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PubMed1987

Expression of fast and slow isoforms of the Ca2+-ATPase in developing chick skeletal muscle.

The expression of fast and slow isoforms of the sarcoplasmic reticulum Ca2+-ATPase was studied in the developing chick embryo and in tissue-cultured myotubes. Monoclonal antibodies specific for each isoform were used as probes of protein expression. Analysis of expression of Ca2+-ATPase isoforms in chick thigh muscles by immunofluorescence microscopy revealed that all muscle fibers expressed both isoforms during their development. Primary generation muscle fibers expressed predominantly the slow isoform. Secondary generation fibers expressed both isoforms at comparable levels. Loss of the "inappropriate" isoforms occurred late in embryonic development. Immunoblot analysis of embryonic thigh muscle proteins indicated that the expression of the slow isoform varied little from embryonic Day 6 (ED6) to ED19, while expression of the fast isoform increased dramatically just prior to ED19. Tissue-cultured myotubes derived from ED12 chick thigh muscle myoblasts, plated at high density, expressed both isoforms of the Ca2+-ATPase at very similar levels. Clonal analysis of myoblasts taken from early (ED6) and late (ED12) chick thigh muscles showed that all muscle colonies expressed both forms, consistent with in vivo results. Fiber-type specific isoforms of the Ca2+-ATPase and myosin heavy chain are not coordinately expressed in developing chick skeletal muscle.

Animals↗

PubMed1990

Cloning of minute virus of mice cDNAs and preliminary analysis of individual viral proteins expressed in murine cells.

cDNAs corresponding to RNA from the autonomous parvovirus minute virus of mice were cloned into constitutive and inducible expression vectors. These clones generate viral NS2, VP1, and VP2 proteins individually. Initial examination of these clones by transient expression analysis and analysis of stably transformed murine cell lines inducibly expressing these constructs indicated that they will be useful tools for characterizing the function of individual minute virus of mice gene products.

Animals↗

PubMed2026

Identification of ultrasound-associated gene candidates in myeloid cells and construction of a prognostic risk model for acute myeloid leukemia.

BACKGROUND: Incorporating ultrasound (US) treatment sensitivity analysis may improve the treatment of acute myeloid leukemia (AML). METHODS: This study integrated single-cell and bulk datasets for analysis. Differential expression analysis between US-treated and control samples was performed using limma package. The AUCell package was used to calculate US-associated scores in the single-cell dataset. Differentially expressed genes (DEGs) between the specific groups were identified, followed by intersection analysis with previously identified DEGs. Univariate regression, Least Absolute Shrinkage and Selection Operator (LASSO) analysis (using the glmnet package), and stepwise multivariate regression (using the MASS package) were used to refine the candidate genes and to construct a risk model. The model genes were validated using in vitro experiments. Enrichment analysis was conducted using gene set enrichment analysis (GSEA), and immune infiltration was evaluate by single-sample GSEA (ssGSEA) and ESTIMATE algorithms. The correlations between RiskScores and drug sensitivity were analyzed by oncoPredict package. Finally, tumor mutational burden (TMB) and genomic mutations were compared between the risk groups. RESULTS: Nine prognostic signatures (SPINK2, HNRNPAB, SH3BGRL3, CLEC11A, ITGA4, RPL39L, MX1, HEXIM1, and MAP4K4) were identified. Particularly, low expression of SPINK2 attenuated the activity and invasion of AML cells. High-risk group had higher immune cell infiltration. Eight drugs were predicted to be correlated with the RiskScore model. DNMT3A and RUNX1 showed higher mutation frequencies in the high-risk group, whereas KIT and MUC16 showed higher mutation frequencies in the low-risk group. CONCLUSION: The RiskScore model established in this study provides a theoretical basis for clinically screening responsive populations and optimizing treatment strategies.

Humans↗

PubMed2026

Transcriptomic responses to developmental temperature in two field-collected Spodoptera exigua populations from Korea.

