novel insights into stress adaptation in mud crab megalopa, Scylla paramamosain after salinity stress
    Zhang Y, Wu Q, Fang S, Li S, Zheng H, Zhang Y, et al.
    BMC Genomics, 2020 Aug 14;21(1):559.
    PMID: 32795331 DOI: 10.1186/s12864-020-06965-5
    BACKGROUND: Mud crab, Scylla paramamosain, a euryhaline crustacean species, mainly inhabits the Indo-Western Pacific region. Wild mud crab spawn in high-salt condition and the salinity reduced with the growth of the hatching larvae. When the larvae grow up to megalopa, they migrate back to estuaries and coasts in virtue of the flood tide, settle and recruit adult habitats and metamorphose into the crablet stage. Adult crab can even survive in a wide salinity of 0-35 ppt. To investigate the mRNA profile after salinity stress, S. paramamosain megalopa were exposed to different salinity seawater (low, 14 ppt; control, 25 ppt; high, 39 ppt).

    RESULTS: Firstly, from the expression profiles of Na+/K+/2Cl- cotransporter, chloride channel protein 2, and ABC transporter, it turned out that the 24 h might be the most influenced duration in the short-term stress. We collected megalopa under different salinity for 24 h and then submitted to mRNA profiling. Totally, 57.87 Gb Clean Data were obtained. The comparative genomic analysis detected 342 differentially expressed genes (DEGs). The most significantly DEGs include gamma-butyrobetaine dioxygenase-like, facilitated trehalose transporter Tret1, sodium/potassium-transporting ATPase subunit alpha, rhodanese 1-like protein, etc. And the significantly enriched pathways were lysine degradation, choline metabolism in cancer, phospholipase D signaling pathway, Fc gamma R-mediated phagocytosis, and sphingolipid signaling pathway. The results indicate that in the short-term salinity stress, the megalopa might regulate some mechanism such as metabolism, immunity responses, osmoregulation to adapt to the alteration of the environment.

    CONCLUSIONS: This study represents the first genome-wide transcriptome analysis of S. paramamosain megalopa for studying its stress adaption mechanisms under different salinity. The results reveal numbers of genes modified by salinity stress and some important pathways, which will provide valuable resources for discovering the molecular basis of salinity stress adaptation of S. paramamosain larvae and further boost the understanding of the potential molecular mechanisms of salinity stress adaptation for crustacean species.

    Matched MeSH terms: Gene Expression Profiling
  4. Fulltext Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development
    Lee XW, Mat-Isa MN, Mohd-Elias NA, Aizat-Juhari MA, Goh HH, Dear PH, et al.
    PLoS One, 2016;11(12):e0167958.
    PMID: 27977777 DOI: 10.1371/journal.pone.0167958
    Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.
    Matched MeSH terms: Gene Expression Profiling
  5. Transcriptome profiling of immune-responsive genes in the intestine of Cynoglossus semilaevis Günther challenged with Shewanella algae
    Han Z, Sun J, Lv A, Xian JA, Sung YY, Sun X, et al.
    Fish Shellfish Immunol, 2018 Sep;80:291-301.
    PMID: 29886138 DOI: 10.1016/j.fsi.2018.06.007
    To better understand gene expression in the intestine after Shewanella algae infection and provide insights into its immune roles in the tongue sole, Cynoglossus semilaevis, sequencing-based high-throughput RNA analysis (RNA-Seq) for the intestines between the control group and 12 h post-injection group was performed. After assembly, there was an average of 23,957,159 raw sequencing reads, and 23,943,491 clean reads were obtained after filtering out low-quality reads. Then, 383 differentially expressed genes (DEGs) in the intestines in response to S. algae infection were identified. Subsequently, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the DEGs were conducted to further explore their functions. Among all of the pathways involved, sixteen pathways were related to the immune system, among which the complement and coagulation cascades pathway was the most prominent for immunity-related DEGs, followed by the leukocyte transendothelial migration pathway. Furthermore, the expression levels of twelve selected DEGs in the immune-related pathways were identified by quantitative real-time polymerase chain reaction, substantiating the reliability and reproducibility of the RNA-Seq results. In summary, this study represents an important genomic resource for understanding the potential immune role of the tongue sole intestine from the perspective of gene expression.
