SEARCH · PubMed Health

Results for “Transcriptomic analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources

PubMed2026

Genome-wide identification of the peanut HD-Zip gene family and AhHDZ15 positively regulating salt and drought stress in heterologously overexpressed Arabidopsis.

Homeodomain-leucine zipper (HD-Zip) transcription factors play important roles in plant growth, development, and abiotic stress responses. However, bioinformatic analyses and functional studies of HD-Zip family in peanut are scarce. In this study, 128 AhHDZ genes were identified and classified into four subfamilies in the phylogenetic analysis. Transcriptomic data and RT-qPCR analysis indicated the expression levels of AhHDZ4 and AhHDZ15 were significantly elevated in response to 12 h of salt stress, while AhHDZ4/15/60/69/126 all showed a progressive increase over time in response to drought stress. AhHDZ15 protein was localized in the nucleus. Under salt and drought stress, the germination rates of AhHDZ15-overexpressing in Arabidopsis were significantly higher than wild-type (WT), and root lengths were also significantly longer than WT. In addition, the SOD, CAT, chlorophyll content, and Relative Leaf Water Content (RLWC) value of leaves in AhHDZ15-overexpressing lines were significantly higher than WT, while the MDA content was significantly lower than WT. The above results indicate that heterologous overexpression of AhHDZ15 enhanced salt and drought tolerance in Arabidopsis. Furthermore, AhHDZ15 could bind to the L1-box element of the AhVNI2 promoter, thereby activating AhVNI2 transcription and enhancing the expression of downstream salt stress-responsive genes. These findings implies a potential function of AhHDZ15 in peanut that requires further validation.

Arabidopsis↗

PubMed2003

Rational antibacterial vaccine design through genomic technologies.

After 200 years of practice, vaccinology has proved to be very effective in preventing infectious diseases. However, several human and animal pathogens exist for which vaccines have not yet been discovered. As for other fields of medical sciences, it is expected that vaccinology will greatly benefit from the emerging genomics technologies such as bioinformatics, proteomics and DNA microarrays. In this review, the potential of these technologies will be illustrated taking into account part of the research activities currently in progress in our laboratories. In particular, I will describe the identification of new vaccine candidates against Meningococcus B through high-throughput cloning and expression of meningococcal antigens selected by: (i) in silico analysis of genome sequence; and (ii) transcriptome analysis of bacteria adherent to epithelial cells. In addition, I will show how the combination of high-throughput cloning and expression technology with two-dimensional gel/mass spectrometry led us to the elucidation of Chlamydia pneumoniae surface protein subproteome and to the identification of potential vaccine candidates.

Animals↗

PubMed2004

Serial analysis of gene expression in methamphetamine- and phencyclidine-treated rodent cerebral cortices: are there common mechanisms?

Pharmacological actions of methamphetamine (METH) and phencyclidine (PCP) are different, but both of them can induce similar psychiatric disorders including abuse, intoxication, withdrawal, and psychotic symptoms like those of schizophrenia. These mental disorders are caused not only by their direct pharmacological effects, but also by secondary brain damage containing gene expression changes. In order to broadly grasp these alterations, we used serial analysis of gene expression (SAGE), a transcriptome analysis. We analyzed three cDNA libraries from cerebral cortices of saline (1 mL/kg)-, METH (4 mg/kg)-, or PCP (10 mg/kg)-treated Wistar rats (one hour after i.p. administration). The numbers of total tags were about 50,000 in each library, and approximately 18,000 kinds of tags were identified respectively. From the comparisons of three groups, we found both METH- and PCP-reactive genes. Upregulated genes contained calmodulin 2, stromal cell-derived factor receptor 1, brain-specific angiogenesis inhibitor 1-associated protein 2, ras homologue enriched in brain, basigin and thyrotropin-releasing hormone receptor. Downregulated genes contained lipocalin 2, aldolase A, importin 13, fatty acid binding protein 3, and glycine receptor alpha2 subunit. These data suggest important clues of common molecular basis in METH- and PCP-related psychiatric disorders.

Animals↗

PubMed2026

Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues.