The beet armyworm, Spodoptera exigua, is a polyphagous insect whose development and seasonal occurrence are strongly influenced by temperature. However, transcriptomic responses to developmental thermal regimes remain insufficiently characterized in field-collected populations. In this study, we compared two Korean field-collected populations of S. exigua: a Haenam population collected in May and initially maintained at 15 ± 1 °C (HN), and a Jeju population collected in July and initially maintained at 27 ± 1 °C (JJ). F1 larvae from each population were reared under three fluctuating developmental temperature regimes: low (15-21 °C), middle (21-27 °C), and high (27-33 °C), followed by RNA-seq analysis. Differential expression analysis revealed population-associated variation in transcriptomic responses across developmental temperatures. HN exhibited a larger number of differentially expressed genes under the high-temperature regime, suggesting stronger transcriptomic sensitivity to elevated developmental temperature. Functional enrichment analyses identified population-associated differences in pathways related to heat response, oxidative metabolism, cytoskeletal organization, cuticle-associated processes, lipid metabolism, and immune-related functions. In JJ, heat-response and cuticle-related expression patterns were more prominent under warmer developmental conditions, whereas HN showed broader changes in stress- and metabolism-associated pathways under high temperature. Overall, this study provides a comparative transcriptomic analysis of two field-collected S. exigua populations under different developmental temperature regimes and identifies RNA-seq-based molecular response patterns associated with population-specific thermal response profiles.

Animals↗

PubMed2025

Genome-wide identification, characterization, and expression pattern analysis of the glyoxalase gene family in Phyllostachys pubescens during abiotic stresses.

BACKGROUND: The glyoxalase pathway comprising of three enzymes i.e., glyoxalase I (GLYI), glyoxalase II (GLYII), and glyoxalase III (GLYIII), which play vital role in mitigating abiotic stresses by detoxifying the stress induced cytotoxic metabolite methylglyoxal (MG). Phyllostachys pubescens an ecologically and economically important forest species, plays vital roles in carbon sequestration and climate change mitigation. A genome-wide study was conducted to identify and characterize GLYI, GLYII, and unique DJ-1/GLYIII gene candidates in P. pubescens. The identified members were evaluated based on phylogenetic analysis, gene structure, chromosomal distribution, gene duplication, presence of conserved domain(s) and cis regulatory region. RESULTS: A total of 19 GLYI, 18 GLYII, and 15 GLYIII members were identified, each featuring characteristic domains: glyoxalase, metallo-β-lactamase, and DJ-1/PfpI, respectively. The presence of different cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under hormonal response, developmental processes and stress adaptation. Besides this, stress responsive transcription factors binding sites also dominated the promoter regions of glyoxalase genes. Expression analysis of various glyoxalase genes demonstrated significant variability under different stress conditions, underscoring their potential roles in stress modulation. Significant upregulation of all of the PhGLYI, PhGLYII, and PhGLYIII were observed under cold, drought, heavy metal and salinity stress suggesting their involvement in oxidative stress management, osmotic regulation and remodelling cellular redox homeostasis. Among the glyoxalase genes, PhGLYI-15, PhGLYII-9, and PhGLYIII-3 showed consistent upregulation under various abiotic stresses. CONCLUSIONS: Our findings reveal that glyoxalase genes crucially contribute towards the improvement of cellular osmotic potential in moso bamboo under different abiotic stresses. This study enhances our understanding of glyoxalase genes' evolution and functional roles in plants and opens new avenues for developing stress resilient crop varieties for sustainable agriculture.

Lactoylglutathione Lyase↗

PubMed2025

Exploring prognostic genes in the immune microenvironment of acute myeloid leukemia via weighted gene co-expression network analysis.