    Matched MeSH terms: Gene Expression Profiling
  6. Fulltext Platelet Transcriptome-based approaches in the fight against dengue and other diseases
    Suppiah, J., Sakinah, S., Chan, S.Y., Wong, Y.P., Subbiah, S.K., Chee, H.Y., et al.
    Pertanika Journal of Science & Technology, 2018;26(3):933-946.
    MyJurnal
    Human platelets are anucleate cells that lack in deoxyribonucleic acid (DNA), thus hampering genomic study on them. However, the presence of their own messenger ribonucleic acid (mRNA) transcript allows functional study via the transcriptome approach. Transcriptome not only allows profiling of platelet but also aids in studying gene regulation in virus infections and other diseases that have an impact on platelets. Some viruses are known to affect the platelet either by causing a reduction or destruction. Dengue virus is one of the most postulated virus having such effect and frequently linked to platelet reduction. The transcriptome approach has a pivotal role in providing a deeper insight to link certain diseases and their effect on platelets. This review critically discusses role of platelet in dengue and other viral diseases of public health relevance, with a specific focus on the methods currently used in platelet transcriptome profiling.
    Matched MeSH terms: Gene Expression Profiling
  7. Fulltext Transcriptomic and Genomic Approaches for Unravelling Candida albicans Biofilm Formation and Drug Resistance-An Update
    Chong PP, Chin VK, Wong WF, Madhavan P, Yong VC, Looi CY
    Genes (Basel), 2018 Nov 07;9(11).
    PMID: 30405082 DOI: 10.3390/genes9110540
    Candida albicans is an opportunistic fungal pathogen, which causes a plethora of superficial, as well as invasive, infections in humans. The ability of this fungus in switching from commensalism to active infection is attributed to its many virulence traits. Biofilm formation is a key process, which allows the fungus to adhere to and proliferate on medically implanted devices as well as host tissue and cause serious life-threatening infections. Biofilms are complex communities of filamentous and yeast cells surrounded by an extracellular matrix that confers an enhanced degree of resistance to antifungal drugs. Moreover, the extensive plasticity of the C. albicans genome has given this versatile fungus the added advantage of microevolution and adaptation to thrive within the unique environmental niches within the host. To combat these challenges in dealing with C. albicans infections, it is imperative that we target specifically the molecular pathways involved in biofilm formation as well as drug resistance. With the advent of the -omics era and whole genome sequencing platforms, novel pathways and genes involved in the pathogenesis of the fungus have been unraveled. Researchers have used a myriad of strategies including transcriptome analysis for C. albicans cells grown in different environments, whole genome sequencing of different strains, functional genomics approaches to identify critical regulatory genes, as well as comparative genomics analysis between C. albicans and its closely related, much less virulent relative, C. dubliniensis, in the quest to increase our understanding of the mechanisms underlying the success of C. albicans as a major fungal pathogen. This review attempts to summarize the most recent advancements in the field of biofilm and antifungal resistance research and offers suggestions for future directions in therapeutics development.
    Matched MeSH terms: Gene Expression Profiling
  8. Fulltext Transcriptome Profiling of the Resistance Response of Musa acuminata subsp. burmannicoides, var. Calcutta 4 to Pseudocercospora musae
    Pinheiro TDM, Rego ECS, Alves GSC, Fonseca FCA, Cotta MG, Antonino JD, et al.
    Int J Mol Sci, 2022 Nov 05;23(21).
