Displaying publications 61 - 80 of 1636 in total

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  1. Fulltext To Establish a Nomogram Prediction of Prostate Cancer Based on Pyroptosis-Related Genes that Affect the Immune Microenvironment
    Ji C, Shrestha S, Jumuddin FA
    Asian Pac J Cancer Prev, 2024 Jul 01;25(7):2319-2327.
    PMID: 39068564 DOI: 10.31557/APJCP.2024.25.7.2319
    BACKGROUND: Prostate cancer is the most common tumor in men worldwide with a poor prognosis. In recent years, studies have revealed that pyroptosis can affect the tumor immune microenvironment. However, the relationship between the immune microenvironment regulated by pyroptosis-related genes and the prognosis of prostate cancer is still unclear.

    METHODS: Thirty-three cell death-associated genes were selected from a literature review. The "DESeq2" R package was used to identify differentially expressed cell death-associated genes between normal prostate tissue (GTEx) and prostate cancer tissue (TCGA) samples. Biological functional enrichment analysis of differentially expressed cell death genes was performed using R statistical software packages, such as "clusterProfiler," "org.Hs.eg.db," "enrichplot," "ggplot2," and "GOplot." Univariate Cox and LASSO Cox regression analyses were conducted to identify prognostic genes associated with the immune microenvironment using the "survival" package. Finally, a predictive model was established based on Gleason score, T stage, and cell death-associated genes.odel was established based on Gleason score, T stage, and cell death-associated genes.

    RESULTS: Seventeen differentially expressed genes related to pyroptosis were screened out. Based on these differentially expressed genes, biological function enrichment analysis showed that they were related to pyroptosis of prostate cells. Based on univariate Cox and (LASSO) Cox regression analysis, four pyroptosis-related genes (CASP3, PLCG1, GSDMB, GPX4) were determined to be related to the prognosis of prostate cancer, and the immune correlation analysis of the four pyroptosis-related genes was performed. The expression of CASP3, PLCG1 and GSDMB was positively correlated with the proportion of immune cells, and the expression of GPX4 was negatively correlated with the proportion of immune cells. A predictive nomogram was established by combining Gleason score, T and pyroptosis genes. The nomogram was accompanied by a calibration curve and used to predict 1 -, 2 -, and 5-year survival in PAAD patients.

    CONCLUSION: Cell death-associated genes (CASP3, PLCG1, GSDMB, GPX4) play crucial roles in modulating the immune microenvironment and can be used to predict the prognosis of prostate cancer.

    Matched MeSH terms: Gene Expression Regulation, Neoplastic
  2. Fulltext RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction
    Wong MY, Govender NT, Ong CS
    BMC Res Notes, 2019 Sep 24;12(1):631.
    PMID: 31551084 DOI: 10.1186/s13104-019-4652-y
    OBJECTIVE: Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presented here aims to identify both the house-keeping and pathogenicity genes of G. boninense using Illumina sequencing reads.

    DESCRIPTION: The hemibiotroph G. boninense establishes via root contact during early stage of colonization and subsequently kills the host tissue as the disease progresses. Information on the pathogenicity factors/genes that causes BSR remain poorly understood. In addition, the molecular expressions corresponding to G. boninense growth and pathogenicity are not reported. Here, six transcriptome datasets of G. boninense from two contrasting conditions (three biological replicates per condition) are presented. The first datasets, collected from a 7-day-old axenic condition provide an insight onto genes responsible for sustenance, growth and development of G. boninense while datasets of the infecting G. boninense collected from oil palm-G. boninense pathosystem (in planta condition) at 1 month post-inoculation offer a comprehensive avenue to understand G. boninense pathogenesis and infection especially in regard to molecular mechanisms and pathways. Raw sequences deposited in Sequence Read Archive (SRA) are available at NCBI SRA portal with PRJNA514399, bioproject ID.

