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PubMed2001

Complementary DNA expression array analysis suggests a lower expression of signal transduction proteins and receptors in cold and hot thyroid nodules.

Autonomously functioning thyroid nodules are characterized by an increased proliferation and function, which is predominantly caused by constitutively activating TSH receptor mutations leading to an activation of cAMP. In contrast to autonomously functioning thyroid nodules, cold thyroid nodules are functionally inactive and less differentiated. Their molecular cause is still unknown. To further investigate the pathophysiological aspects of autonomously functioning thyroid nodules and to elucidate the molecular etiology of cold thyroid nodules, it is essential to identify genes with differential expression in autonomously functioning thyroid nodules and cold thyroid nodules and to compare this expression to that in normal surrounding tissue. The list of possible candidates for differential regulation ranges from growth factors and their receptors to transcription factors or oncogenes. Therefore, we evaluated the potential of cDNA arrays and studied the expression of 588 known genes from 6 different classes of proteins in thyroid nodules characterized for their function. Forty-seven genes showed a differential expression between nodular and surrounding tissue identified by the expression arrays. The differential expression of 15 transcripts was verified by real-time PCR. About 25% of the transcripts determined by LightCycler PCR are considered false positives because data from PCR and array analysis did not agree. This indicates the reliability of cDNA expression arrays to identify differentially expressed genes in thyroid nodules compared with their surrounding tissue. The 15 selected genes were additionally quantified by real-time PCR in 7 additional cold thyroid nodules, autonomously functioning thyroid nodules, and their surrounding tissues. The highest number of differentially expressed genes was in the group of signal transduction proteins (4 of 38 detectable genes) and extracellular cell signaling and communication proteins (2 of 62 detectable genes). In contrast, transcripts of other classes of proteins were unchanged (e.g. DNA-binding molecules and stress responses). Most of the transcripts were down-regulated in autonomously functioning thyroid nodule and cold thyroid nodule compared with the respective surrounding tissue. This finding could be the result of a dominant activation of a signal transduction pathway, with the cAMP pathway being the likely candidate for autonomously functioning thyroid nodules. The qualitatively similar pattern of changes in this limited number of genes in autonomously functioning thyroid nodules and cold thyroid nodules could suggest a similar dominant activation of a specific signaling cascade in cold thyroid nodules as the constitutively activating mutations in autonomously functioning thyroid nodules.

Adult↗

PubMed2026

Integrative haplotype and SNP-based GWAS supports the identification of stable genomic loci controlling yield-related traits in soybean.

Soybean yield is vulnerable to environmental variation, therefore, it is important to detect and implement stable genomic regions associated with yield-related traits in soybean breeding programs. In this study, SNP and haplotype-based GWAS were conducted to reveal important candidate genomic regions and putative candidate genes associated with soybean yield-related traits. This study demonstrates that the integration of haplotype and SNP-based GWAS could improve the detection of genomic regions associated with complex traits, enhance statistical power, and facilitate the identification of biologically relevant candidate genes. Ten stable haplotype blocks and six stable SNPs were detected based on the integration of haplotype and SNP-based GWAS, respectively. Furthermore, multiple candidate genes associated with the yield-related traits were identified. For instance, six genes were identified as transporters, including Glyma.15G092800, encoding serine-type endopeptidase activity, Glyma.15G203300 encoding a major facilitator superfamily (MFS) sugar transporter, Glyma.04G163000, transmembrane transporter, and Glyma.04G164100, leucine-rich repeat receptor-like protein kinase (LRR-RLK), as the most promising candidate genes. Additionally, three genes involved in signaling and pathways of various phytohormones can be promising candidates for increasing seed yield through improving plant architecture in soybean plants. The identified superior haplotypes with favourable alleles will be useful for marker-assisted selection in future breeding programs in soybean.

DArT markers↗

PubMed2005

Modified anthrax fusion proteins deliver HIV antigens through MHC Class I and II pathways.

T cell-based HIV vaccine candidates have focused on eliciting both CD4- and CD8-mediated responses. One challenge in vaccine development is the successful introduction and presentation of exogenous antigen to elicit an immune response. Modified bacterial toxins have been studied extensively as intracellular delivery agents because of their unique capability to translocate antigen across the cell membrane without affecting cell viability. Modified anthrax toxin lethal factor (LFn) fusion protein is able to effectively induce anti-HIV cytotoxic T lymphocytes in the absence of protective antigen (PA) and is being evaluated as a vaccine candidate. Here we describe, for the first time, the processing and presentation of LFn fusion proteins by the MHC Class II pathway. The ability of LFn--HIV to induce both CD8- and CD4-mediated responses may have relevance in current approaches to vaccine design. Furthermore, the translocation and presentation of antigens occurs in the absence of PA, which proposes a modified molecular mechanism of antigen presentation by the anthrax toxin model. Additionally, we found that LFn--HIV is specific and sensitive in detecting HIV-specific CD4(+) and CD8(+) T cell responses in T cell assays, further broadening the value of this antigen delivery system as a useful immunologic tool.