    PMID: 36362377 DOI: 10.3390/ijms232113589
    Banana (Musa spp.), which is one of the world's most popular and most traded fruits, is highly susceptible to pests and diseases. Pseudocercospora musae, responsible for Sigatoka leaf spot disease, is a principal fungal pathogen of Musa spp., resulting in serious economic damage to cultivars in the Cavendish subgroup. The aim of this study was to characterize genetic components of the early immune response to P. musae in Musa acuminata subsp. burmannicoides, var. Calcutta 4, a resistant wild diploid. Leaf RNA samples were extracted from Calcutta 4 three days after inoculation with fungal conidiospores, with paired-end sequencing conducted in inoculated and non-inoculated controls using lllumina HiSeq 4000 technology. Following mapping to the reference M. acuminata ssp. malaccensis var. Pahang genome, differentially expressed genes (DEGs) were identified and expression representation analyzed on the basis of gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes orthology and MapMan pathway analysis. Sequence data mapped to 29,757 gene transcript models in the reference Musa genome. A total of 1073 DEGs were identified in pathogen-inoculated cDNA libraries, in comparison to non-inoculated controls, with 32% overexpressed. GO enrichment analysis revealed common assignment to terms that included chitin binding, chitinase activity, pattern binding, oxidoreductase activity and transcription factor (TF) activity. Allocation to KEGG pathways revealed DEGs associated with environmental information processing, signaling, biosynthesis of secondary metabolites, and metabolism of terpenoids and polyketides. With 144 up-regulated DEGs potentially involved in biotic stress response pathways, including genes involved in cell wall reinforcement, PTI responses, TF regulation, phytohormone signaling and secondary metabolism, data demonstrated diverse early-stage defense responses to P. musae. With increased understanding of the defense responses occurring during the incompatible interaction in resistant Calcutta 4, these data are appropriate for the development of effective disease management approaches based on genetic improvement through introgression of candidate genes in superior cultivars.
    Matched MeSH terms: Gene Expression Profiling
  9. Fulltext Data on RNA-seq analysis of Garcinia mangostana L. seed development
    Mazlan O, Abdul-Rahman A, Goh HH, Aizat WM, Mohd Noor N
    Data Brief, 2018 Feb;16:90-93.
    PMID: 29188226 DOI: 10.1016/j.dib.2017.11.001
    Mangosteen (Garcinia mangostana L.) has exceptional potential for commercial and pharmaceutical applications due to its delicious fruit and medicinal properties. Nevertheless, the molecular mechanism of mangosteen seed development is poorly understood. In this study, we performed transcriptomic analysis of four seed developmental stages; eight, ten, twelve and fourteen weeks after anthesis. Illumina HiSeq™ 4000 sequencer was used to generate raw data of approximately 68 Gb in size. From 451,495,326 raw reads, 406,143,756 clean reads were obtained. The raw data were uploaded to SRA database and the BioProject ID is PRJNA395504. These data provide the basis for further exploration and understanding of the molecular mechanism in mangosteen seed development.
    Matched MeSH terms: Gene Expression Profiling
  10. Fulltext Circular RNA- and microRNA-Mediated Post-Transcriptional Regulation of Preadipocyte Differentiation in Adipogenesis: From Expression Profiling to Signaling Pathway
    Huang CJ, Choo KB
    Int J Mol Sci, 2023 Feb 25;24(5).
    PMID: 36901978 DOI: 10.3390/ijms24054549
    Adipogenesis is an indispensable cellular process that involves preadipocyte differentiation into mature adipocyte. Dysregulated adipogenesis contributes to obesity, diabetes, vascular conditions and cancer-associated cachexia. This review aims to elucidate the mechanistic details on how circular RNA (circRNA) and microRNA (miRNA) modulate post-transcriptional expression of targeted mRNA and the impacted downstream signaling and biochemical pathways in adipogenesis. Twelve adipocyte circRNA profiling and comparative datasets from seven species are analyzed using bioinformatics tools and interrogations of public circRNA databases. Twenty-three circRNAs are identified in the literature that are common to two or more of the adipose tissue datasets in different species; these are novel circRNAs that have not been reported in the literature in relation to adipogenesis. Four complete circRNA-miRNA-mediated modulatory pathways are constructed via integration of experimentally validated circRNA-miRNA-mRNA interactions and the downstream signaling and biochemical pathways involved in preadipocyte differentiation via the PPARγ/C/EBPα gateway. Despite the diverse mode of modulation, bioinformatics analysis shows that the circRNA-miRNA-mRNA interacting seed sequences are conserved across species, supporting mandatory regulatory functions in adipogenesis. Understanding the diverse modes of post-transcriptional regulation of adipogenesis may contribute to the development of novel diagnostic and therapeutic strategies for adipogenesis-associated diseases and in improving meat quality in the livestock industries.
    Matched MeSH terms: Gene Expression Profiling
  11. scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network
    Huang Z, Wang J, Lu X, Mohd Zain A, Yu G
    Brief Bioinform, 2023 Mar 19;24(2).