    Matched MeSH terms: Gene Expression Regulation, Bacterial*; Gene Expression Profiling/methods*; Gene Expression Profiling/statistics & numerical data
  3. 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 Regulation, Plant/genetics; Gene Expression Profiling/methods; Gene Expression Profiling/trends*
  4. Fulltext Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer
    Zainul Abidin FN, Westhead DR
    Nucleic Acids Res, 2017 04 20;45(7):e53.
    PMID: 27994031 DOI: 10.1093/nar/gkw1270
    Clustering is used widely in 'omics' studies and is often tackled with standard methods, e.g. hierarchical clustering. However, the increasing need for integration of multiple data sets leads to a requirement for clustering methods applicable to mixed data types, where the straightforward application of standard methods is not necessarily the best approach. A particularly common problem involves clustering entities characterized by a mixture of binary data (e.g. presence/absence of mutations, binding, motifs and epigenetic marks) and continuous data (e.g. gene expression, protein abundance, metabolite levels). Here, we present a generic method based on a probabilistic model for clustering this type of data, and illustrate its application to genetic regulation and the clustering of cancer samples. We show that the resulting clusters lead to useful hypotheses: in the case of genetic regulation these concern regulation of groups of genes by specific sets of transcription factors and in the case of cancer samples combinations of gene mutations are related to patterns of gene expression. The clusters have potential mechanistic significance and in the latter case are significantly linked to survival. The method is available as a stand-alone software package (GNU General Public Licence) from http://github.com/BioToolsLeeds/FlexiCoClusteringPackage.git.
    Matched MeSH terms: Gene Expression Regulation, Fungal; Gene Expression Regulation, Neoplastic*; Gene Expression Profiling/methods*
  5. Relative quantification of human β‑defensins gene expression in pterygium and normal conjunctiva samples
    Abubakar SA, Isa MM, Omar N, Tan SW
    Mol Med Rep, 2020 Dec;22(6):4931-4937.
    PMID: 33174018 DOI: 10.3892/mmr.2020.11560
    The human ocular surface produces highly conserved cationic peptides. Human β‑defensins (HBDs) serve an important role in innate and adaptive immunity. They are primarily expressed in epithelial cells in response to infection and provide the first line of defence against invading microbes. Defensin β1 (DEFB1) is constitutively expressed and regulated by inflammatory mediators including interferon‑γ, lipopolysaccharide and peptidoglycans. DEFB4A is locally induced in response to microbial infection while DEFB109 is induced via Toll‑like receptor 2. The present study examined the expression of the HBD DEFB1, DEFB4A and DEFB109 genes in pterygium. The pterygium tissues and normal conjunctiva samples were obtained from 18 patients undergoing pterygium surgery. The reverse transcription‑quantitative polymerase chain reaction method was employed to determine the expression of DEFB1, DEFB4A and DEFB109 genes. The results revealed that the expression of DEFB1 and DEFB4A was significantly higher and upregulated in pterygium samples when compared with normal conjunctiva samples from each patient (P<0.05), while the expression of DEFB109 was observed to be lower in pterygium samples when compared with normal samples from the same patient. Previous studies have revealed that DEFB1 and DEFB4A genes are present in low concentrations inside the human eye, and they are upregulated during the maturation of keratinocytes, suggesting a possible role in cell differentiation. The DEFB109 gene is present in higher concentrations inside the human eye, though it is newly discovered. It has also been reported that DEFB1 may be involved in carcinogenesis epithelial tumours. Collectively, the current data suggests that HBDs may serve a crucial role in the pathogenesis and development of pterygia, and thus may be considered as novel molecular targets in understanding pterygia development.
    Matched MeSH terms: Gene Expression Regulation/genetics; Gene Expression/genetics; Gene Expression Profiling/methods
  6. Fulltext A hybrid distance measure for clustering expressed sequence tags originating from the same gene family
    Ng KH, Ho CK, Phon-Amnuaisuk S
    PLoS One, 2012;7(10):e47216.