Antigen Presentation↗

PubMed2006

Sleep deprivation and activation of morning levels of cellular and genomic markers of inflammation.

BACKGROUND: Inflammation is associated with increased risk of cardiovascular disorders, arthritis, diabetes mellitus, and mortality. The effects of sleep loss on the cellular and genomic mechanisms that contribute to inflammatory cytokine activity are not known. METHODS: In 30 healthy adults, monocyte intracellular proinflammatory cytokine production was repeatedly assessed during the day across 3 baseline periods and after partial sleep deprivation (awake from 11 pm to 3 am). We analyzed the impact of sleep loss on transcription of proinflammatory cytokine genes and used DNA microarray analyses to characterize candidate transcription-control pathways that might mediate the effects of sleep loss on leukocyte gene expression. RESULTS: In the morning after a night of sleep loss, monocyte production of interleukin 6 and tumor necrosis factor alpha was significantly greater compared with morning levels following uninterrupted sleep. In addition, sleep loss induced a more than 3-fold increase in transcription of interleukin 6 messenger RNA and a 2-fold increase in tumor necrosis factor alpha messenger RNA. Bioinformatics analyses suggested that the inflammatory response was mediated by the nuclear factor kappaB inflammatory signaling system as well as through classic hormone and growth factor response pathways. CONCLUSIONS: Sleep loss induces a functional alteration of the monocyte proinflammatory cytokine response. A modest amount of sleep loss also alters molecular processes that drive cellular immune activation and induce inflammatory cytokines; mapping the dynamics of sleep loss on molecular signaling pathways has implications for understanding the role of sleep in altering immune cell physiologic characteristics. Interventions that target sleep might constitute new strategies to constrain inflammation with effects on inflammatory disease risk.

Adult↗

PubMed1982

Does occupational exposure to silica cause lung cancer?

Silica is not generally considered to be a carcinogen, however, occupations characterized by high exposure to crystalline silica have excessive rates of lung cancer mortality. Respiratory cancer excesses have been reported from North America and from Europe for the following dusty trades in which exposure to silica is a common factor: iron and steel foundry workers, steel casting workers, sand blasters, metal molders, non-uranium miners, and ceramic workers. These findings have been reinforced by two reports from the Swedish Pneumoconiosis Register and the Ontario Ministry of Labor indicating that silicotics have statistically significant risks of lung cancer mortality. Animal studies suggest that silica can be an initiating carcinogen or can act as a cocarcinogen or promoter when combined with benzo(a)pyrene. We propose three candidate hypotheses and two pathways for silicocarcinogenesis.

Animals↗

PubMed2004

Differential expression of immunoregulatory genes in male and female Norway rats following infection with Seoul virus.

Males of many species are more susceptible than females to infections caused by parasites, bacteria, fungi, and viruses. Following inoculation with Seoul virus, male rats have more virus present in target organs and shed virus longer than females. The goal of this study was to test the hypothesis that variation in the expression of genes associated with immune function mediates sex differences in hantavirus infection. Using DNA microarrays, we examined changes in gene expression in lung tissue during the early (when animals are viremic and shedding virus; Day 15 post-inoculation (p.i.)) and late (animals have low levels of infectious virus, but high antibody titers; Day 40 p.i.) phases of infection in adult male and female rats. After normalizing the gene expression levels from infected animals to the gene expression levels from same-sex uninfected controls, our data revealed that 1,813 genes were differentially expressed between the sexes during infection. The expression of key transcriptional factors (e.g., eIF-2 alpha, NF-kappa B, IRF-1, NF-IL-6, and STAT6) and genes that encode for proinflammatory (e.g., TNF alpha R, IL-1R, and IL-1RAcP), antiviral (e.g., IFN gamma R and Mx proteins), T cell (e.g., CD3 and TCR), and Ig superfamily (e.g., IgM, IgG, and MHC class I and II) proteins was higher in females than males. Conversely, males had higher expression of heat shock protein genes (e.g., hsp70) suggesting that cellular stress is elevated in males. These data provide candidate genes and cellular pathways that may underlie sex differences in responses to Seoul virus and possibly other hemorrhagic fever viruses.