Cell and tissue functions arise from complex interactions among numerous genes, and a systematic understanding of these functions requires isoform-resolved transcriptomic analysis of single cells with high spatial resolution. Here, we introduce an in situ RNA amplification method and its integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) to detect short RNA sequences and enable whole-transcriptome-scale, isoform-resolved spatial transcriptomics of individual cells in intact tissues. Using this approach, we imaged ∼33,000 distinct RNAs-including ∼23,000 genes and ∼10,000 isoforms-in the mouse brain. Our data enabled systematic analyses of region- and cell-type-specific gene programs and ligand-receptor-based cell-cell communications. These data further revealed rich spatial diversity and cell-type specificity in isoform usage across numerous genes, as well as brain structures particularly rich in isoform specificity. We anticipate broad application of this method for characterizing the molecular and cellular basis of tissue functions, unlocking previously inaccessible discoveries in cell and organismal biology.

Animals↗

PubMed2026

Precision-Based Filtering Facilitates Cross-Referencing of Conventional and Single-Nucleus Transcriptomes to Identify Time- and Temperature-Sensitive Cell Populations.

Transcriptome analysis via RNA sequencing (RNAseq) has become a ubiquitous method of molecular characterization from whole organisms, dissected tissues, and single cells. These experiments continue to provide an extraordinary volume of data describing molecular states and responses to many conditions. However, standard approaches to RNAseq analysis commonly use expression level filters that eliminate potentially useful data in the service of decreasing noise. Here we describe the implementation of a coefficient of variation-based filter for RNAseq gene expression data. This filter prioritizes consistent data across replicates, allowing lowly-expressed genes with low-variation measurements to be retained for downstream analysis. We show, using two independent Arabidopsis RNAseq datasets, that this filter allows for the inclusion of many more transcription factors than even a low-stringency expression level filter. This effect is independent of sequencing depth. We find that these lowly-expressed genes mark specific cell clusters in our single-nucleus (sn)RNAseq dataset and may facilitate future characterization of currently unknown cell types or states. We further characterize communities of co-expressed genes, sampled across the day at two growth temperatures, in relation to snRNAseq cell clusters, finding evidence for a highly photosynthetic cell population, and a cell state marked by high cell division and translation. These methods can be expanded to RNAseq analysis in many systems, facilitating the construction of more detailed models of tissue-specific gene regulatory networks.

Transcriptome analysis↗

PubMed2005

Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth.

A combined proteomic and transcriptomic analysis of Staphylococcus aureus strain N315 was performed to study a sequenced strain at the system level. Total protein and membrane protein extracts were prepared and analyzed using various proteomic workflows including: 2-DE, SDS-PAGE combined with microcapillary LC-MALDI-MS/MS, and multidimensional liquid chromatography. The presence of a protein was then correlated with its respective transcript level from S. aureus cells grown under the same conditions. Gene-expression data revealed that 97% of the 2'596 ORFs were detected during the post-exponential phase. At the protein level, 23% of these ORFs (591 proteins) were identified. Correlation of the two datasets revealed that 42% of the identified proteins (248 proteins) were amongst the top 25% of genes with highest mRNA signal intensities, and 69% of the identified proteins (406 proteins) were amongst the top 50% with the highest mRNA signal intensities. The fact that the remaining 31% of proteins were not strongly expressed at the RNA level indicates either that some low-abundance proteins were identified or that some transcripts or proteins showed extended half-lives. The most abundant classes identified with the combined proteomic and transcriptomic approach involved energy production, translational activities and nucleotide transport, reflecting an active metabolism. The simultaneous large-scale analysis of transcriptomes and proteomes enables a global and holistic view of the S. aureus biology, allowing the parallel study of multiple active events in an organism.

Bacterial Proteins↗

PubMed2005

Transcriptome and proteome analysis of soleus muscle of hormone-sensitive lipase-null mice.

Hormone-sensitive lipase (HSL), a key enzyme in fatty acid mobilization in adipocytes, has been demonstrated also in skeletal muscle. To gain further insight into the role and importance of HSL in skeletal muscle, a transcriptome analysis of soleus muscle of HSL-null mice was performed. A total of 161 transcripts were found to be differentially expressed. Increased mRNA levels of fructose-1,6-bisphosphatase, fructose-2,6-bisphosphatase, and phosphorylase kinase gamma1A suggest a higher glycogen flux in soleus muscle of HSL-null mice. An observed increase in the utilization of glycogen stores supports this finding. Moreover, an increased amount of intramyocellular lipid droplets, observed by transmission electron microscopy, suggests decreased mobilization of lipid stores in HSL-null mice. To complement the transcriptome data, protein expression analysis was performed. Five spots were found to be differentially expressed: pyruvate dehydrogenase E1alpha, creatine kinase (CK), ankyrin-repeat domain 2, glyceraldehyde-3-phosphate dehydrogenase, and one protein yet to be identified. The increased protein level of CK indicates creatine phosphate degradation to be of increased importance in HSL-null mice. The results of this study suggest that in the absence of HSL, a metabolic switch from reliance on lipid to carbohydrate energy substrates takes place, supporting an important role of HSL in soleus muscle lipid metabolism.