    PMID: 23071763 DOI: 10.1371/journal.pone.0047216
    Clustering is a key step in the processing of Expressed Sequence Tags (ESTs). The primary goal of clustering is to put ESTs from the same transcript of a single gene into a unique cluster. Recent EST clustering algorithms mostly adopt the alignment-free distance measures, where they tend to yield acceptable clustering accuracies with reasonable computational time. Despite the fact that these clustering methods work satisfactorily on a majority of the EST datasets, they have a common weakness. They are prone to deliver unsatisfactory clustering results when dealing with ESTs from the genes derived from the same family. The root cause is the distance measures applied on them are not sensitive enough to separate these closely related genes.
    Matched MeSH terms: Gene Expression Profiling/methods*
  7. Gene expression profiling and cancer-related pathways in type I endometrial carcinoma
    Saghir FS, Rose IM, Dali AZ, Shamsuddin Z, Jamal AR, Mokhtar NM
    Int. J. Gynecol. Cancer, 2010 Jul;20(5):724-31.
    PMID: 20973258
    INTRODUCTION: Malignant transformation of type I endometrium involves alteration in gene expression with subsequent uncontrolled proliferation of altered cells.

    OBJECTIVE: The main objective of the present study was to identify the cancer-related genes and gene pathways in the endometrium of healthy and cancer patients.

    MATERIALS AND METHODS: Thirty endometrial tissues from healthy and type I EC patients were subjected to total RNA isolation. The RNA samples with good integrity number were hybridized to a new version of Affymetrix Human Genome GeneChip 1.0 ST array. We analyzed the results using the GeneSpring 9.0 GX and the Pathway Studio 6.1 software. For validation assay, quantitative real-time polymerase chain reaction was used to analyze 4 selected genes in normal and EC tissue.

    RESULTS: Of the 28,869 genes profiled, we identified 621 differentially expressed genes (2-fold) in the normal tissue and the tumor. Among these genes, 146 were up-regulated and 476 were down-regulated in the tumor as compared with the normal tissue (P < 0.001). Up-regulated genes included the v-erb-a erythroblastic leukemia viral oncogene homolog 3 (ErbB3), ErbB4, E74-like factor 3 (ELF3), and chemokine ligand 17 (CXCL17). The down-regulated genes included signal transducer and activator transcription 5B (STAT5b), transforming growth factor A receptor III (TGFA3), caveolin 1 (CAV1), and protein kinase C alpha (PKCA). The gene set enrichment analysis showed 10 significant gene sets with related genes (P < 0.05). The quantitative polymerase chain reaction of 4 selected genes using similar RNA confirmed the microarray results (P < 0.05).

    CONCLUSIONS: Identification of molecular pathways with their genes related to type I EC contribute to the understanding of pathophysiology of this cancer, probably leading to identifying potential biomarkers of the cancer.

    Matched MeSH terms: Gene Expression Profiling*
  8. Gene expressions screening of human cell line exposed to locally produced biomaterial
    Azlina A, Samsudin AR
    Med J Malaysia, 2004 May;59 Suppl B:166-7.
    PMID: 15468870
    In Malaysia, the field of genomics in toxicology is still in infancy. The purpose of this study is to focus on the use of toxicogenomics for determination of gene expressions changes in cultured human fibroblast cells treated with genotoxicology free biomaterial (using Ames test), a locally produced hyroxyapatite. Dose and time response is similar to Ames test with time interval up to 21 days. mRNA is extracted, followed with RT-PCR and polyacrilamide gel electrophoresis. Changes of the gene expressions compared to the non-treated fibroblast mRNA would suggest some gene interactions in the molecule level associated with the exposure of the fibroblast cell line to the biomaterials. Further analysis (cloning & sequencing) shall be carried out to investigate the genes involved as simple changes might not signified toxicity.
    Matched MeSH terms: Gene Expression Profiling*
  9. A Comprehensive Review of the Cosmeceutical Benefits of Vanda Species (Orchidaceae)
    Hadi H, Razali SN, Awadh AI
    Nat Prod Commun, 2015 Aug;10(8):1483-8.
