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PubMed1997

Molecular cloning and expression analysis of dihydroflavonol 4-reductase gene in flower organs of Forsythia x intermedia.

The expression, during flower development, of the gene encoding the anthocyanin pathway key enzyme dihydroflavonol 4-reductase (DFR) was investigated in floral organs of Forsythia x intermedia cv. 'Spring Glory'. Full-length DFR and partial chalcone synthase (CHS) cDNAs, the gene of interest and a flavonoid pathway control gene respectively, were obtained from petal RNA by reverse transcription PCR. Whereas for CHS northern blot analysis enabled the study of its expression pattern, competitive PCR assays were necessary to quantify DFR mRNA levels in wild-type plants and in petals of 2 transgenic clones containing a CaMV 35S promoter-driven DFR gene of Antirrhinum majus. Results indicated a peak of CHS and DFR transcript levels in petals at the very early stages of anthesis, and different expression patterns in anthers and sepals. In comparison to wild-type plants, transformants showed a more intense anthocyanin pigmentation of some vegetative organs, and a dramatic increase in DFR transcript concentration and enzymatic activity in petals. However, petals of transformed plants did not accumulate any anthocyanins. These results indicate that other genes and/or regulatory factors should be considered responsible for the lack of anthocyanin production in Forsythia petals.

Alcohol Oxidoreductases↗
PubMed2006

Regulating the regulator: factors that control levels and activity of the aryl hydrocarbon receptor.

The aryl hydrocarbon receptor (AHR) participates in a wide range of critical cellular events in response to endogenous signals or xenobiotic chemicals. Hence, it is important that AHR levels and activity themselves be well controlled in target tissues. The AHR is essentially ubiquitous in its distribution in mammalian tissues. However, levels of the receptor vary widely across different tissues and among different cell types. AHR levels and activity are modulated by exposure to the receptor's own ligands and are influenced by other xenobiotic chemicals. Many different factors impinge on AHR levels and AHR activity. These factors may alter responsiveness of downstream pathways, thereby affecting normal physiologic functions as well as responses to toxic environmental chemicals such as dioxins. Our commentary appraises the current literature on factors that regulate AHR levels/activity and attempts to identify fruitful strategies towards discovery of key pathways by which AHR levels are modulated in response to endogenous signals and in response to xenobiotic chemicals. An extraordinarily large number of agents alter the level or activity of the AHR. We have not yet entered an age of enlightenment sufficient to achieve true understanding of the interplay of mechanisms that regulate AHR expression in space and in time.

Animals↗
PubMed2005

A novel regulation of IRS1 (insulin receptor substrate-1) expression following short term insulin administration.

Reduced insulin-mediated glucose transport in skeletal muscle is a hallmark of the pathophysiology of T2DM (Type II diabetes mellitus). Impaired intracellular insulin signalling is implicated as a key underlying mechanism. Attention has focused on early signalling events such as defective tyrosine phosphorylation of IRS1 (insulin receptor substrate-1), a major target for the insulin receptor tyrosine kinase. This is required for normal induction of signalling pathways key to many of the metabolic actions of insulin. Conversely, increased serine/threonine phosphorylation of IRS1 following prolonged insulin exposure (or in obesity) reduces signalling capacity, partly by stimulating IRS1 degradation. We now show that IRS1 levels in human muscle are actually increased 3-fold following 1 h of hyperinsulinaemic euglycaemia. Similarly, transient induction of IRS1 (3-fold) in the liver or muscle of rodents occurs following feeding or insulin injection respectively. The induction by insulin is also observed in cell culture systems, although to a lesser degree, and is not due to reduced proteasomal targeting, increased protein synthesis or gene transcription. Elucidation of the mechanism by which insulin promotes IRS1 stability will permit characterization of the importance of this novel signalling event in insulin regulation of liver and muscle function. Impairment of this process would reduce IRS1 signalling capacity, thereby contributing to the development of hyperinsulinaemia/insulin resistance prior to the appearance of T2DM.

Adult↗
PubMed2001

Regulation of Kv1.3 channels in activated human T lymphocytes by Ca(2+)-dependent pathways.