Animals↗

PubMed2026

Antibacterial mechanisms and pathogen-dependent protective effects of the golden pompano LEAP2-derived peptide TroLEAP2-21.

Antimicrobial peptides (AMPs) are essential components of the innate immune system, with liver-expressed antimicrobial peptide 2 (LEAP2) playing a pivotal role in fish immunity. This study investigated the antimicrobial activity and mechanisms of TroLEAP2-21, a 21-amino-acid short peptide from golden pompano (Trachinotus ovatus), against Gram-positive (Lactococcus garvieae, Staphylococcus epidermidis) and Gram-negative (Vibrio alginolyticus, Vibrio harveyi) bacteria. The predicted three-dimensional structure and helical wheel projection of TroLEAP2-21 suggested typical AMP-like physicochemical features. troleap2 expression in the liver and intestine of T. ovatus was significantly upregulated post L. garvieae or V. harveyi infection, suggesting its potential involvement in antibacterial defense. In vitro, TroLEAP2-21 exhibited antibacterial activity against the tested bacterial strains, with membrane disruption, increased membrane permeability, cytoplasmic leakage, and membrane depolarization observed after peptide treatment. Gel retardation assays further indicated species-dependent association of TroLEAP2-21 with bacterial genomic DNA. In vivo, under the tested intraperitoneal injection conditions, TroLEAP2-21 was associated with improved survival and reduced tissue damage in V. harveyi-infected T. ovatus, whereas no significant survival benefit was observed against L. garvieae. Transcriptomic analysis at 48 h post-infection showed transcriptional changes in immune-related DEGs (rsad2, mx1/mx2, il-8) and enrichment of TLR and Jak-STAT signaling pathways at the transcriptional level in peptide-treated fish. FISH showed the tissue localization of tnf-α and nf-κb transcripts and revealed treatment-associated changes in fluorescence signals, and qRT-PCR of eight immune genes supported transcriptomic results in tissues at 48 h post-infection. Collectively, these findings characterize TroLEAP2-21 as a short LEAP2-derived peptide with antibacterial and immunomodulatory activities. Its comparative advantages over other LEAP2-related peptides and its practical application potential remain to be further investigated.

AMPs↗

PubMed2026

Grafting and biodynamic nanosilica-induced physiological and transcriptomic modulation of chilli (Capsicum annuum L.) under drought stress.

Chilli (Capsicum annuum L.) is an economically important vegetable crop cultivated worldwide. Increasing drought stress associated with climate change has severely reduced chilli productivity. Although grafting and silicon-based nanomaterials have each been investigated independently as drought mitigation strategies in Solanaceae crops, this study represents, to our knowledge, the first investigation of their combined physiological, yield, and genome-wide transcriptomic effects in chilli under experimentally validated drought stress. Biodynamic nanosilica (BNS) is an α-quartz nanoparticle preparation (20-200 nm) derived from the biodynamic agricultural preparation BD501 through a vortex-triturating process, and distinct from chemically synthesised nanosilica in preparation method and surface bioavailability, applied as a foliar spray at 50 mg L-1. Five treatments were established: well-watered (WW), drought (D), grafting + BNS + drought (G+B+D), grafting + drought (G+D), and BNS + drought (B+D), each with three independent biological replicates. Under moderate-to-severe drought conditions (DSI 62-64%; VWC ~12% v/v at 14 days), the combined G+B+D treatment significantly improved plant height (3.05-fold over D), leaf relative water content (83% vs 49% in D), net photosynthetic rate (2.0-fold over D), water-use efficiency (+40%), and antioxidant enzyme activities (SOD: 3.1-fold; CAT: 2.8-fold over D), while reducing lipid peroxidation by 76%. Root architecture was also substantially enhanced, with a 4.1-fold increase in root length and a 3.1-fold increase in root surface area relative to D. Fruit yield increased by 79% relative to drought-stressed non-grafted plants. Transcriptomic analysis using Illumina NovaSeq 6000 identified 1,051 DEGs (431 upregulated, 620 downregulated; FDR < 0.05, |log2FC| > 1). Integrated transcriptomic-phenotypic concordance analysis revealed enrichment of MAPK signalling, ABA-mediated regulation (including ABA binding and (+)-ABA 8'-hydroxylase activity), and phenylpropanoid biosynthesis as the enriched pathways. Protein-protein interaction network analysis further revealed coordinated regulation of redox homeostasis, drought-responsive hormone signalling, and water transport gene modules in the combined treatment. These findings demonstrate that integrating grafting with biodynamic nanosilica is a promising strategy to enhance drought resilience and productivity in chilli, offering a sustainable approach for vegetable production under drought.