    PMID: 26434147
    Orchidaceae is the largest family of flowering plants with over 35,000 species and 850 genera. About 3300 species of orchids are found in Malaysia and the diversity is highest in the Main, Keledang, Bintang and Tahan Ranges. Apart from being prized for their beauty, orchids have long been used by humans for medicinal purposes. Today the uses of orchids have been expanded to the food and cosmetics industries. Many cosmeceutical companies use orchid extracts as an active ingredient in their products. Previous studies provide riveting insights into the potential uses of orchid extracts as an active agent in cosmetics. This paper describes the cosmeceutical potential of orchids as an anti-aging, and skin moisturizing agent. Orchid extracts from Vanda coerulea and V. teres delay aging caused by reactive oxygen species (ROS) following LV irradiation through their antioxidant and anti-inflammatory activity. These extracts also show anti-aging properties by stimulating cytochrome c oxidase (complex IV), which is part of the electron transport chain in mitochondria. Stimulation of cytochrome c oxidase improves the respiratory function of mitochondria in keratinocytes. The presence of mucilage in orchids enables them to maintain skin hydration. Mucilage functions as a moisturizer and emollient due to its high water binding capacity. Additionally, orchid extracts provide skin hydration by stimulating aquaporin 3 (AQP3) and LEKTI protein expression. The presence of AQP3 leads to a five-fold increase in water permeability, which subsequently increases stratum corneum hydration. Increased LEKTI protein expression mediated by orchid extracts reduces the degradation of desmoglein-1 and enhances the structural function of desmosomes, which play important roles in preventing water evaporation.
    Matched MeSH terms: Gene Expression/drug effects
  10. Proteomics of Sago Palm Towards Identifying Contributory Proteins in Stress-Tolerant Cultivar
    Hussain H, Mustafa Kamal M, Al-Obaidi JR, Hamdin NE, Ngaini Z, Mohd-Yusuf Y
    Protein J, 2020 02;39(1):62-72.
    PMID: 31863255 DOI: 10.1007/s10930-019-09878-9
    Metroxylon sagu Rottb. or locally known as sago palm is a tropical starch crop grown for starch production in commercial plantations in Malaysia, especially in Sarawak, East Malaysia. This plant species accumulate the highest amount of edible starch compared to other starch-producing crops. However, the non-trunking phenomenon has been observed to be one of the major issues restricting the yield of sago palm starch. In this study, proteomics approach was utilised to discover differences between trunking and non-trunking proteomes in sago palm leaf tissues. Total protein from 16 years old trunking and non-trunking sago palm leaves from deep peat area were extracted with PEG fractionation extraction method and subjected to two-dimensional gel electrophoresis (2D PAGE). Differential protein spots were subjected to MALDI-ToF/ToF MS/MS. Proteomic analysis has identified 34 differentially expressed proteins between trunking and non-trunking sago samples. From these protein spots, all 19 proteins representing different enzymes and proteins have significantly increased in abundance in non-trunking sago plant when subjected to mass spectrometry. The identified proteins mostly function in metabolic pathways including photosynthesis, tricarboxylic acid cycle, glycolysis, carbon utilization and oxidative stress. The current study indicated that the several proteins identified through differentially expressed proteome contributed to physical differences in trunking and non-trunking sago palm.
    Matched MeSH terms: Gene Expression/physiology
  11. Functional identification of the prnABCD operon and its regulation in Serratia plymuthica
    Liu X, Yu X, Yang Y, Heeb S, Gao S, Chan KG, et al.
    Appl Microbiol Biotechnol, 2018 Apr;102(8):3711-3721.