    PMID: 36733262 DOI: 10.1093/bib/bbad040
    Single-cell RNA sequencing (scRNA-seq) data are typically with a large number of missing values, which often results in the loss of critical gene signaling information and seriously limit the downstream analysis. Deep learning-based imputation methods often can better handle scRNA-seq data than shallow ones, but most of them do not consider the inherent relations between genes, and the expression of a gene is often regulated by other genes. Therefore, it is essential to impute scRNA-seq data by considering the regional gene-to-gene relations. We propose a novel model (named scGGAN) to impute scRNA-seq data that learns the gene-to-gene relations by Graph Convolutional Networks (GCN) and global scRNA-seq data distribution by Generative Adversarial Networks (GAN). scGGAN first leverages single-cell and bulk genomics data to explore inherent relations between genes and builds a more compact gene relation network to jointly capture the homogeneous and heterogeneous information. Then, it constructs a GCN-based GAN model to integrate the scRNA-seq, gene sequencing data and gene relation network for generating scRNA-seq data, and trains the model through adversarial learning. Finally, it utilizes data generated by the trained GCN-based GAN model to impute scRNA-seq data. Experiments on simulated and real scRNA-seq datasets show that scGGAN can effectively identify dropout events, recover the biologically meaningful expressions, determine subcellular states and types, improve the differential expression analysis and temporal dynamics analysis. Ablation experiments confirm that both the gene relation network and gene sequence data help the imputation of scRNA-seq data.
    Matched MeSH terms: Gene Expression Profiling
  12. Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica
    Ong SN, Tan BC, Hanada K, Teo CH
    Gene, 2023 Aug 20;878:147579.
    PMID: 37336274 DOI: 10.1016/j.gene.2023.147579
    Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.
    Matched MeSH terms: Gene Expression Profiling
  13. Gene expression profiling of host lipid metabolism in SARS-CoV-2 infected patients: a systematic review and integrated bioinformatics analysis
    Munawar WASWA, Elias MH, Addnan FH, Hassandarvish P, AbuBakar S, Roslan N
    BMC Infect Dis, 2024 Jan 23;24(1):124.
    PMID: 38263024 DOI: 10.1186/s12879-024-08983-0
    BACKGROUND: The Coronavirus disease 2019 (COVID-19) pandemic occurred due to the dispersion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe symptoms can be observed in COVID-19 patients with lipid-related comorbidities such as obesity and diabetes. Yet, the extensive molecular mechanisms of how SARS-CoV-2 causes dysregulation of lipid metabolism remain unknown.

    METHODS: Here, an advanced search of articles was conducted using PubMed, Scopus, EBSCOhost, and Web of Science databases using terms from Medical Subject Heading (MeSH) like SARS-CoV-2, lipid metabolism and transcriptomic as the keywords. From 428 retrieved studies, only clinical studies using next-generation sequencing as a gene expression method in COVID-19 patients were accepted. Study design, study population, sample type, the method for gene expression and differentially expressed genes (DEGs) were extracted from the five included studies. The DEGs obtained from the studies were pooled and analyzed using the bioinformatics software package, DAVID, to determine the enriched pathways. The DEGs involved in lipid metabolic pathways were selected and further analyzed using STRING and Cytoscape through visualization by protein-protein interaction (PPI) network complex.

    RESULTS: The analysis identified nine remarkable clusters from the PPI complex, where cluster 1 showed the highest molecular interaction score. Three potential candidate genes (PPARG, IFITM3 and APOBEC3G) were pointed out from the integrated bioinformatics analysis in this systematic review and were chosen due to their significant role in regulating lipid metabolism. These candidate genes were significantly involved in enriched lipid metabolic pathways, mainly in regulating lipid homeostasis affecting the pathogenicity of SARS-CoV-2, specifically in mechanisms of viral entry and viral replication in COVID-19 patients.

    CONCLUSIONS: Taken together, our findings in this systematic review highlight the affected lipid-metabolic pathways along with the affected genes upon SARS-CoV-2 invasion, which could be a potential target for new therapeutic strategies study in the future.

    Matched MeSH terms: Gene Expression Profiling
  14. De Novo Transcriptomic and Life-History Responses of Moina Micrura Under Stress Environment Conditions
    Razak MR, Aris AZ, Yusoff FM, Yusof ZNB, Kim SD, Kim KW
    Mar Biotechnol (NY), 2023 Jun;25(3):473-487.