Activated T lymphoblasts respond more effectively to mitogenic stimuli than resting T cells, partly through differences in Ca(2+) signaling, which in turn depend on K(+) channel activity. Both Kv1.3 and Ca(2+)-activated K(+) (SK4) channels are up-regulated in T lymphoblasts. Since Ca(2+)- and calmodulin (CaM)-dependent signal-ing are key pathways in T-cell activation, we investigated their involvement in regulating the Kv1.3 current. Kv1.3 in lymphoblasts was significantly inhibited by elevating internal Ca(2+) to the micromolar level. It was also reduced in a Ca(2+)-dependent manner by inhibiting CaM with W-7 or calmidazolium. Part of the CaM-dependence is likely through CaM kinase since the current was also inhibited by the antagonist, KN-62, but not by the inactive analogue, KN-04. Kinase inhibition, unlike CaM inhibition, was only effective at physiological temperatures, a difference that implies involvement of more than one mechanism. We demonstrated a biochemical association of Kv1.3 protein in lymphoblasts with the multifunctional type II CaM kinase, but not with calmodulin. Thus, Kv1.3 forms a multi-protein complex with CaM kinase II (which binds to Ca(2+)/CaM) and previously identified proteins (e.g., PSD-95, src tyrosine kinase) that position the channel to respond to signaling pathways that are crucial for T-cell activation and proliferation.

Calcium↗
PubMed2000

Metaplasticity of mossy fiber synaptic transmission involves altered release probability.

Activity-dependent synaptic plasticity is a fundamental feature of CNS synapses. Intriguingly, the capacity of synapses to express plastic changes is itself subject to considerable activity-dependent variation, or metaplasticity. These forms of higher order plasticity are important because they may be crucial to maintain synapses within a dynamic functional range. In this study, we asked whether neuronal activity induced in vivo by application of kainate can induce lasting changes in mossy fiber short- and long-term plasticity. Several weeks after kainate-induced status epilepticus, the mossy fiber, but not the associational-commissural pathway, exhibits a marked loss of paired-pulse facilitation, augmentation, and long-term potentiation (LTP). Because the adenylyl cyclase-protein kinase A cascade is involved in mossy fiber LTP induction, we have tested the integrity of this key pathway by pharmacological activation of either adenylyl cyclase or protein kinase A. These treatments resulted in LTP in control, but not in kainate-treated animals, indicating that status-induced changes occur downstream of protein kinase A. To test whether altered neurotransmitter release might account for these changes, we measured the size of the releasable pool of glutamate in mossy fiber terminals. We find that the size of the releasable pool of glutamate was significantly increased in kainate-treated rats, indicating an increased release probability at the mossy fiber-CA3 synapse. Therefore, we suggest that lasting changes in neurotransmitter release probability caused by neuronal activity may be a powerful mechanism for metaplasticity that modulates both short- and long-term plasticity in the mossy fiber-CA3 synapse after status epilepticus.

Animals↗
PubMed1999

Signaling and effector pathways.

There is increasing evidence that distinct signaling and effector pathways in the rheumatoid synovium result in a cascade of pathophysiologic events. These interactions, which finally lead to progressive joint destruction, are different from all other joint diseases in numerous aspects. As outlined in this review, molecular biology techniques allow detection of key pathways ranging from external stimuli to subcellular gene regulation mechanisms operative in various cells within the rheumatoid synovium. To alter these pathways, inhibitory factors need to be applied to these "hot zones" for an extended period, which can be achieved either by repeated drug administration or by local synthesis using genetically altered synovial cells. Both adenovirus and retroviral constructs, as well as ex vivo and in vivo strategies, can be used for gene transfer into these cells, and routine delivery of "protective" genes into the affected joints might be achieved within the next decade.

Arthritis, Rheumatoid↗
PubMed1993

Role of excitotoxins in heredito-degenerative neurologic diseases.

In summary, EAA play an important role in neurodegenerative disorders simply by virtue of the pathways in brain that utilize EAA as neurotransmitters. Thus, the striatum, which is so strikingly affected in Huntington's disease, receives massive EAAergic input from all regions of the cerebral cortex and from the thalamus. In Parkinson's disease, some of the key pathways projecting into the substantia nigra pars compacta and to the subthalamic nucleus and basal ganglia output zones also use EAA as neurotransmitters. In Alzheimer's disease, the cerebral cortex and hippocampus are dependent on EAAergic neurotransmission for normal function. Drugs that manipulate these neurotransmitter inputs and outputs could be very helpful in the symptomatic relief of all these neurodegenerative disorders. In addition, there may be secondary excitotoxic effects of EAA on neuronal function in neurodegenerative disorders. Genetic abnormalities may render subsets of neurons more vulnerable to changes in ion concentration or energy demands and thus more susceptible to EAA-induced neurotoxicity. Although EAA themselves may not be the primary culprit in a disease, EAA-induced toxicity may cause significant damage as a secondary phenomenon. If so, the neuronal damage could potentially be attenuated by the use of EAA antagonists. Future research on these problems hold great promise.