    PMID: 29511844 DOI: 10.1007/s00253-018-8857-0
    The antibiotic pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite that plays an important role in the biocontrol of plant diseases due to its broad-spectrum of antimicrobial activities. The PRN biosynthetic gene cluster remains to be characterised in Serratia plymuthica, though it is highly conserved in PRN-producing bacteria. To better understand PRN biosynthesis and its regulation in Serratia, the prnABCD operon from S. plymuthica G3 was cloned, sequenced and expressed in Escherichia coli DH5α. Furthermore, an engineered strain prnind which is a conditional mutant of G3 prnABCD under the control of the Ptac promoter was constructed. This mutant was able to overproduce PRN with isopropylthiogalactoside (IPTG) induction by overexpressing prnABCD, whilst behaving as a conditional mutant of G3 prnABCD in the absence of IPTG. These results confirmed that prnABCD is responsible for PRN biosynthesis in strain G3. Further experiments involving lux-/dsRed-based promoter fusions, combined with site-directed mutagenesis of the putative σS extended -10 region in the prnA promoter, and liquid chromatography-mass spectrometry (LC-MS) analysis extended our previous knowledge about G3, revealing that quorum sensing (QS) regulates PRN biosynthesis through cross talk with RpoS, which may directly activated prnABCD transcription. These findings suggest that PRN in S. plymuthica G3 is produced in a tightly controlled manner, and has diverse functions, such as modulation of cell motility, in addition to antimicrobial activities. Meanwhile, the construction of inducible mutants could be a powerful tool to improve PRN production, beyond its potential use for the investigation of the biological function of PRN.
    Matched MeSH terms: Gene Expression Regulation, Bacterial*
  12. Contribution of transposable elements in the plant's genome
    Sahebi M, Hanafi MM, van Wijnen AJ, Rice D, Rafii MY, Azizi P, et al.
    Gene, 2018 Jul 30;665:155-166.
    PMID: 29684486 DOI: 10.1016/j.gene.2018.04.050
    Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.
    Matched MeSH terms: Gene Expression Regulation, Plant/physiology*
  13. Characterization and expression of Xiphophorus maculatus microsatellite Msb069 full sequence in subgenus Poecilia
    Poh KB, Roslan ZM, Misnan R, Sinang SC
    J Genet, 2018 Sep;97(4):817-824.
    PMID: 30262693
    Msb069 primer pairs encompassed region is believed to be associated with a quantitative trait loci (QTL) of dorsal fin length in subgenus Poecilia. However, detailed investigation on Msb069 which originated from Xiphophorus on subgenus Poecilia remains unexplored. In this study, full sequence of Msb069 was characterized by sequencing bioinformatics analysis and gene expression. The sequence analysis of Msb069 primer pairs encompassed region on three species of Poecilia revealed higher number of microsatellite tandem repeats in Poecilia latipinna (ATG
    16
    ) compared to P. sphenops (ATG
    13-14
    ). There is no notable pattern of ATGtandem repeats discovered in the hybrids. The full sequence of Msb069 is 734 bp in length and showed a 233 bp conserved region between Xiphophorus and Poecilia. BLAST search performed on this sequence revealed no significant similarities. Nonquantitative RT-PCR exhibited the presence of Msb069 transcripts in three different tissues in subgenus Poecilia. Meanwhile, quantitative RTPCR expression on two different tissues showed relatively higher expression of Msb069 transcript in P. latipinna dorsal fin tissues in both male and female fishes, suggesting a repressive function of this transcript with respect to dorsal fin length. However the exact gene expression event of Msb069 is still unknown and requires further investigation.
    Matched MeSH terms: Gene Expression/genetics
  14. Fulltext ROS Homeostasis in Abiotic Stress Tolerance in Plants
    Nadarajah KK
    Int J Mol Sci, 2020 Jul 23;21(15).
    PMID: 32717820 DOI: 10.3390/ijms21155208
    Climate change-induced abiotic stress results in crop yield and production losses. These stresses result in changes at the physiological and molecular level that affect the development and growth of the plant. Reactive oxygen species (ROS) is formed at high levels due to abiotic stress within different organelles, leading to cellular damage. Plants have evolved mechanisms to control the production and scavenging of ROS through enzymatic and non-enzymatic antioxidative processes. However, ROS has a dual function in abiotic stresses where, at high levels, they are toxic to cells while the same molecule can function as a signal transducer that activates a local and systemic plant defense response against stress. The effects, perception, signaling, and activation of ROS and their antioxidative responses are elaborated in this review. This review aims to provide a purview of processes involved in ROS homeostasis in plants and to identify genes that are triggered in response to abiotic-induced oxidative stress. This review articulates the importance of these genes and pathways in understanding the mechanism of resistance in plants and the importance of this information in breeding and genetically developing crops for resistance against abiotic stress in plants.
