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Results for “Candidate pathways”

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PubMed2003

Nereistoxin and cartap neurotoxicity attributable to direct block of the insect nicotinic receptor/channel.

Nereistoxin (NTX) (4-dimethylamino-1,2-dithiolane) is the naturally occurring prototype for cartap [the bis(thiocarbamate) derivative of the NTX dithiol], which is generally regarded as a proinsecticide reverting to NTX. The aim of this study is to define the target site(s) for dithiolanes and dithiol esters. The affinity of [(3)H]NTX was not suitable for binding assays with honeybee (Apis mellifera) head membranes. However, NTX and cartap are equally potent, direct-acting, and competitive displacers of [(3)H]thienylcyclohexylpiperidine binding at the noncompetitive blocker (NCB) site of the Apis nicotinic acetylcholine receptor (nAChR)/channel. NTX also binds at the Apis [(3)H]imidacloprid agonist site, but cartap does not. As candidate metabolic pathways, sequential N-desmethylation and S-oxidation of NTX progressively reduce its potency at the NCB site and toxicity to houseflies. A P450 inhibitor reduces the toxicity of NTX and enhances it with cartap. Surprisingly, cartap is not just a pro-NTX but instead directly induces inhibitory neurotoxicity by blocking the nAChR/channel, whereas NTX may have dual NCB and agonist targets.

Animals↗

PubMed1998

Role of the NF-ATc transcription factor in morphogenesis of cardiac valves and septum.

In lymphocytes, the expression of early immune response genes is regulated by NF-AT transcription factors which translocate to the nucleus after dephosphorylation by the Ca2+-dependent phosphatase, calcineurin. We report here that mice bearing a disruption in the NF-ATc gene fail to develop normal cardiac valves and septa and die of circulatory failure before day 14.5 of development. NF-ATc is first expressed in the heart at day 7.5, and is restricted to the endocardium, a specialized endothelium that gives rise to the valves and septum. Within the endocardium, specific inductive events appear to activate NF-ATc: it is localized to the nucleus only in endocardial cells that are adjacent to the interface with the cardiac jelly and myocardium, which are thought to give the inductive stimulus to the valve primordia. Treatment of wild-type embryos with FK506, a specific calcineurin inhibitor, prevents nuclear localization of NF-ATc. These data indicate that the Ca2+/calcineurin/NF-ATc signalling pathway is essential for normal cardiac valve and septum morphogenesis; hence, NF-ATc and its regulatory pathways are candidates for genetic defects underlying congenital human heart disease.

Animals↗

PubMed2004

[Infectious features of atherosclerosis].

As an inflammatory focus, the atherosclerotic plaque is viewed as a response to aggressions. Suppressing these causal injuries appears as the best means for preventing the disease. Infection is among the clues for answering the etiological challenge of atherosclerosis. Through direct or indirect, and specific or non specific pathways, some candidate viruses or bacteria are suspected to induce or stimulate plaque formation or complications. Yet, none of these working hypotheses has reached the level of proof required for establishing a valid concept. Although submitted to intensive investigations, anti-infectious drugs and antimicrobial vaccinations are still far-sighted expectations in the treatment and prevention of coronary artery disease.

Animals↗

PubMed2024

Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

Vitis↗

PubMed2004

Multiple fatty acid sensing mechanisms operate in enteroendocrine cells: novel evidence for direct mobilization of stored calcium by cytosolic fatty acid.

Fatty acids (FA) with at least 12 carbon atoms increase intracellular Ca(2+) ([Ca(2+)](i)) to stimulate cholecystokinin release from enteroendocrine cells. Using the murine enteroendocrine cell line STC-1, we investigated whether candidate intracellular pathways transduce the FA signal, or whether FA themselves act within the cell to release Ca(2+) directly from the intracellular store. STC-1 cells loaded with fura-2 were briefly (3 min) exposed to saturated FA above and below the threshold length (C(8), C(10), and C(12)). C(12), but not C(8) or C(10), induced a dose-dependent increase in [Ca(2+)](i), in the presence or absence of extracellular Ca(2+). Various signaling inhibitors, including d-myo-inositol 1,4,5-triphosphate receptor antagonists, all failed to block FA-induced Ca(2+) responses. To identify direct effects of cytosolic FA on the intracellular Ca(2+) store, [Ca(2+)](i) was measured in STC-1 cells loaded with the lower affinity Ca(2+) dye magfura-2, permeabilized by streptolysin O. In permeabilized cells, again C(12) but not C(8) or C(10), induced release of stored Ca(2+). Although C(12) released Ca(2+) in other permeabilized cell lines, only intact STC-1 cells responded to C(12) in the presence of extracellular Ca(2+). In addition, 30 min exposure to C(12) induced a sustained elevation of [Ca(2+)](i) in the presence of extracellular Ca(2+), but only a transient response in the absence of extracellular Ca(2+). These results suggest that at least two FA sensing mechanisms operate in enteroendocrine cells: intracellularly, FA (>/=C(12)) transiently induce Ca(2+) release from intracellular Ca(2+) stores. However, they also induce sustained Ca(2+) entry from the extracellular medium to maintain an elevated [Ca(2+)](i).