    PMID: 37310522 DOI: 10.1007/s10126-023-10220-9
    Moina micrura represents a promising model species for ecological and ecotoxicological investigations in tropical freshwater ecosystems. Illumina NovaSeq™ 6000 sequencing was employed in this study to analyze M. micrura across three distinct developmental stages: juvenile, adult, and male. Current study successfully annotated 51,547 unigenes (73.11%) derived from seven (7) different databases. A total of 554 genes were found to be significantly upregulated, while 452 genes showed significant downregulation between juvenile and male. Moreover, 1001 genes were upregulated, whereas 830 genes exhibited downregulation between the adult and male. Analysis of differentially expressed genes revealed upregulation of chitin, cuticle, myosin (MYO), mitogen-activated protein kinases (MAPK), fibrillin (FBN), cytochrome (CYP), glutathione s-transferase (GST), vitellogenin (VTG), acetylcholinesterase (AChE), and transforming growth factor beta (TGFB) under unfavorable environmental conditions (male), as compared to favorable environmental conditions (juveniles and adults). These alterations in gene expression significantly impact the phenological and life-history traits of M. micrura. Furthermore, the upregulation of hemoglobin (HMB), doublesex (DSX), juvenile hormone analogs (JHA), heat shock protein (HSP), and methyltransferase (METT) genes in males initiates the sex-switching effects observed in M. micrura. These findings hold substantial value for researchers interested in determining M. micrura sequences for future investigations of gene expression and comparative reproductive genome analysis within the Moina genus and cladoceran families.
    Matched MeSH terms: Gene Expression Profiling
  15. Fulltext HDG-select: A novel GUI based application for gene selection and classification in high dimensional datasets
    Hameed SS, Hassan R, Hassan WH, Muhammadsharif FF, Latiff LA
    PLoS One, 2021;16(1):e0246039.
    PMID: 33507983 DOI: 10.1371/journal.pone.0246039
    The selection and classification of genes is essential for the identification of related genes to a specific disease. Developing a user-friendly application with combined statistical rigor and machine learning functionality to help the biomedical researchers and end users is of great importance. In this work, a novel stand-alone application, which is based on graphical user interface (GUI), is developed to perform the full functionality of gene selection and classification in high dimensional datasets. The so-called HDG-select application is validated on eleven high dimensional datasets of the format CSV and GEO soft. The proposed tool uses the efficient algorithm of combined filter-GBPSO-SVM and it was made freely available to users. It was found that the proposed HDG-select outperformed other tools reported in literature and presented a competitive performance, accessibility, and functionality.
    Matched MeSH terms: Gene Expression Profiling
  16. Fulltext Exploring the current landscape of single-cell RNA sequencing applications in gastric cancer research
    Awuah WA, Roy S, Tan JK, Adebusoye FT, Qiang Z, Ferreira T, et al.
    J Cell Mol Med, 2024 Apr;28(7):e18159.
    PMID: 38494861 DOI: 10.1111/jcmm.18159
    Gastric cancer (GC) represents a major global health burden and is responsible for a significant number of cancer-related fatalities. Its complex nature, characterized by heterogeneity and aggressive behaviour, poses considerable challenges for effective diagnosis and treatment. Single-cell RNA sequencing (scRNA-seq) has emerged as an important technique, offering unprecedented precision and depth in gene expression profiling at the cellular level. By facilitating the identification of distinct cell populations, rare cells and dynamic transcriptional changes within GC, scRNA-seq has yielded valuable insights into tumour progression and potential therapeutic targets. Moreover, this technology has significantly improved our comprehension of the tumour microenvironment (TME) and its intricate interplay with immune cells, thereby opening avenues for targeted therapeutic strategies. Nonetheless, certain obstacles, including tumour heterogeneity and technical limitations, persist in the field. Current endeavours are dedicated to refining protocols and computational tools to surmount these challenges. In this narrative review, we explore the significance of scRNA-seq in GC, emphasizing its advantages, challenges and potential applications in unravelling tumour heterogeneity and identifying promising therapeutic targets. Additionally, we discuss recent developments, ongoing efforts to overcome these challenges, and future prospects. Although further enhancements are required, scRNA-seq has already provided valuable insights into GC and holds promise for advancing biomedical research and clinical practice.