    Matched MeSH terms: Gene Expression Regulation, Plant/physiology*
  15. Role of the Tristetraprolin (Zinc Finger Protein 36 Homolog) Gene in Cancer
    Gupta G, Bebawy M, Pinto TJA, Chellappan DK, Mishra A, Dua K
    Crit Rev Eukaryot Gene Expr, 2018;28(3):217-221.
    PMID: 30311568 DOI: 10.1615/CritRevEukaryotGeneExpr.2018021188
    Cancer is a complicated transformational progression that fiercely changes the appearance of cell physiology as well as cells' relations with adjacent tissues. Developing an oncogenic characteristic requires a wide range of modifications in a gene expression at a cellular level. This can be achieved by activation or suppression of the gene regulation pathway in a cell. Tristetraprolin (TTP or ZFP36) associated with the initiation and development of tumors are regulated at the level of mRNA decay, frequently through the activity of AU-rich mRNA-destabilizing elements (AREs) located in their 3'-untranslated regions. TTP is an attractive target for therapeutic use and diagnostic tools due to its characteristic appearance in cancer tissue alone. Thus, the illumination of TTP in diverse types of cancer might deliver additional effective remedies in the coming era for cancer patients. The objective of this review is to familiarize the reader with the TTP proteins, focus on efficient properties that endow them with their effective oncogenic potential, describe their physiological role in cancer cells, and review the unique properties of TT, and of TTP-driven cancer.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic/genetics
  16. Potential muscle activity disturbance in Penaeus monodon during Acute Hepatopancreatic Necrosis Disease (AHPND) infection: Inference through gene expression, calcium concentration, and MicroRNA
    Soo TCC, See SA, Bhassu S
    J Invertebr Pathol, 2020 11;177:107497.
    PMID: 33130047 DOI: 10.1016/j.jip.2020.107497
    Global shrimp aquaculture farmers have suffered major economic losses due to disease outbreaks. A notable shrimp disease is Acute Hepatopancreatic Necrosis Disease (AHPND), which is caused by a new strain of Vibrio parahaemolyticus bacteria (VpAHPND) that mainly inhabits the shrimp gut and damages the hepatopancreas. Fewer studies have investigated whether this disease will affect shrimp muscle functioning or cause any muscle damage. We challenged Penaeus monodon shrimp with VpAHPND bacteria using an immersion method. Expression of Dystrophin gene, an important regulatory gene for maintenance of muscle integrity, was quantified from muscle samples using qRT-PCR. Additional verification was conducted by determining calcium concentration and bta-miR-4286 and dre-miR-107b miRNAs expression. P. monodon dystrophin gene demonstrated the highest expression level during AHPND infection when muscle calcium concentration was detected at its lowest level at 6 h post-infection (hpi). The highest muscle calcium concentration, determined at 36 hpi, was supported by higher bta-miR-4286 miRNA expression and lower dre-miR-107b miRNA expression in VpAHPND-infected samples compared to uninfected samples at the same time point. We deduced an interactive relationship between dystrophin gene expression, calcium concentration, and miRNA expression in P. monodon muscle tissues triggered by the invading VpAHPND bacterium.
    Matched MeSH terms: Gene Expression*
  17. Use of control analysis to study the regulation of plant lipid biosynthesis
    Ramli US, Baker DS, Quant PA, Harwood JL
    Biochem Soc Trans, 2002 Nov;30(Pt 6):1043-6.
    PMID: 12440968
    Control analysis is a powerful method to quantify the regulation of metabolic pathways. We have applied it to lipid biosynthesis for the first time by using model tissue culture systems from the important oil crops, olive ( Olea europaea L.) and oil palm ( Elaeis guineensis Jacq.). By the use of top-down control analysis, fatty acid biosynthesis has been shown to exert more control than lipid assembly under different experimental conditions. However, both parts of the lipid biosynthetic pathway are important, so that attempts to alter oil yield by manipulating the activity of a single enzyme step are very unlikely to produce significant increases.