Animals↗

PubMed2005

High density lipoprotein endocytosis by scavenger receptor SR-BII is clathrin-dependent and requires a carboxyl-terminal dileucine motif.

The high density lipoprotein (HDL) receptor Scavenger Receptor BII (SR-BII) is encoded by an alternatively spliced mRNA from the SR-BI gene and is expressed in various tissues. SR-BII protein differs from SR-BI only in the carboxyl-terminal cytoplasmic tail, which, as we showed previously, must contain a signal that confers predominant intracellular expression and rapid endocytosis of HDL. We have shown that SR-BII mediates HDL endocytosis through aclathrin-dependent, caveolae-independent pathway. Two candidate amino acid motifs were identified in the tail that could mediate association with clathrin-containing endocytic vesicles: a putative dileucine motif at position 492-493 and an overlapping tyrosine-based YXXZ motif starting at position 489. Although substitution of tyrosine at position 489 with alanine or histidine did not affect endocytosis, substitution L492A resulted in increased surface binding of HDL and reduced HDL particle endocytosis. Substitution L493A had a less dramatic effect. No other regions in the carboxyl-terminal tail appeared to contain motifs required for HDL endocytosis. Substitutions of leucine at position 492 with the hydrophobic amino acids valine or phenylalanine also reduced HDL endocytosis, stressing the importance of leucine at this position. Introducing the SR-BII YTPLL motif into the carboxyl-terminal cytoplasmic tail of SR-BI converted SR-BI into an endocytic receptor resembling SR-BII. These results demonstrated that SR-BII differs from SR-BI in subcellular localization and trafficking and suggest that the two isoforms differ in the manner in which they target ligands intracellularly.

Amino Acid Motifs↗

PubMed2001

The possible anti-inflammatory role of circulating human leukocyte antigen levels in women with endometriosis after treatment with danazol and leuprorelin acetate depot.

BACKGROUND: Endometriosis is defined as an inflammatory condition of the female reproductive tract, a state often associated with infertility and miscarriage. Many exogenously administered factors (treatments) control the disease via as yet unknown pathways. Possible candidate molecules involved in these mechanisms could be the serum-soluble human leukocyte antigens (sHIA) that have been detected in a variety of human body fluids and that are associated with several diseases. AIMS: We here examine how danazol and leuprorelin acetate depot treatments exert their anti-inflammatory action. It is plausible that subtle alterations mediated by these treatments and in relation to sHLA may explain the pathophysiology of endometriosis and provide insights towards new therapeutic protocols. METHODS: Indirect enzyme-linked immunosorbent assay (ELISA), using specific monoclonal antibodies, determined serum-soluble class-I and class-II HLA levels. ELISA readings from treated women were compared with normal healthy subjects. RESULTS: Serum-soluble class-I and class-II HLA levels are statistically significantly lower (P < 0.001) in women with endometriosis than in the control groups. However, danazol but not leuprorelin acetate depot administration augments soluble HLA class I and class II (P < 0.01 and P < 0.001, respectively) to normal levels during the treatment period, an increase that may account for the anti-inflammatory effect and the remission observed. CONCLUSIONS: It is shown that one of the underlying causes of endometriosis may be the lack of both circulating class-I and class-II antigen levels. Danazol administration acts via an induced release of these antigens, whose presence correlates with the degree of the inflammatory alleviation obtained. We thus provide evidence that the inflammatory state of the disease appears to be associated with soluble HLA levels because, 3 months after ceasing therapy, the circulating antigens in the serum return to the same levels that correspond to the pathological condition.

Adult↗

PubMed1999

Physical mapping of porcine seasonality genes.