BACKGROUND: Acute myeloid leukemia (AML) is a heterogeneous blood cancer that arises from transformed myeloid precursor cells in a compromised bone marrow microenvironment. This environment is essential for AML initiation, progression, and relapse. Alongside oncogenic changes in hematopoietic cells, immunological dysregulation also contributes to leukemogenesis. The present study is aimed to identify prognostic genes in stromal and immune cells associated with AML using the weighted gene co-expression network analysis (WGCNA). METHODS: Gene expression profiles were retrieved from The Cancer Genome Atlas database, and immune and stromal cell scores were calculated using the ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) method. These scores helped identify differentially expressed genes (DEGs), which were then used to create gene clusters through WGCNA. To explore the functions of genes linked to AML subtypes, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed. A protein-protein interaction network was developed to identify hub genes. The top 18 hub genes were identified using the cytoHubba plug-in in Cytoscape software, and survival analysis was conducted with the Gene Expression Profiling Interactive Analysis 2 online tool. RESULTS: A total of 1097 DEGs were identified, with 601 being upregulated and 496 downregulated. WGCNA analysis indicated that the gray module, comprising 165 genes, had the strongest association with AML subtypes (Cor > 0.3; P < .05). Gene Ontology enrichment analysis demonstrated that the 18 identified hub genes were predominantly associated with neutrophil activation, immune response, secretory granule membrane, and pattern recognition receptor activity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the DEGs were mainly involved in pathways related to phagosome, lysosome, tuberculosis, leishmaniasis, and neutrophil extracellular trap formation. Kaplan-Meier survival analysis of the top 18 hub genes indicated that ITGAM, IL10, and CD163 were significantly correlated with survival outcomes in AML. CONCLUSION: Key stromal and immune-related genes influencing AML patient outcomes were identified, highlighting their potential as therapeutic targets. These discoveries provide deeper insights into the molecular mechanisms driving AML pathogenesis and subtype differentiation.

Leukemia, Myeloid, Acute↗

PubMed1995

Establishment and characterization of an uveal-melanoma cell line.

A human uveal melanoma cell line (92-1) was established from a primary uveal melanoma, and has now been maintained in culture for over 2 1/2 years. Light microscopy of the cultured cells demonstrated extremely pleiomorphic cells with large prominent nucleoli. Cell proliferation was determined with a non-radioactive propidium-iodide assay and indicated an in vitro doubling time of approximately 58 hr. Furthermore, the cell line was characterized by cytogenetic analysis, electron microscopy, immunocytochemistry and Northern blotting for HLA and c-myc-mRNA analysis. Cytogenetic analysis revealed numerical abnormalities of chromosome 8 and structural abnormalities of chromosome 6. By electron microscopy, different stages of melanosome development were observed. Immunocytochemical analysis demonstrated expression of the melanoma-associated antigen gp 100. Expression analysis of HLA antigens revealed a very low level of, in particular, the HLA-B locus products, which could be induced by interferon-alpha or -gamma treatment. Likewise, Northern-blot experiments revealed decreased levels of HLA-B mRNA as compared with HLA-A. In addition, high levels of c-myc expression were observed. The phenotypic characteristics of the cultured cells indicate that we have established an uveal melanoma cell line. This now well-characterized uveal melanoma cell line can be used in future studies.

Aged↗

PubMed1985

Expression of hybrid class I genes of the major histocompatibility complex in mouse L cells.

The class I genes of the major histocompatibility complex of the mouse can be divided into two categories: those encoding the transplantation antigens and those encoding the Qa and Tla antigens. The inbred BALB/c mouse has 28 potential Qa/Tla genes. The sites of tissue expression, developmental regulation, and functions of these genes are virtually unknown. We have used the technique of exon shuffling to construct hybrid genes between each of three Qa region genes (Q5, Q7, and Q8) and two other class I genes (H-2Ld and Q6). The hybrid genes have been transfected into mouse L cells, in which intact transplantation antigen genes generally are expressed and in which intact Qa genes generally are not expressed. Analysis of expression of the hybrid gene constructs indicates that the 5' half of two of the Qa genes (Q5 and Q8) can readily be expressed in the context of a hybrid molecule, whereas the 3' half prevents cell-surface expression. The exon shuffling approach described here will be useful in characterizing Qa/Tla genes and in identifying or producing new reagents to study the Qa/Tla gene products, their tissue distribution, their developmental stages of expression, and, ultimately, their functions.