    Matched MeSH terms: Gene Expression Regulation, Plant*
  18. Fulltext Regulation of autophagy by microRNAs in human breast cancer
    Chong ZX, Yeap SK, Ho WY
    J Biomed Sci, 2021 Mar 25;28(1):21.
    PMID: 33761957 DOI: 10.1186/s12929-021-00715-9
    Breast cancer is the most common solid cancer that affects female population globally. MicroRNAs (miRNAs) are short non-coding RNAs that can regulate post-transcriptional modification of multiple downstream genes. Autophagy is a conserved cellular catabolic activity that aims to provide nutrients and degrade un-usable macromolecules in mammalian cells. A number of in vitro, in vivo and clinical studies have reported that some miRNAs could modulate autophagy activity in human breast cancer cells, and these would influence human breast cancer progression and treatment response. Therefore, this review was aimed to discuss the roles of autophagy-regulating miRNAs in influencing breast cancer development and treatment response. The review would first introduce autophagy types and process, followed by the discussion of the roles of different miRNAs in modulating autophagy in human breast cancer, and to explore how would this miRNA-autophagy regulatory process affect the disease progression or treatment response. Lastly, the potential applications and challenges of utilizing autophagy-regulating miRNAs as breast cancer biomarkers and novel therapeutic agents would be discussed.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic*
  19. Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana
    Ong WD, Okubo-Kurihara E, Kurihara Y, Shimada S, Makita Y, Kawashima M, et al.
    Plant Cell Physiol, 2017 01 01;58(1):95-105.
    PMID: 28011868 DOI: 10.1093/pcp/pcw181
    Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes. By combining chemicals and analyzing the effects they have on plant morphology, we identified a chemical, 3-bromo-7-nitroindazole (3B7N), that promotes hypocotyl elongation of wild-type Arabidopsis only under continuous blue light. Further evaluation with loss-of-function mutants confirmed that 3B7N inhibits photomorphogenesis through cryptochrome-mediated light signaling. Microarray analysis demonstrated that the effect of 3B7N treatment on gene expression in cry1cry2 is considerably smaller than that in the wild type, indicating that 3B7N specifically interrupts cryptochrome function in the control of seedling development in a light-dependent manner. We demonstrated that 3B7N directly binds to CRY1 protein using an in vitro binding assay. These results suggest that 3B7N is a novel chemical that directly inhibits plant cryptochrome function by physical binding. The application of 3B7N can be used on other plants to study further the blue light mechanism and the genetic control of cryptochromes in the growth and development of plant species.
    Matched MeSH terms: Gene Expression Regulation, Plant/drug effects; Gene Expression Regulation, Plant/radiation effects; Gene Expression Regulation, Developmental/drug effects; Gene Expression Regulation, Developmental/radiation effects; Gene Expression Profiling/methods
  20. Missing-Values Imputation Algorithms for Microarray Gene Expression Data
    Moorthy K, Jaber AN, Ismail MA, Ernawan F, Mohamad MS, Deris S
    Methods Mol Biol, 2019;1986:255-266.
    PMID: 31115893 DOI: 10.1007/978-1-4939-9442-7_12
    In gene expression studies, missing values are a common problem with important consequences for the interpretation of the final data (Satija et al., Nat Biotechnol 33(5):495, 2015). Numerous bioinformatics examination tools are used for cancer prediction, including the data set matrix (Bailey et al., Cell 173(2):371-385, 2018); thus, it is necessary to resolve the problem of missing-values imputation. This chapter presents a review of the research on missing-values imputation approaches for gene expression data. By using local and global correlation of the data, we were able to focus mostly on the differences between the algorithms. We classified the algorithms as global, hybrid, local, or knowledge-based techniques. Additionally, this chapter presents suitable assessments of the different approaches. The purpose of this review is to focus on developments in the current techniques for scientists rather than applying different or newly developed algorithms with identical functional goals. The aim was to adapt the algorithms to the characteristics of the data.
    Matched MeSH terms: Gene Expression Profiling*
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