Seasonal infertility in sows is a problem in the pig industry characterized by delayed onset of puberty in summer and decreased farrowing rate resulting from silent oestrus and aborted pregnancy. Summer infertility is thought to be influenced by heat, sunburn and stress. However, the strongest contributory factor is photoperiod. The difference in seasonality between wild boar and commercial pig breeds suggests that there may be a genetic component to this trait. The maps and associated molecular tools emerging from the pig genome project have created opportunities to examine the genetic component of seasonal infertility. We are identifying and mapping genes that are likely to be involved in biological clock mechanisms and the melatonin pathways as candidate seasonality genes.

Abortion, Veterinary↗

PubMed2003

Gene expression profile changes are commonly modulated across models and species after traumatic brain injury.

Brain trauma is a major cause of morbidity and mortality, both in adult and pediatric populations. Much of the functional deficit derives from delayed cell death resulting from induction of neurotoxic factors that overwhelm endogenous neuroprotective responses. To identify the potential molecular mechanisms underlying such delayed responses, we compared gene expression patterns using high-density oligonucleotide arrays at 4, 8, 24, and 72 h after moderate levels of lateral fluid percussion-induced brain injury in rats and lateral controlled cortical impact injury in mice (a total of 47 profiles). Expression of 82 genes in 12 functional categories was significantly changed in both species after trauma. The largest number of gene expression changes were found in the functional groups related to inflammation (17%), transcription regulation (16%), and cell adhesion/extracellular matrix (15%). Fifty percent of genes similarly altered across models had not been previously implicated in traumatic brain injury. Of particular interest were expression changes in genes linked to neurodegeneration, such as ATF3 and lysosomal membrane glycoprotein 2, and to neuroprotection including lipocortin 1, calponin 3, gelsolin, Id-1, and p45 NF-E2. Gene expression profiling across species and models may help identify candidate molecular pathways induced by brain injury, some of which may provide novel targets for therapeutic intervention.

Animals↗

PubMed1985

The response of the colon to eating.

Much evidence indicates that there is an increased motor activity in the colon from eating in several species of animals. Though some of this effect may be cephalic in origin, the greater part of the response results from the arrival of food in the stomach and proximal intestine. Chemoreceptor stimulation appears to be more important than mechanoreceptor stimulation in bringing about this effect. The means by which this effect comes about could be either hormonal or neural. Several polypeptide hormones released from the proximal gut by eating are candidates. Neural pathways through both parasympathetic and sympathetic systems could be responsible. The exact nature of the change in colonic motility that is produced is unknown. It could involve changes in the pacemakers for colonic contractions (the electrical slow waves of the colon and the migrating spike burst of the colon), changes in the excitability of the colonic musculature or changes in colonic mucosal function.

Animals↗

PubMed1992

Characterization of the T cell antigen receptor--p60fyn protein tyrosine kinase association by chemical cross-linking.

Engagement of the TCR by specific antigen results in activation of a tyrosine kinase pathway. A candidate for the kinase responsible for the rapid tyrosine phosphorylation detected with T cell activation is p60fyn, a member of the src kinase family. In an earlier study [Samelson et al. (1990) Proc. Natl Acad. Sci. USA 87:4358] this enzyme was co-immunoprecipitated with the TCR from T cells solubilized in digitonin. In that study a sensitive in vitro kinase assay was used to detect the associated p60fyn. It was subsequently found that the reproducibility of the interaction depended on lot-to-lot variations in digitonin. To eliminate the possibility that the association of antigen receptor and kinase is an artifact of solubilization with ill-defined digitonin preparations, a cross-linking protocol was developed to stabilize the interaction between the TCR and p60fyn. T cells were permeabilized with tetanolysin and proteins were cross-linked with the water soluble chemical cross-linker, 3,3' dithiobis(sulfosuccinimidylpropionate). These experiments allowed the confirmation of the interaction between the TCR, p60fyn, and several additional proteins. The cross-linking studies also enabled the mapping of the interaction of p60fyn and associated proteins to the TCR zeta-chain. This technique should have a general use in stabilizing interactions between other receptors and molecules required for intracellular signaling.

Animals↗

PubMed2004

Prenatal choline supplementation advances hippocampal development and enhances MAPK and CREB activation.