Alzheimer Disease↗
PubMed2004

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.

BACKGROUND: Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory sequence detection and analysis of genomic context. RESULTS: In the genomes of delta-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA, sigma-32), four types of metabolite-binding riboswitches (RFN-, THI-, B12-elements and S-box), and new binding sites for the FUR, ModE, NikR, PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions. CONCLUSIONS: Phylogenetically diverse delta-proteobacteria appear to have homologous regulatory components. This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria. Recent efforts in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions.

Bacterial Proteins↗
PubMed2026

Transcriptomic analysis identifies novel ferroptosis-related biomarkers and therapeutic targets in pulmonary arterial hypertension.

BACKGROUND: Ferroptosis plays a significant role in pulmonary arterial hypertension (PAH), although its underlying mechanisms and key pathogenic genes remain unclear. METHODS: Transcriptomic data from human PAH and control lung tissue were obtained from the Gene Expression Omnibus (GEO) database, whereas ferroptosis-related genes (FRGs) were sourced from the MsigDb and FerrDb databases. Differentially expressed FRGs (DE-FRGs) were identified through the intersection of FRGs with differentially expressed genes (DEGs). Functional enrichment analysis was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Key hub genes were identified through Least Absolute Shrinkage and Selection Operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and weighted correlation network analysis (WGCNA). Gene set enrichment analysis (GSEA) was conducted to explore the functional roles and associated pathways of hub genes. The relationship between hub genes and immune infiltration was investigated. Expression levels of potential biomarkers were validated via Quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) in two PAH animal models (monocrotaline-induced and Sugen5416 plus hypoxia-induced PAH). Finally, molecular docking was employed to screen potential therapeutic compounds. RESULTS: A total of 133 DE-FRGs were identified, with KEGG and GO analyses highlighting their involvement in intracellular iron homeostasis and ferroptosis. Hub genes, notably FZD7 and NFE2, were identified using LASSO, SVM-RFE, and WGCNA. Immune infiltration analysis suggested that monocytes and neutrophils play key roles in PAH pathogenesis. Validation in PAH animal models showed significant upregulation of Fzd7 and downregulation of Nfe2 in lung tissues of both MCT- and SuHx-induced PAH models. Molecular docking identified tetrachlorodibenzodioxin (TCDD) has good binding affinity. CONCLUSION: In summary, we investigated two ferroptosis-related biomarkers, FZD7 and NFE2, in PAH using transcriptomics, offering new insights into molecular mechanisms and potential targeted therapies for the disease.

Ferroptosis↗
PubMed2003

Human neutrophils utilize a Rac/Cdc42-dependent MAPK pathway to direct intracellular granule mobilization toward ingested microbial pathogens.

Elevated levels of mitogen-activated protein kinase/extracellular regulatory kinase (MAPK/ERK) activity are frequently found in some cancer cells. In efforts to reduce tumor growth, attempts have been made to develop cancer therapeutic agents targeting the MAPK. Here, by use of biologic, biochemical, and gene manipulation methods in human polymorphonuclear neutrophils (PMNs), we have identified a key pathway important in normal cell function involving MAPK/ERK in PMNs for growth inhibition of Candida albicans. Contact with C albicans triggered MAPK/ERK activation in PMNs within 5 minutes, and blocking of MAPK/ERK activation, either by the pharmacologic reagent PD098059 or by dominant-negative MAPK kinase (MEK) expression via vaccinia viral delivery, suppressed antimicrobial activity. Rac and Cdc42, but not Ras or Rho, were responsible for this MAPK/ERK activation. Expression of dominant-negative Rac (N17Rac) or Cdc42 (N17Cdc42) eliminated not only C albicans- mediated ERK phosphorylation but also phagocytosis and granule migration toward the ingested microbes, whereas dominant-negative Ras (N17Ras) and Rho (N19Rho) did not. PAK1 (p21-activated kinase 1) activation is induced by C albicans, suggesting that PAK1 may also be involved in the Rac1 activation of MAPK/ERK. We conclude from these data that Rac/Cdc42-dependent activation of MAPK/ERK is a critical event in the immediate phagocytic response of PMNs to microbial challenge. Therefore, use of MAPK pharmacologic inhibitors for the treatment of cancer may result in the interruption of normal neutrophil function. A balance between therapeutic outcome and undesirable side effects must be attained to achieve successful and safe anticancer therapy.