Animals↗

PubMed1996

The human skeletal muscle glycogenin gene: cDNA, tissue expression and chromosomal localization.

Glycogen synthesis is impaired in first degree relatives of subjects with non-insulin-dependent diabetes mellitus and genes relevant to this metabolic pathway are considered reasonable candidates in the pathogenesis of the disease. In skeletal muscle the de novo synthesis of glycogen in primed by an enzyme named glycogenin. We have cloned the glycogenin cDNA from human skeletal muscle mRNA: human glucogenin is a 333 amino acid protein exhibiting 93% identity with rabbit glycogenin. A single transcript of about 2.4 kb, prominent in skeletal muscle, was detected by Northern blot analysis. In situ hybridization unequivocally located the human glycogenin gene to chromosome 3q25.1. Furthermore, we mapped two intronless glycogenin-related sequences to human chromosomes 12 and 13.

Amino Acid Sequence↗

PubMed2000

Evidence that Src-type tyrosine kinase activity is necessary for initiation of calcium release at fertilization in sea urchin eggs.

The initiation of Ca(2+) release from internal stores in the egg is a hallmark of egg activation. In sea urchins, PLCgamma activity is necessary for the production of IP(3), which leads to the initial rise in Ca(2+). To examine the possible function of a tyrosine kinase in activating PLCgamma at fertilization, sea urchin eggs were treated with the specific Src kinase inhibitor PP1 or microinjected with recombinant Src-family SH2-domain proteins, which act as dominant interfering inhibitors of Src-family kinase function. Both modes of inhibiting Src-family kinases resulted in a specific and dose-dependent delay in the onset of Ca(2+) release from the endoplasmic reticulum at fertilization. The rise in cytoplasmic pH at fertilization also was inhibited by microinjection of Src-family SH2-domain proteins. Further, an antibody directed against Src-type kinases recognized a protein of ca. M(r) 57K that was enriched in the membrane fraction of eggs. The kinase activity of this protein was stimulated rapidly and transiently at fertilization, as measured by autophosphorylation and by phosphorylation of an exogenous substrate. Together, these data indicate that a Src-type tyrosine kinase is necessary for the initiation of Ca(2+) release from the egg ER at fertilization and identify a Src-type p57 protein as a candidate in the signaling pathway leading to this Ca(2+) release.

Animals↗

PubMed1984

Mitochondrial oxidative phosphorylation: tissue oxygen sensor for regulation of coronary flow.

The observation that mitochondrial oxidative phosphorylation in vivo is dependent on oxygen tension throughout the physiological range (Wilson et al., 1979a , 1979b ) has made this metabolic pathway the most probable candidate for the tissue oxygen sensor in the regulation of local blood flow. We have utilized the oxygen dependent regulatory system for coronary blood flow to examine this possibility. Alterations in coronary flow were induced by: 1. Varied work load; 2. Infusion of Amytal (an inhibitor of mitochondrial respiration); 3. Infusion of DNP; 4. Hypoxia. Increased work load caused increased coronary flow with no decrease in effluent oxygen tension while Amytal infusion and hypoxia caused vasodilation with increased and decreased O2 tension respectively. This indicates that oxygen tension per se cannot be responsible for the observed vasodilation. Tissue energy metabolism was evaluated by measuring metabolite levels in hearts which were freeze-clamped in each state of perfusion. In all four methods of vasodilation, a decrease in cellular energy state ratio ([ATP]f/[ADP]f[Pi]) expressed as the calculated ratio of free adenine nucleotides, was observed for conditions which increased flow. Systematic variation of work load, Amytal or DNP concentration resulted in quantitatively the same correlation between tissue [ATP]f/[ADP]f[Pi] and coronary flow. It is concluded that mitochondrial oxidative phosphorylation is the oxygen sensor for the regulation of coronary blood flow by tissue oxygen tension. Infusion of adenosine, a known coronary vasodilator, induced vasodilation which was completely blocked by theophylline.(ABSTRACT TRUNCATED AT 250 WORDS)

2,4-Dinitrophenol↗

PubMed1982

Close apposition of muscle cells in the longitudinal bands of the body wall of a holothurian, Isostichopus badionotus.

Electron microscopy reveals that sarcolemmata of adjacent muscle cells form pentalaminar junctions by fusion of apposed trilaminar double leaflet membranes. These junctions appear to be candidates for low resistance pathways between muscle fibers. The muscles depolarize slowly when bathed in solutions containing elevated concentrations of KCl, and the sucrose gap method can then be used to measure the potential difference between polarized and depolarized regions. Thus the junctions which we have observed may provide the structural basis for electrical transmission through the sucrose gap.