    Matched MeSH terms: Gene Expression Profiling
  17. The cadmium tolerance and bioaccumulation mechanism of Tetratostichococcus sp. P1: insight from transcriptomics analysis
    Sahabudin E, Kubo S, Yuzir MAM, Othman N, Nadia Md Akhir F, Suzuki K, et al.
    Bioengineered, 2024 Dec;15(1):2314888.
    PMID: 38375815 DOI: 10.1080/21655979.2024.2314888
    Cadmium (Cd) has become a severe issue in relatively low concentration and attracts expert attention due to its toxicity, accumulation, and biomagnification in living organisms. Cd does not have a biological role and causes serious health issues. Therefore, Cd pollutants should be reduced and removed from the environment. Microalgae have great potential for Cd absorption for waste treatment since they are more environmentally friendly than existing treatment methods and have strong metal sorption selectivity. This study evaluated the tolerance and ability of the microalga Tetratostichococcus sp. P1 to remove Cd ions under acidic conditions and reveal mechanisms based on transcriptomics analysis. The results showed that Tetratostichococcus sp. P1 had a high Cd tolerance that survived under the presence of Cd up to 100 µM, and IC50, the half-maximal inhibitory concentration value, was 57.0 μM, calculated from the change in growth rate based on the chlorophyll content. Long-term Cd exposure affected the algal morphology and photosynthetic pigments of the alga. Tetratostichococcus sp. P1 removed Cd with a maximum uptake of 1.55 mg g-1 dry weight. Transcriptomic analysis revealed the upregulation of the expression of genes related to metal binding, such as metallothionein. Group A, Group B transporters and glutathione, were also found upregulated. While the downregulation of the genes were related to photosynthesis, mitochondria electron transport, ABC-2 transporter, polysaccharide metabolic process, and cell division. This research is the first study on heavy metal bioremediation using Tetratostichococcus sp. P1 and provides a new potential microalga strain for heavy metal removal in wastewater.[Figure: see text]Abbreviations:BP: Biological process; bZIP: Basic Leucine Zipper; CC: Cellular component; ccc1: Ca (II)-sensitive cross complementary 1; Cd: Cadmium; CDF: Cation diffusion facilitator; Chl: Chlorophyll; CTR: Cu TRansporter families; DAGs: Directed acyclic graphs; DEGs: Differentially expressed genes; DVR: Divinyl chlorophyllide, an 8-vinyl-reductase; FPN: FerroportinN; FTIR: Fourier transform infrared; FTR: Fe TRansporter; GO: Gene Ontology; IC50: Growth half maximal inhibitory concentration; ICP: Inductively coupled plasma; MF: molecular function; NRAMPs: Natural resistance-associated aacrophage proteins; OD: Optical density; RPKM: Reads Per Kilobase of Exon Per Million Reads Mapped; VIT1: Vacuolar iron transporter 1 families; ZIPs: Zrt-, Irt-like proteins.
    Matched MeSH terms: Gene Expression Profiling
  18. Comparative transcriptomics of the chilling stress response in two Asian mangrove species, Bruguiera gymnorhiza and Rhizophora apiculata
    Short AW, Sebastian JSV, Huang J, Wang G, Dassanayake M, Finnegan PM, et al.
    Tree Physiol, 2024 Feb 11;44(3).
    PMID: 38366388 DOI: 10.1093/treephys/tpae019
    Low temperatures largely determine the geographic limits of plant species by reducing survival and growth. Inter-specific differences in the geographic distribution of mangrove species have been associated with cold tolerance, with exclusively tropical species being highly cold-sensitive and subtropical species being relatively cold-tolerant. To identify species-specific adaptations to low temperatures, we compared the chilling stress response of two widespread Indo-West Pacific mangrove species from Rhizophoraceae with differing latitudinal range limits-Bruguiera gymnorhiza (L.) Lam. ex Savigny (subtropical range limit) and Rhizophora apiculata Blume (tropical range limit). For both species, we measured the maximum photochemical efficiency of photosystem II (Fv/Fm) as a proxy for the physiological condition of the plants and examined gene expression profiles during chilling at 15 and 5 °C. At 15 °C, B. gymnorhiza maintained a significantly higher Fv/Fm than R. apiculata. However, at 5 °C, both species displayed equivalent Fv/Fm values. Thus, species-specific differences in chilling tolerance were only found at 15 °C, and both species were sensitive to chilling at 5 °C. At 15 °C, B. gymnorhiza downregulated genes related to the light reactions of photosynthesis and upregulated a gene involved in cyclic electron flow regulation, whereas R. apiculata downregulated more RuBisCo-related genes. At 5 °C, both species repressed genes related to CO2 assimilation. The downregulation of genes related to light absorption and upregulation of genes related to cyclic electron flow regulation are photoprotective mechanisms that likely contributed to the greater photosystem II photochemical efficiency of B. gymnorhiza at 15 °C. The results of this study provide evidence that the distributional range limits and potentially the expansion rates of plant species are associated with differences in the regulation of photosynthesis and photoprotective mechanisms under low temperatures.