Candida albicans↗
PubMed2025

BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies.

Cancer drug resistance remains a major barrier to durable treatment success, often leading to relapse despite advances in precision oncology. While combination therapies are being increasingly investigated, such as chemotherapy with small molecule inhibitors, predicting drug response and identifying rational drug combinations based on resistance mechanisms remain major challenges. Therefore, a proteome-wide, single-gene overexpression screening platform is essential for guiding rational therapy selection. Here, we present BOGO (Bxb1-landing pad human ORFeome-integrated system for a proteome-wide Gene Overexpression), a robust, scalable, and reproducible screening platform that enables single-copy, site-specific integration and overexpression of ~19,000 human open across cancer cell models. Using BOGO, we identified drug-specific response drivers for 16 chemotherapeutic agents and integrated clinical datasets to uncover proliferation and resistance-associated genes with prognostic potential. Drug response similarity networks revealed both shared and unique mechanisms, highlighting key pathways such as autophagy, apoptosis, and Wnt signaling, and notable resistance-associated genes including BCL2, POLD2, and TRADD. In particular, we proposed a synergistic combination of the BCL2 family inhibitor ABT-263 (Navitoclax®) and the DNA analog TAS-102 (Lonsurf®), which revealed that lysosomal modulation is a key mechanism driving DNA analog resistance. This combination therapy selectively enhanced cytotoxicity in colorectal and pancreatic cancer cells in vitro, and demonstrated therapeutic benefit in vivo in both cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. Together, these findings establish BOGO as a powerful gene overexpression perturbation platform for systematically identifying chemoresistance and chemosensitization drivers, and for discovering rational combination therapies. Its scalability and reproducibility position BOGO as a broadly applicable tool for functional genomics and therapeutic discovery beyond cancer resistance.

Journal Article↗
PubMed2003

[Pleiotropic function of phosphoenolpyruvate-dependent phosphotransferase system in bacteria. Report 1].

Modern data (collected mainly in the 1998-2001 studies) about the transport of carbohydrates in bacteria, about the regulation of utilization of sugars via the glycolytic pathway as well as about the regulation of transformation of pyruvat into the products of secondary metabolism and of tricarboxylic acid cycle are presented in the survey. Issues, related with the regulation of synthesis of enzymes involved in the last mentioned process, are discussed in detail. Besides, the key pathways pertaining to the regulation of synthesis and activity of adenylate cyclase; elimination of the inductor in the gram-negative bacteria and entry of phage lambda DNA into E. coli are described. As for the gram-positive bacteria, properties of their main components (involved in catabolic repression), i.e. HPr, K/P, CcpA, CCpB and CcpC, cre, are presented. The mechanisms of catabolic repressions and of catabolic activation in bacteria are in the focus of attention. Finally, issues related with the structural organization of PTS as well as molecular-and-biological aspects of the interaction of proteins of the mentioned system are considered in the survey.

Adenosine Triphosphate↗
PubMed2001

Sex related embryo development.

Although sexual dimorphic development in the mammalian embryo prior to differentiation of the gonad has been documented, there are many seemingly conflicting observations and gaps in our understanding of this process. Conditions that influence the process include gamete interaction, that might give one sex and advantage in the fertilization process and in rates of blastomere cleavage that would allow one sex to accumulate cells at a faster rate. In this scenario, males could accumulate more cells within a defined window of development. Another key difference between males and females is the number of copies of genes located on the sex chromosomes. Transcripts from the Y-chromosome are thought to function as transcription factors, which could accelerate development. Conversely, the X-chromosome contains genes that code for rate limiting steps in pathways key to embryo metabolism and stress reduction. It can be envisioned that prior to X-chromosome inactivation in females, elevated levels of transcripts for such genes may enable greater protection from environmental stress and regulate growth. As we gain a better understanding of how males and female develop we will be able to exert greater control over the manipulation of the sex ratio for the offspring of domestic animals.

Animals↗
PubMed2026

Therapeutic Potential of Terpenes in Lung Cancer: Modulation of 4-Oxo- Retinoic Acid, TNF-α, NF-κB, and HDAC2 Pathways.