Animals↗

PubMed2024

Differential expression and regulation of ADAD1, DMRTC2, PRSS54, SYCE1, SYCP1, TEX101, TEX48, and TMPRSS12 gene profiles in colon cancer tissues and their in vitro response to epigenetic drugs.

Colon cancer (CC) is a significant cause of death worldwide, particularly in Saudi Arabia. To increase the accuracy of diagnosis and treatment, it is important to discover new specific biomarkers for CC. The main objectives of this research are to identify potential specific biomarkers for the early diagnosis of CC by analyzing the expressions of eight cancer testis (CT) genes, as well as to analyze how epigenetic mechanisms control the expression of these genes in CC cell lines. Tissue samples were collected from 15 male patients with CC tissues and matched NC tissues for gene expression analysis. The expression levels of specific CT genes, including ADAD1, DMRTC2, PRSS54, SYCE1, SYCP1, TEX101, TEX48, and TMPRSS12, were assessed using quantitative techniques. To validate the gene expression patterns, we used publicly available CC statistics. To investigate the effect of inhibition of DNA methylation and histone deacetylation on CT gene expression, in vitro experiments were performed using HCT116 and Caco-2 cell lines. There was no detected expression of the genes neither in the patient samples nor in NC tissues, except for TEX48, which exhibited upregulation in CC samples compared to NC tissues in online datasets. Notably, CT genes showed expression in testis samples. In vitro, experiments demonstrated significant enhancement in mRNA expression levels of ADAD1, DMRTC2, PRSS54, SYCE1, SYCP1, TEX101, TEX48, and TMPRSS12 following treatment with 5-aza-2'-deoxycytidine and trichostatin A in HCT116 and Caco-2 cell lines. Epigenetic treatments modify the expression of CT genes, indicating that these genes can potentially be used as biomarkers for CC. The importance of conducting further research to understand and target epigenetic mechanisms to improve CC treatment cannot be overemphasized.

Humans↗

PubMed1987

The invected gene of Drosophila: sequence analysis and expression studies reveal a close kinship to the engrailed gene.

The invected and engrailed genes are juxtaposed in the Drosophila genome and are closely related in sequence and pattern of expression. The structure of the most abundant invected transcript was defined by obtaining the full-length cDNA sequence and by S1 nuclease sensitivity and primer extension studies; a partial sequence of the invected gene was determined; and the developmental profile of invected expression was characterized by Northern analysis and by in situ localization. The invected gene, like the engrailed gene, is expressed in the embryonic and larval cells of the posterior developmental compartments and in the embryonic hindgut, clypeolabrum, and nervous system. Like the engrailed gene, the invected gene can encode a protein of approximately 60 kD that contains a homeo box near its carboxyl terminus; indeed, a sequence of 117 amino acids in the carboxy-terminal region of both proteins is almost identical. The developmental role of the invected gene is not known.

Amino Acid Sequence↗

PubMed1986

Murine plasmacytomas constitute a class of natural heat-shock variants in which the major inducible hsp-68 gene is not expressed.

Analysis of the heat-shock response in murine plasmacytomas reveals that, as demonstrated previously for the MPC-11 cell line, the genes coding for the 68-kilodalton heat-shock protein (hsp-68) are not expressed upon heat shock or sodium arsenite treatment. Noninduction is unique to the normally coordinated set of three hsp-68 genes since at least two other heat-shock protein genes (hsp-70 and hsp-89) are properly induced. No other lymphoid cell line was found to possess silent hsp-68 genes. Cell lines examined included a T lymphoma, a pre-B lymphocyte, and a non-B-non-T tumor cell line, as well as an Ig-nonproducing myeloma of undetermined differentiated status. Nonexpression is strain-independent as observed in BALB/c and C3H plasmacytomas. Based on S1 nuclease analysis using a cloned genomic hsp-68 probe, nonexpression is caused by the absence of hsp-68 mRNA following heat shock. A time-course experiment suggests that rapid degradation of mRNA does not occur, implying that the block is most likely at the transcriptional level. Southern blot analysis does not indicate any minor deletions around the region of transcription initiation, at least in the probed hsp-68 gene. These results suggest that the absence of hsp-68 gene expression may be a reflection of the differentiated and (or) transformed state of murine plasma cells, possibly through the absence or deregulation of a regulatory factor required for induction of heat-shock genes.