    Matched MeSH terms: Gene Expression Profiling
  19. Transcriptome analysis of feline infectious peritonitis virus infection
    Mehrbod P, Harun MS, Shuid AN, Omar AR
    Methods Mol Biol, 2015;1282:241-50.
    PMID: 25720485 DOI: 10.1007/978-1-4939-2438-7_20
    Feline infectious peritonitis (FIP) is a lethal systemic disease caused by FIP virus (FIPV). There are no effective vaccines or treatment available, and the virus virulence determinants and pathogenesis are not fully understood. Here, we describe the sequencing of RNA extracted from Crandell Rees Feline Kidney (CRFK) cells infected with FIPV using the Illumina next-generation sequencing approach. Bioinformatics analysis, based on Felis catus 2X annotated shotgun reference genome, using CLC bio Genome Workbench is used to map both control and infected cells. Kal's Z test statistical analysis is used to analyze the differentially expressed genes from the infected CRFK cells. In addition, RT-qPCR analysis is used for further transcriptional profiling of selected genes in infected CRFK cells and Peripheral Blood Mononuclear Cells (PBMCs) from healthy and FIP-diagnosed cats.
    Matched MeSH terms: Gene Expression Profiling*
  20. Expression profiling of choline and ethanolamine kinases in MCF7, HCT116 and HepG2 cells, and the transcriptional regulation by epigenetic modification
    Ling CS, Yin KB, Cun ST, Ling FL
    Mol Med Rep, 2015 Jan;11(1):611-8.
    PMID: 25333818 DOI: 10.3892/mmr.2014.2707
    The function of choline kinase (CK) and ethanolamine kinase (EK) is to catalyse the phosphorylation of choline and ethanolamine, respectively, in order to yield phosphocholine (PCho) and phosphoethanolamine (PEtn). A high expression level of PCho, due to elevated CK activity, has previously been associated with malignant transformation. In the present study, a quantitative polymerase chain reaction was performed to determine the mRNA expression profiles of ck and ek mRNA variants in MCF7 breast, HCT116 colon and HepG2 liver cancer cells. The ck and ek mRNA expression profiles showed that total ckα was expressed most abundantly in the HepG2 cells. The HCT116 cells exhibited the highest ckβ and ek1 mRNA expression levels, whereas the highest ek2α mRNA expression levels were detected in the MCF7 cells. The ckβ variant had higher mRNA expression levels, as compared with total ckα, in both the MCF7 and HCT116 cells. Relatively low ek1 mRNA expression levels were detected, as compared with ek2α in the MCF7 cells; however, this was not observed in the HCT116 and HepG2 cells. Notably, the mRNA expression levels of ckα2 were markedly low, as compared with ckα1, in all three cancer cell lines. The effects of epigenetic modification on ck and ek mRNA expression, by treatment of the cells with the histone deacetylase inhibitor trichostatin A (TSA), were also investigated. The results of the present study showed that the mRNA expression levels of ckα, ckβ and ek2α were affected by TSA. An increase >8-fold was observed in ek2α mRNA expression upon treatment with TSA, in a concentration- and time-dependent manner. In conclusion, the levels of ck and ek transcript variants in the three cancer cell lines were varied. The effects of TSA treatment on the mRNA expression levels of ck and ek imply that ck and ek mRNA expression may be regulated by epigenetic modification.
    Matched MeSH terms: Gene Expression Profiling*
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links