Capsicum↗

PubMed2026

Transcriptome sequencing provides novel insights into larval development and sexual dimorphism in the firefly Aquatica leii (Coleoptera: Lampyridae).

Fireflies are regarded as one of the most charismatic beetles due to their bioluminescence and ecological importance as bioindicators of freshwater quality. However, molecular mechanisms of larval development and sexual dimorphism in aquatic species remain poorly understood. Here, we performed multi-stage transcriptomic analysis of the aquatic firefly Aquatica leii across larval instars from L2 to L6, together with adult females and males, with three biological replicates per stage. Using time-series expression clustering, differential expression analysis, and weighted gene co-expression network analysis (WGCNA), we characterized the transcriptional dynamics of continuous larval development and the onset of sex-biased gene expression. We identified a critical transcriptional transition occurred at L5-L6, marked by downregulation of early morphogenetic genes and upregulation of juvenile hormone metabolism, oxidoreductase activity, and muscle contraction genes, indicating a shift from growth to metamorphic preparation. WGCNA identified a module strongly correlated with L6 (R = 0.97) enriched for the same functions, confirming a coordinated late-larval program. Notably, genes exhibiting sex-biased expression in adults were already expressed during late larval stages (L5 and L6), and 123 genes progressively upregulated from L2 to L6 showed enrichment in chitin biosynthesis, heart contraction, and ion transport; among these, six genes maintained high expression in adults with clear male-biased (Alei052192, Alei006658, and Alei087054) or female-biased (Alei003725, Alei096818, and Alei074026) patterns. These findings establish that transcriptional foundations for sexual dimorphism and adult tissue formation are laid during late larval stages, providing the first multi-stage transcriptomic resource for aquatic firefly conservation and breeding.

Animals↗

PubMed2026

Unlocking antifungal mechanisms of natural 3-(oxazole-5-yl) indole compound derived from Streptomyces syringium against plant gray mold caused by Botrytis cinerea.

BACKGROUND: Plant fungal diseases cause significant agricultural losses, and Streptomyces-derived antifungal compounds offer a promising biocontrol strategy. This study aimed to isolate and characterize bioactive metabolites from Streptomyces syringium LZ036 and evaluate their activity and mechanism of action against Botrytis cinerea. RESULTS: A strain LZ036 with broad-spectrum antifungal activity was identified as Streptomyces syringium. The 3-(oxazole-5-yl) indole compound NL3 isolated from this strain exhibited potent broad-spectrum antifungal activity, especially against Botrytis cinerea. Compound NL3 inhibited fungal growth and development by inducing severe oxidative damage and membrane disruption. And it could trigger jasmonic acid (JA)-dependent induced systemic resistance (ISR) in plants. Transcriptomic analysis of compound NL3-treated Botrytis cinerea revealed genome-wide transcriptional alterations, including disruption of energy metabolism and mitochondrial function. Key genes related to mitogen-activated protein kinase (MAPK) signaling pathway down-regulated significantly, among which the catalytic S_TKc domain of Bcste7 exhibited a predicted interaction with compound NL3 through hydrophobic interactions and hydrogen bonding. CONCLUSION: The Streptomyces syringium-derived compound NL3 shows high potential as a green fungicide, acting through multiple mechanisms. These findings advance the development of Streptomyces-based antifungal agents. © 2026 Society of Chemical Industry.

3‐(oxazole‐5‐yl) indole compo↗

PubMed2026

Morphological, Physiological and Transcriptomic Changes in Response to Water Deficit Stress in Brassica napus L.