Animals↗

PubMed1992

Cloning of GT box-binding proteins: a novel Sp1 multigene family regulating T-cell receptor gene expression.

Analysis of a T-cell antigen receptor (TCR) alpha promoter from a variable gene segment (V) revealed a critical GT box element which is also found in upstream regions of several V alpha genes, TCR enhancer, and regulatory elements of other genes. This element is necessary for TCR gene expression and binds several proteins. These GT box-binding proteins were identified as members of a novel Sp1 multigene family. Two of them, which we term Sp2 and Sp3, were cloned. Sp2 and Sp3 contain zinc fingers and transactivation domains similar to those of Sp1. Like Sp1, Sp2 and Sp3 are expressed ubiquitously, and their in vitro-translated products bind to the GT box in TCR V alpha promoters. Sp3, in particular, also binds to the Sp1 consensus sequence GC box and has binding activity similar to that of Sp1. As the GT box has also previously been shown to play a role in gene regulation of other genes, these newly isolated Sp2 and Sp3 proteins might regulate expression not only of the TCR gene but of other genes as well.

Amino Acid Sequence↗

PubMed1985

3' end structure of the human (2'-5') oligo A synthetase gene: prediction of two distinct proteins with cell type-specific expression.

Analysis of the sizes of the (2'-5') oligo A synthetase polyadenylated transcripts in various human cell lines by hybridization with a cDNA probe revealed that the pattern of the transcripts was cell-type specific. In order to investigate whether the 1.6 Kb, 1.8 Kb and 3.6 Kb mRNA, which are predominantly expressed in different cell-lines, encode different proteins or could differ in the size of their 3' or 5' untranslated sequences, the corresponding gene was isolated. On Southern blots of human genomic RNA, the cDNA probe hybridize to a 3.1 Kb EcoRI fragment. Three overlapping genomic clones were isolated which contain the same 3.1 Kb EcoRI fragment. Transcriptional mapping of the 3' end of the gene by Northern blots, hybridization translation experiments and sequencing showed that the 1.6 and 1.8 Kb mRNA are produced by a differential processing at the 3' end of the primary transcript of the same gene. The polyadenylation site of the 1.6 Kb mRNA is located 1.9 Kb upstream to the one of the 1.8 Kb mRNA. To produce the latter transcript, a portion of the last exon of the 1.6 Kb mRNA (including a segment coding for a very hydrophobic sequence of 18 amino acids and 3' untranslated sequence) is spliced out. The two mRNAs thus encode two different proteins which could have different affinity for cellular elements. The 3.6 Kb transcript has the same polyadenylation site as the 1.8 Kb mRNA, but contains additional unspliced 3' intron sequences.

2',5'-Oligoadenylate Synthetase↗

PubMed1978

X-linked and autosomal genes controlling mouse alpha-galactosidase expression.

Analysis of F2 and backcross animals has confirmed the X-chromosome linkage of Ags, the structural locus for mouse alpha-galactosidase. The position of Ags has been located in the X chromosome, 9 centimorgans from Mo, and the gene order is centromere-Hq-Bn-Ta-Mo-Ags. A variation in the developmental expression of alpha-galactosidase activity, inherited as an autosomal trait, has been characterized using recombinant inbred lines of mice. Among certain recombinant inbred lines, the variation appears to segregate as a single major locus.