Choline is an essential nutrient for animals and humans. Previous studies showed that supplementing the maternal diet with choline during the second half of gestation in rats permanently enhances memory performance of the adult offspring. Here we show that prenatal choline supplementation causes a 3-day advancement in the ability of juvenile rats to use relational cues in a water maze task, indicating that the treatment accelerates hippocampal maturation. Moreover, phosphorylation and therefore activation of hippocampal mitogen-activated protein kinase (MAPK) and cAMP-response element binding protein (CREB) in response to stimulation by glutamate, N-methyl-D-aspartate, or depolarizing concentrations of K+ were increased by prenatal choline supplementation and reduced by prenatal choline deficiency. These data provide the first evidence that developmental plasticity of the hippocampal MAPK and CREB signaling pathways is controlled by the supply of a single essential nutrient, choline, during fetal development and point to these pathways as candidate mechanisms for the developmental and long-term cognitive enhancement induced by prenatal choline supplementation.

Animals↗

PubMed2001

Molecular pathways that modify tumor radiation response.

Aberrant expression of signal transduction molecules in pathways controlling cell survival, proliferation, death, or differentiation are a common feature of all tumors. The identification of the molecules that are involved allows the development of novel tumor-specific strategies. Not surprisingly, targeting these pathways often also results in radiosensitization. The efficacy of such directed therapies may, however, be limited by the heterogeneity and the multiple mutations that are associated with the cancerous state. A more robust alternative may be to target global mechanisms of cellular control. The ubiquitin/proteasome degradation pathway is one candidate for such therapeutic intervention. This pathway is the main posttranscriptional mechanism that controls levels of many short-lived proteins involved in regulation of cell cycle progression, DNA transcription, DNA repair, and apoptosis. Many of these proteins are involved in various malignancies and/or radiation responses. In recent years, proteasome inhibitors have gained interest as a promising new group of antitumor drugs. PS-341, a reversible inhibitor of proteasome chymotryptic activity, is currently being tested in phase I clinical trials. In this study, we show that proteasome inhibition by PS-341 can alter cellular radiosensitivity in vitro and in vivo, in addition to having direct antitumor effects.

Animals↗

PubMed2005

Valproic acid-induced skeletal malformations: associated gene expression cascades.

OBJECTIVES: Valproic acid (VPA) is a widely used anticonvulsant medication with well-known teratogenic effects in both humans and in experimental animal model systems. The most commonly observed malformations induced by VPA in experimental animals include neural and skeletal defects. In this study the potential alterations in somitic tissue gene expression relative to the development of observed axial skeletal defects were examined. METHODS: SWV mice were treated at 8.5 days post coitum (d.p.c.) with 1.36 mmol/kg or 2.72 mmol/kg VPA by i.p. injection. At 18.5 d.p.c., animals were killed and stained for morphological and skeletal examination. Cervical malformations consisting of vertebral fusions and cervical ribs were consistently observed. Phenotypic analysis confirmed the presence of dose-dependent axial skeletal malformations induced by in-utero VPA-exposure. Using antisense RNA amplification and cDNA microarrays, we examined the expression of approximately 5700 genes in the first six postotic somites of control and treated embryos at 6, 12, 18 and 24 h after the 8.5 d.p.c. VPA treatment. RESULTS: Analysis indicated that several ontological groups (e.g. histone deacetylase complex, guanosine triphosphatases, cell proliferation and cytoskeletal) have significantly enriched gene expression changes in response to the teratogenic insult. The RNA from 6 h post-treatment was also subjected to a microarray cross-platform validation, and genes identified on both platforms are presented. CONCLUSION: These data were then used to deduce candidate cellular pathways that may be responsible for the VPA-induced teratogenic skeletal phenotypes.

Abnormalities, Drug-Induced↗

PubMed1997

Code Stroke: rapid transport, triage and treatment using rt-PA therapy. The NINDS rt-PA Stroke Study Group.

With the approval of rt-PA therapy for ischemic stroke, stroke care has acutely transitioned from focusing on rehabilitative services to emergency services. This treatment, which must be initiated within the first three hours after the onset of stroke symptoms, requires reorganization of current management approaches. Developing a Code Stroke Team facilitates this process and helps to identify potential thrombolysis candidates. A pathway to deliver rapid care begins with 911 notification and transport, emergency department triage and procedures, and moves through the initiation of thrombolytic therapy. We call this pathway "Code Stroke".