Yield losses due to water-deficit (WD) conditions, especially during the reproductive stages of plant development, pose a significant threat to global canola (Brassica napus L.) production. Therefore, it is critical to investigate traits contributing to improved productivity under increased WD conditions. Here we present phenotypic, physiological and transcriptomic changes in response to WD across contrasting canola accessions exhibiting variation in drought resistance-related traits. WD significantly reduced shoot biomass, plant height, harvest index, leaf water content, photosynthetic CO2 assimilation rate, intrinsic water-use efficiency and carbon isotope discrimination. WD caused 49 to 100% of the seed yield reduction: the minimum seed yield reduction (49.66%) was observed in a doubled-haploid (DH) line, 06-5101.137, while the maximum yield reduction (94.1 to 100%) occurred in the late-flowering DH lines (06.5101.088 and 06-5101.306). Seed yield showed a positive correlation (r = 0.29 to 0.95) with shoot biomass and harvest index, leaf water content, photosynthetic CO2 assimilation rate, intrinsic water use efficiency and carbon isotope discrimination. However, it showed negative correlations with days to flower, leaf specific weight, root length, root biomass (r = -0.04 to -0.79) across water treatments. The specific leaf transcriptome analysis of the two parental lines of DH population that exhibit variation for effective water use under well-watered and water-deficient conditions revealed different categories of differentially expressed genes (DEGs): WD-responsive DEGs in BC1329 parental line (1116) and BC9102 (1205) with 754 and 853 DEGs unique to BC1329 and BC9102, respectively, WD-responsive DEGs (906), genotype-dependent DEGs (8465) and genotype × treatment interaction DEGs (353). DEG annotations revealed that the WD-treatment-affected genes were involved in stress responses and growth and development. We further located 235 DEGs within the QTL regions underlying agronomic and physiological performance. Our study provides a conceptual framework for the morphological, physiological and molecular determinants involved in water-use efficiency. Seedlings' traits with high heritability values, such as shoot biomass, leaf weight, leaf water content and Δ13C, serve as proxies for trait-based selection for improved seed yield under both water-limited and non-water-limited conditions.

Brassica napus↗

PubMed2026

Functional characterization of SHC-like triterpene cyclase genes in azole response and virulence-related traits of Aspergillus fumigatus.

Aspergillus fumigatus is a major opportunistic fungal pathogen, and increasing azole resistance poses a challenge for aspergillosis treatment. Squalene is an upstream precursor of ergosterol biosynthesis and may also be utilized by SHC-like triterpene cyclases, suggesting a potential link between squalene-associated metabolism, membrane adaptation, and azole response. However, the roles of SHC-like triterpene cyclase genes in A. fumigatus remain unclear. Here, we characterized three candidates, shc1, shc2, and shc3, using comparative bioinformatic analysis, gene deletion, phenotypic assays, azole susceptibility testing, transcriptomics, and host-interaction models. Sequence, genomic-context, phylogenetic, and structural analyses suggested divergence among the three candidates. Individual shc deletion caused limited effects on vegetative growth, whereas loss of shc1 mildly reduced susceptibility to voriconazole and posaconazole, as reflected by twofold MIC increases and lower inhibition rates. Transcriptomic analysis revealed distinct remodeling patterns, with Δshc3 showing the broadest transcriptional changes despite no detectable MIC shift. Targeted metabolite profiling and PI uptake analysis further supported an association between shc deletion, sterol/hopane-type triterpenoid balance, and membrane-associated properties. shc deletion also altered epithelial cell interaction phenotypes, while Δshc1 showed reduced lethality in Galleria mellonella. In clinical isolates, elevated shc transcription was associated with azole-resistant backgrounds. These findings suggest functional diversification among SHC-like triterpene cyclase genes and indicate that shc1 may contribute to azole-associated adaptation and virulence-related traits in A. fumigatus.

Aspergillus fumigatus↗

PubMed2004

CEBS object model for systems biology data, SysBio-OM.

MOTIVATION: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). RESULTS: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. AVAILABILITY: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Database Management Systems↗

PubMed2005

Laser capture microdissection of hepatic stages of the human parasite Plasmodium falciparum for molecular analysis.

Despite the sequencing of parasite genomes and development of DNA microarray technology, gene profiling of parasites remains a difficult task. For example, transcriptome analysis cannot currently be applied to the hepatic stages of the malaria parasite Plasmodium falciparum due to difficulties in obtaining sufficient amounts of parasite material that lies among the large excess of host cell RNA. Here, we describe the isolation of P. falciparum-infected human hepatocytes by a laser capture microdissection approach. Reverse transcriptase polymerase chain reaction amplification of several P. falciparum transcripts demonstrates the high quality of the RNA recovered after microdissection. This approach should enable analysis of P. falciparum transcriptome during its hepatic development, a major step toward the identification of new therapeutic and vaccine targets.

Animals↗

PubMed2003

Proteomics and transcriptomics analyses of secretagogin down-regulation in human non-functional pituitary adenomas.