Animals↗

PubMed1994

[Transcriptional regulation in airway epithelial cell gene expression].

Analysis of molecular mechanisms that regulate transcription in airway epithelial cells is important not only in understanding the principles of development and differentiation of the airway but also in unravelling the function of proteins encoded in the genes analysed. In addition, a well-characterized promoter of a gene can be used as to regulate the expression of a gene or genes introduced into the airway for gene therapy. For these reasons, we studied the cell-specific transcription of the secretory leukoprotease inhibitor gene and found a cis-element specific to airway epithelial cells in the promoter of this gene.

Amino Acid Sequence↗

PubMed1991

A marsupial beta-lactoglobulin gene: characterization and prolactin-dependent expression.

Analysis of the tammar wallaby beta-lactoglobulin cDNA and inferred amino acid sequences reveal extensive sequence divergence from the eutherian beta-lactoglobulins. Conserved residues include the cysteines and a number of individual amino acids involved in structure and ligand-binding. The only region of extended similarity is a heptapeptide sequence which may impart specificity to its interaction with a receptor protein. Northern analysis of total mammary RNA revealed two transcripts which result from differential utilization of polyadenylation signals. The concentration of beta-lactoglobulin mRNA increased in late lactation and correlates with increases in milk production and levels of milk fat. Quantification of beta-lactoglobulin mRNA levels in hormone-stimulated mammary gland explants from tammars in late pregnancy suggests that maximal induction of the gene is dependent on prolactin alone and that expression is not modulated by other hormones known to play a role in the initiation of lactation in eutherians.

Amino Acid Sequence↗

PubMed1990

Critical regions of the Vibrio fischeri luxR protein defined by mutational analysis.

Expression of Vibrio fischeri luminescence genes requires an inducer, termed autoinducer, and a positive regulatory element, the luxR gene product. A plasmid containing a tac promoter-controlled luxR was mutagenized in vitro with hydroxylamine, and luxR mutant plasmids were identified by their inability to complement a luxR deletion mutation in trans. Sixteen luxR mutant plasmids were obtained, ten of which encoded full-length but inactive luxR gene products as demonstrated by a Western immunoblot analysis. The effects of 1 of the 10 mutations could be overcome by the addition of autoinducer at a high concentration. The mutations in each of the 10 mutant plasmids that directed the synthesis of an inactive LuxR protein were identified by DNA sequencing. Of the 10 proteins encoded by the mutant luxR plasmids, 9 differed from the normally active LuxR in only a single amino acid residue. The amino acid residue substitutions in the proteins encoded by the nine mutant luxR genes clustered in two regions. One region around the middle of the polypeptide encoded by luxR was hypothesized to represent an autoinducer-binding domain, and the other region towards the carboxy terminus of the gene product was hypothesized to constitute a lux operator DNA-binding domain or a lux operator DNA recognition domain.

Bacterial Proteins↗

PubMed1988

Immune system of swine: dissection of mononuclear leucocyte subpopulations by means of two-colour cytofluorometric analysis.

Expression of the differentiation antigen 8/1, a porcine leucocyte marker for which no counterpart is known as yet in other species, was tested in relation to the expression of surface Ig and the monocyte marker 74-22-15. B lymphocytes and T lymphocytes can be typified by the exclusive expression of surface Ig and 8/1, respectively, while all monocytes defined by the expression of the 74-22-15 antigen co-express 8/1 with the highest staining density observed for this marker. 8/1+ T lymphocyte subsets defined by the expression of CD4 and CD8 cell surface antigens differed in the expression of 8/1 with the staining density being high in CD4+ T lymphocytes, intermediate in CD8+ as well as in CD4+CD8+ T lymphocytes, and low in the CD4-CD8- subset. Practically all mononuclear leucocytes present in peripheral blood are included in the subpopulations defined by this kit of reagents, and thus it can be predicted that if mononuclear leucocytes which do not belong to any of these subpopulations exist at all, these must be rare and will not be accessible to an analysis without enrichment.

Animals↗