Cerebrovascular Disorders↗

PubMed2025

Inflammatory pathways and immune dysregulation in pediatric postoperative septic shock: A study integrating transcriptomics, machine learning and molecular docking.

This study elucidates the molecular and immune regulatory mechanisms of pediatric postoperative septic shock. Transcriptomic data were obtained from the Gene Expression Omnibus database. Differentially expressed genes were identified using the limma package, and gene co-expression modules were constructed using Weighted Gene Co-expression Network Analysis. Functional enrichment was performed via gene set enrichment analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses. Immune cell infiltration was assessed using ESTIMATE and CIBERSORT. Mendelian randomization was applied to explore causal relationships between gene expression and septic shock. Feature genes were selected using machine learning algorithms, and a diagnostic nomogram model was constructed. Finally, molecular docking analysis was performed to screen and evaluate the binding affinity of traditional Chinese medicine monomers to core target proteins. A total of 1331 differentially expressed genes were identified, and the turquoise module was strongly correlated with septic shock. Enrichment analysis revealed significant activation of IL-6/JAK/STAT3, TNF-α/NF-κB, and PI3K/Akt/mTOR pathways. Immune infiltration analysis indicated suppressed immune scores and imbalances in neutrophils, macrophages, T cells, and B cells. Mendelian randomization confirmed causal associations for 6 genes, including PIM3. The predictive model based on feature genes demonstrated high diagnostic performance. Molecular docking suggested that quercetin and astramembrannin I could stably bind PIM3. This study systematically identified core genes, dysregulated immune pathways, and candidate small-molecule interventions in pediatric septic shock, providing novel insights for early diagnosis and targeted therapy.

Humans↗

PubMed2005

The Pun1 gene for pungency in pepper encodes a putative acyltransferase.

Pungency in Capsicum fruits is due to the accumulation of the alkaloid capsaicin and its analogs. The biosynthesis of capsaicin is restricted to the genus Capsicum and results from the acylation of an aromatic moiety, vanillylamine, by a branched-chain fatty acid. Many of the enzymes involved in capsaicin biosynthesis are not well characterized and the regulation of the pathway is not fully understood. Based on the current pathway model, candidate genes were identified in public databases and the literature, and genetically mapped. A published EST co-localized with the Pun1 locus which is required for the presence of capsaicinoids. This gene, AT3, has been isolated and its nucleotide sequence has been determined in an array of genotypes within the genus. AT3 showed significant similarity to acyltransferases in the BAHD superfamily. The recessive allele at this locus contains a deletion spanning the promoter and first exon of the predicted coding region in every non-pungent accession tested. Transcript and protein expression of AT3 was tissue-specific and developmentally regulated. Virus-induced gene silencing of AT3 resulted in a decrease in the accumulation of capsaicinoids, a phenotype consistent with pun1. In conclusion, gene mapping, allele sequence data, expression profile and silencing analysis collectively indicate that the Pun1 locus in pepper encodes a putative acyltransferase, and the pun1 allele, used in pepper breeding for nearly 50 000 years, results from a large deletion at this locus.

Acyltransferases↗

PubMed2006

Association analysis of genes in the renin-angiotensin system with subclinical cardiovascular disease in families with Type 2 diabetes mellitus: the Diabetes Heart Study.

AIMS: Cardiovascular disease (CVD) is a major complication of Type 2 diabetes mellitus. The renin-angiotensin system (RAS) and nitric oxide production are both important regulators of vascular function and blood pressure. Genes encoding proteins involved in these pathways are candidates for a contribution to CVD in diabetic patients. We have investigated variants of the angiotensinogen (AGT), angiotensin converting enzyme (ACE), angiotensin type 1 receptor (AT1R) and endothelial nitric oxide synthase (NOS3) genes for association with subclinical measures of CVD in families with Type 2 diabetes mellitus (T2DM). METHODS: Atherosclerosis was measured by carotid intima-media thickness and calcification of the carotid and coronary arteries in 620 European Americans and 117 African Americans in the Diabetes Heart Study. Because of the role of these systems in blood pressure regulation, blood pressure was also investigated. RESULTS: Compelling evidence of association was not detected with any of the SNPs with any outcome measures after adjustments for covariates despite sufficient power to detect relatively small differences in traits for specific genotype combinations. CONCLUSIONS: Genetic variation of the RAS and NOS3 genes do not appear to strongly influence subclinical cardiovascular disease or blood pressure in this diabetic population.

Adult↗