Non-small cell lung cancer (NSCLC) includes various epithelial malignancies, such as squamous cell carcinoma, large cell carcinoma, and adenocarcinoma. Despite advancements in surgical resection, chemoradiotherapy, and multimodal therapies, NSCLC prognosis remains challenging due to its complex molecular landscape, drug resistance, and high treatment costs. Recent research highlights the potential of natural compounds, particularly terpenes and terpenoids, derived from essential oils (EOs), to enhance NSCLC treatment. These compounds exhibit anticancer properties and modulate key pathways like the 4-oxo-retinoic acid pathway, TNF-α signaling, NF-κB activation, and histone deacetylases (HDACs). Retinoids, a subclass of terpenes, show both chemopreventive and therapeutic benefits, especially when combined with other agents, though challenges in dosing and delivery methods limit their clinical application. Terpenes may also synergize with emerging therapies, such as antiangiogenic treatments and immunotherapy, to improve outcomes. Biomarkers, including genomic, epigenomic, and proteomic markers, play a critical role in predicting responses to terpene-based treatments, supporting personalized medicine. The integration of terpenes into existing regimens, in combination with conventional therapies, holds promise in overcoming clinical challenges, improving patient outcomes, and advancing natural compound use in modern oncology. Future research should focus on optimizing terpene therapies and addressing clinical hurdles.

Humans↗
PubMed2003

Amyotrophic lateral sclerosis: a novel hypothesis involving a gained 'loss of function' in the JNK/SAPK pathway.

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease that mainly affects motor neurons. Despite intensive research efforts inspired by the mile-stone discovery linking the Cu/Zn superoxide dismutase 1 (SOD1) gene to a subset of familial cases, the mechanisms underlying disease pathogenesis are still largely unknown. Nonetheless, the recent finding of a second gene associated with familial form of the disease, ALS2, is likely to be of great help in elucidating the key pathways involved in motor neuron degeneration. Here, we provide evidence that the JNK/SAPK pathway plays a critical neuroprotective role in susceptible motor neurons in ALS. The involvement of the JNK/SAPK pathway integrates our knowledge about these two known genetic factors into a single pathogenic pathway involved in both sporadic and familial ALS.

Amyotrophic Lateral Sclerosis↗
PubMed2000

The role of orphan nuclear receptors in the regulation of cholesterol homeostasis.

Cholesterol balance is maintained by a series of regulatory pathways that control the acquisition of cholesterol from endogenous and exogenous sources and the elimination of cholesterol, facilitated by its conversion to bile acids. Over the past decade, investigators have discovered that a family of membrane-bound transcription factors, sterol regulatory element-binding proteins (SREBPs), mediate the end-product repression of key enzymes of cholesterol biosynthesis. Recently orphan members of another family of transcription factors, the nuclear hormone receptors, have been found to regulate key pathways in bile acid metabolism, thereby controlling cholesterol elimination. The study of these orphan nuclear receptors suggests their potential as targets for new drug therapies.

Animals↗
PubMed2006

A complex of Yos9p and the HRD ligase integrates endoplasmic reticulum quality control into the degradation machinery.

A quality-control system surveys the lumen of the endoplasmic reticulum for terminally misfolded proteins. Polypeptides singled out by this system are ultimately degraded by the cytosolic ubiquitin-proteasome pathway. Key components of both the endoplasmic reticulum quality-control system and the degradation machinery have been identified, but a connection between the two systems has remained elusive. Here, we report an association between the endoplasmic reticulum quality-control lectin Yos9p and Hrd3p, a component of the ubiquitin-proteasome system that links these pathways. We identify designated regions in the luminal domain of Hrd3p that interact with Yos9p and the ubiquitin ligase Hrd1p. Binding of misfolded proteins occurs through Hrd3p, suggesting that Hrd3p recognises proteins that deviate from their native conformation, whereas Yos9p ensures that only terminally misfolded polypeptides are degraded.

Blotting, Western↗
PubMed2004

The adaptive imbalance to genotoxic stress: genome guardians rear their ugly heads.

An adaptive response of the genome-protection machinery occurs in cells exposed to genotoxic stress. This machinery includes the p53 and retinoblastoma protein pathways, which are not mutually exclusive from other adapting machinery including DNA repair, cell cycle checkpoints, apoptosis and endogenous metabolizing and antioxidant enzymes. The adaptive changes occur in chronic inflammation and in cigarette smokers associated with a high cancer risk, and are an attempt to keep cells healthy. However, there is increasing evidence that this response may have deleterious effects. Here, key pathways that adaptively respond to genotoxic stress are reviewed and mechanisms by which this response may have pro-carcinogenic implications are discussed.

Animals↗