Animals↗

PubMed2003

Molecular mapping of capsaicinoid biosynthesis genes and quantitative trait loci analysis for capsaicinoid content in Capsicum.

Quantitative variation in the accumulation of two major capsaicinoids responsible for pungency in the fruit of chile peppers, capsaicin and dihydrocapsaicin, was analyzed in a cross between the non-pungent Capsicum annuum parent cv. Maor and a pungent Capsicum frutescens parent, accession BG 2816. In order to identify quantitative trait loci (QTLs) for capsaicinoid content, we employed the bulked segregant analysis method and screened bulked DNA from F2 individuals at the extremes of the distribution of capsaicinoid content with RAPD primers. Screening with 400 primers allowed the identification of three loci that were polymorphic between the bulks. These RAPD markers were converted to SCARs and subsequently mapped with additional RFLP markers to chromosome 7 of pepper. QTL interval analysis for individual and total capsaicinoid content identified a major QTL, termed cap, which explained 34-38% of the phenotypic variation for this trait in two growing environments. For all measurements, the allele of the pungent parent BG 2816 at cap contributed to the increased level of pungency. To determine whether known structural genes in the pathway could define a candidate for this QTL, 12 clones obtained from differentially expressed transcripts from placental tissue in pungent peppers were also mapped. None of them had a significant effect on this trait, nor did the allelic state at the locus C, the on/off switch for pungency in pepper, located on chromosome 2. The identity of cap and its effect on capsaicin content in other backgrounds will be addressed in future studies.

Alleles↗

PubMed2006

Gene-dosage effect on chromosome 21 transcriptome in trisomy 21: implication in Down syndrome cognitive disorders.

In the era of human functional genomics, the chromosome 21 has represented a prototype for pioneering global biotechnologies. Its relatively low gene content enabled studying Down syndrome at the chromosomal scale, for which the last years have seen intense research activity aiming at genotype-phenotype correlations. The global gene-dose dependent upregulation of gene expression seen in the context of trisomy and preliminary functional annotation of chromosome 21 genes points towards candidate genes and molecular pathways potentially associated with the cognitive defects observed in Down syndrome.

Chromosome Mapping↗

PubMed2006

Challenges identifying genetic determinants of pediatric cancers--the childhood leukemia experience.

Pediatric cancers affect approximately 1 in every 500 children before the age of 15. Little is known about the etiology of this heterogeneous group of diseases despite the fact they constitute the major cause of death by disease among this population. Because of its relatively high prevalence, most of the work done in pediatric oncogenetics has been focused on leukemias, particularly acute lymphoblastic leukemia (ALL). Although it is now well accepted that genetic variation plays a significant role in determining individual's cancer susceptibility, few studies have explored genetic susceptibility to childhood leukemia with respect to common polymorphisms. The biochemical and genetic mechanisms contributing to cancer susceptibility are numerous and can be grouped into broad categories: (1) cellular growth and differentiation, (2) DNA replication and repair, (3) metabolism of carcinogens (4) apoptosis, (5) oxidative stress response and (6) cell cycle. To evaluate whether candidate genes in these pathways are involved in childhood leukemogenesis, we conducted case-control studies. We showed that leukemogenesis in children may be associated with DNA variants in some of these genes and that the combination of genotypes seems to be more predictive of risk than either of them independently. We also observed that, at least at some loci, the parental genetics might be important in predicting the risk of cancer in this pediatric model of a complex disease. Taken together, these results indicate that the investigation of a single enzyme and/or a single genotype might not be sufficient to explain the etiology of childhood leukemia because of the complexity of the environment and that of the inter-individual variability in cancer susceptibility.

Child↗

PubMed1986

Organization of the pathway of de novo pyrimidine nucleotide biosynthesis in pea (Pisum sativum L. cv Progress No. 9) leaves.

The organization of the enzymes of de novo pyrimidine nucleotide biosynthesis in pea (Pisum sativum L. cv Progress No. 9) has been studied. The first three enzymes of the pathway, carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, and dihydroorotase, are readily separable from one another; they are not part of a multifunctional complex. The final two activities of the pathway, orotate phosphoribosyltransferase and orotidylate decarboxylase, copurify and appear to be complexed in vivo. This organizational pattern is distinct from those reported for bacteria, yeast, and mammals. The differences in organization, in a pathway which is present in all organisms, make the pyrimidine biosynthetic pathway a very interesting candidate for evolutionary studies.