In order to explore the presence of, and the potential role of, secretagogin in human pituitary adenomas, an analytical strategy that integrated comparative proteomics and comparative transcriptomics was used to detect the protein and the mRNA expression, respectively, of secretagogin in human non-functional pituitary adenomas compared to controls. Proteomics methods included two-dimensional gel electrophoresis, 2D gel image analysis, mass spectrometry [matrix-assisted laser desorption/ionization-time of flight-peptide mass fingerprinting (MALDI-TOF PMF) and liquid chromatography-electrospray ionization-quadrupole-ion trap tandem mass spectrometry (LC-ESI-Q-IT MS/MS)], and database analysis. Transcriptomics methods included the GeneChip microarray, image processing, and data analysis. The proteomics and transcriptomics data demonstrated that secretagogin was significantly down-regulated at the protein and mRNA levels, respectively, in the human non-functional (NF) pituitary adenomas (NF-, LH+, FSH+, and FSH+ + LH+). For the secretagogin protein, the expression level was NF- < FSH+ + LH+ < FSH+ < LH+ < Control, with a range of down-regulation of 2.2-6.9 fold in non-functional pituitary adenomas compared to controls, with a significant difference (p < 0.001). For secretagogin mRNA, the expression level was NF- < LH+ < FSH+ + LH+ < FSH+ < Control, with a range of down-regulation of 1.8-18.6 fold in non-functional pituitary adenomas compared to controls that was significant (p < 0.05). The secretagogin protein expression correlated significantly with its mRNA expression. Those results suggest that secretagogin might play a role in human non-functional pituitary adenomas. This novel finding may provide clues to clarify the basic molecular mechanisms of pituitary adenoma formation, and to identify new tumor-related markers.

Adenoma↗

PubMed2005

Transcriptional profiles of the human pathogenic fungus Paracoccidioides brasiliensis in mycelium and yeast cells.

Paracoccidioides brasiliensis is the causative agent of paracoccidioidomycosis, a disease that affects 10 million individuals in Latin America. This report depicts the results of the analysis of 6,022 assembled groups from mycelium and yeast phase expressed sequence tags, covering about 80% of the estimated genome of this dimorphic, thermo-regulated fungus. The data provide a comprehensive view of the fungal metabolism, including overexpressed transcripts, stage-specific genes, and also those that are up- or down-regulated as assessed by in silico electronic subtraction and cDNA microarrays. Also, a significant differential expression pattern in mycelium and yeast cells was detected, which was confirmed by Northern blot analysis, providing insights into differential metabolic adaptations. The overall transcriptome analysis provided information about sequences related to the cell cycle, stress response, drug resistance, and signal transduction pathways of the pathogen. Novel P. brasiliensis genes have been identified, probably corresponding to proteins that should be addressed as virulence factor candidates and potential new drug targets.

Blotting, Northern↗

PubMed2026

Effects of rumen fluid transplantation on longissimus dorsi muscle development in Xizang sheep: An association analysis based on transcriptomic and serum metabolomic profiles.

This study aimed to investigate the effects of rumen fluid transplantation (RFT) on the growth and development of the longissimus dorsi muscle in female Xizang sheep. After RFT, muscle lightness differed significantly between the two groups, with the LDC group showing significantly higher lightness than the LDT group. In contrast, no significant differences were observed between groups in other muscle phenotypic traits, including drip loss, pH, cooking loss, shear force, redness, and yellowness. Antioxidant-related indices (SOD, GSH-PX, MDA, CAT, and T-AOC) also showed no significant differences between groups. Histological analysis revealed that muscle fiber length, width, and density were significantly greater in the experimental group than in the control group. Transcriptomic analysis identified 515 differentially expressed genes (DEGs), of which 419 were downregulated. KEGG analysis indicated that genes involved in muscle development-related pathways, such as cell adhesion and the PI3K-Akt signaling pathway, were predominantly downregulated. Key serum metabolites (L-kynurenine, IPA, allantoin, and propionylcarnitine) showed highly significant positive correlations with muscle fiber growth indices. In contrast, metabolites such as l-carnitine, acetylcarnitine, and citrulline were negatively correlated with muscle fiber growth, but positively correlated with the expression of muscle structure-related genes (COL11A1 and EFNA5) and with meat lightness. Overall, this study provides new insights into the potential molecular basis by which RFT influences muscle growth and development. However, the mechanisms by which RFT affects muscle development and meat quality-related traits remain unclear and warrant further investigation.

Animals↗