Aspartate Carbamoyltransferase↗

PubMed1985

Activation of lumbar spinoreticular neurons by stimulation of muscle, cutaneous and sympathetic afferents.

Forty-four spinal neurons located mainly in laminae IV-VII of the L7 and S1 segments projected primarily contralaterally and to the lateral reticular nucleus. Muscle and cutaneous input was via group II and III afferents, whereas sympathetic input was via group III or IV afferents. Close-arterial injection of bradykinin and/or capsaicin excited most of the neurons so tested. These responses make these neurons likely candidates for the ascending pathway of the exercise pressor reflex.

Animals↗

PubMed1994

Recovery of olfactory behavior. I. Recovery after a complete olfactory bulb lesion correlates with patterns of olfactory nerve penetration.

The olfactory system is an excellent system in which to study issues related to potential functional recovery after a debilitating brain injury. The olfactory system is well-characterized, easily accessible and there are a vast number of studies available from a variety of perspectives. The experimental aim of this research is to examine the anatomical correlates associated with potential behavioral recovery in rats that receive complete olfactory bulb lesions as neonates or as adults. The results show that behavioral recovery occurs only when olfactory nerve penetration of the central nervous system is observed. Further, both olfactory nerve penetration and behavioral recovery are age-dependent phenomena. The olfactory nerve penetration only occurs when the olfactory bulb lesion is performed in neonates. Behavioral recovery of olfactory ability follows a linear trend and reaches near normal levels during the six weeks behavioral testing period. Histological analysis using an antibody for olfactory marker protein (an olfactory nerve-specific marker) reveals two potential candidates for the anatomical pathway responsible for behavioral recovery: olfactory nerve to orbital frontal cortex and olfactory nerve to olfactory peduncle. This report presents evidence that recovery of olfactory ability can occur in the absence of the olfactory bulb if the lesion is performed when the rat is still a neonate.

Animals↗

PubMed1994

Polymorphism of antigen processing (TAP, LMP) and HLA class II genes in celiac disease.

Susceptibility to CD is strongly associated with particular HLA class II molecules. However, additive genetic factors are likely to be required for the development of the disease. The polymorphic TAP and LMP genes, located within the HLA class II region, are involved in the antigen presentation pathway and thus represent candidate susceptibility genes. HLA class II DRB1, DRB3, DQA1, DQB1, and DPB1 as well as TAP1, TAP2, and LMP2 polymorphism was studied in 80 Caucasian CD patients and 213 normal controls by DNA oligotyping. The DQB1*0201 allele was found in 96.3% of CD patients and provided the highest risk (RR = 50), whereas only 89% of CD patients carried the DQ alpha 501/beta 201 heterodimer (RR = 30). The participation of the DRB3 and DPB1 locus was ruled out as it was attributed to a linkage disequilibrium on the DR3 haplotype. TAP1 and LMP2 allelic distribution was not significantly different among CD patients and controls. The TAP2-C allele was completely absent from the CD population, while it was found in 22.5% of controls. Although linkage disequilibrium between TAP2 and class II loci clearly exists in some haplotypes, TAP could act as additional susceptibility genes.

Adolescent↗

PubMed1993

Recombinant yeast in drug metabolism.

The usefulness of cDNA-directed expression of human hepatic P450s in yeast for the in vitro study of drug metabolism is emphasized. The major advantages of yeast expression are: (i) relatively high yields of heterologous P450 (approximately 5-10 nmol/l of culture medium) can be obtained; (ii) the expressed P450s are directly active in yeast microsomes, allowing the determination of specific catalytic activities of individual isoforms, which is a prerequisite for the prediction of metabolic pathways for new drug candidates; (iii) transformed yeast microsomes can also be used to study the specific affinity of individual P450s for various substrates and the formation of P450-metabolite complexes by difference visible spectroscopy; such studies can help to predict drug interactions. The advantages of expression in yeast with respect to biochemical studies of drug metabolism are illustrated with data about P450 NF25 (P450 3A4), the major form of human liver. Expressed P450 NF25 is obtained in a functionally active state, and some specific catalytic activities observed in liver microsomes could be reproduced directly with transformed yeast microsomes. The use of genomically modified yeast strains coexpressing human cytochrome b5 and/or overexpressing yeast P450-reductase allowed us to optimize these catalytic activities. In particular, this coexpression system was useful in the study of the in vitro formation of a P450 NF25 Fe(II)-RNO complex. Such inhibitory complexes have been implied in numerous drug interactions involving P450 3A4.

Animals↗