Carbide and nitride phase characterization in a transition metal carbo-nitride using x-ray spectroscopy and atom probe tomography.

A multi-phase hafnium carbo-nitride was investigated by various analytical methods. Incomplete homogenization between mixed HfC-HfN starting powders subjected to hot isostatic pressing resulted in both carbon-rich and nitrogen-rich phases. The compositions of these two phases were quantified in detail by wavelength dispersive spectroscopy and atom probe tomography, with the atom probe tips having either a small or a large shank angle geometry. For each of the two phases, an agreement of the compositions obtained by wavelength dispersive spectroscopy and atom probe tomography was found. However, the quality of the mass spectrum and hit multiplicity (single hits) were generally higher for the carbon-rich as compared to the nitrogen-rich carbo-nitride. Though the atom probe tip geometry does not appear to influence the composition, the mass resolving power did improve with the larger shank angle geometry while the hit multiplicity deteriorated slightly. Finally, our results demonstrate that hafnium carbide requires less thermal assistance to field evaporate than hafnium nitride.

Estimation of dislocation density from precession electron diffraction data using the Nye tensor.

The Nye tensor offers a means to estimate the geometrically necessary dislocation density of a crystalline sample based on measurements of the orientation changes within individual crystal grains. In this paper, the Nye tensor theory is applied to precession electron diffraction automated crystallographic orientation mapping (PED-ACOM) data acquired using a transmission electron microscope (TEM). The resulting dislocation density values are mapped in order to visualize the dislocation structures present in a quantitative manner. These density maps are compared with other related methods of approximating local strain dependencies in dislocation-based microstructural transitions from orientation data. The effect of acquisition parameters on density measurements is examined. By decreasing the step size and spot size during data acquisition, an increasing fraction of the dislocation content becomes accessible. Finally, the method described herein is applied to the measurement of dislocation emission during in situ annealing of Cu in TEM in order to demonstrate the utility of the technique for characterizing microstructural dynamics.

Farnesoid X receptor responds to bile acids and represses cholesterol 7alpha-hydroxylase gene (CYP7A1) transcription.

Cholesterol 7alpha-hydroxylase gene (CYP7A1) transcription is repressed by bile acids. The goal of this study is to elucidate the mechanism of CYP7A1 transcription by bile acid-activated farnesoid X receptor (FXR) in its native promoter and cellular context and to identify FXR response elements in the gene. In Chinese hamster ovary cells transfected with retinoid X receptor alpha (RXRalpha)/FXR, only chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA) were able to stimulate a heterologous promoter/reporter containing an ecdysone response element. In HepG2 cells, all bile acids (25 microM) were able to repress CYP7A1/luciferase reporter activity, and only CDCA and DCA further repressed reporter activity when cotransfected with RXRalpha/FXR. The concentration of CDCA required to inhibit 50% of reporter activity (IC(50)) was determined to be approximately 25 microM without FXR and 10 microM with FXR. Deletion analysis revealed that the bile acid response element located between nucleotides -148 and -128 was the FXR response element, but RXRalpha/FXR did not bind to this sequence. These results suggest that bile acid-activated FXR exerts its inhibitory effect on CYP7A1 transcription by an indirect mechanism, in contrast to the stimulation and binding of FXR to intestinal bile acid-binding protein gene promoter. Results also reveal that bile acid receptors other than FXR are present in HepG2 cells.

Phytol metabolites are circulating dietary factors that activate the nuclear receptor RXR.

RXR is a nuclear receptor that plays a central role in cell signaling by pairing with a host of other receptors. Previously, 9-cis-retinoic acid (9cRA) was defined as a potent RXR activator. Here we describe a unique RXR effector identified from organic extracts of bovine serum by following RXR-dependent transcriptional activity. Structural analyses of material in active fractions pointed to the saturated diterpenoid phytanic acid, which induced RXR-dependent transcription at concentrations between 4 and 64 microM. Although 200 times more potent than phytanic acid, 9cRA was undetectable in equivalent amounts of extract and cannot be present at a concentration that could account for the activity. Phytanic acid, another phytol metabolite, was synthesized and stimulated RXR with a potency and efficacy similar to phytanic acid. These metabolites specifically displaced [3H]-9cRA from RXR with Ki values of 4 microM, indicating that their transcriptional effects are mediated by direct receptor interactions. Phytol metabolites are compelling candidates for physiological effectors, because their RXR binding affinities and activation potencies match their micromolar circulating concentrations. Given their exclusive dietary origin, these chlorophyll metabolites may represent essential nutrients that coordinate cellular metabolism through RXR-dependent signaling pathways.

Convergence of three steroid receptor pathways in the mediation of nongenotoxic hepatocarcinogenesis.

The mechanisms by which peroxisome proliferators are able to regulate metabolic processes such as fat metabolism, while at the same time creating an environment for the development of hepatocellular carcinomas, is a central issue in the non-genotoxic carcinogenesis field. The convergence of two members of the steroid receptor family (peroxisome proliferator-activated receptor, PPAR; and retinoid X receptor, RXR) has provided strong support for an oxidative stress component in this carcinogenesis process, but has yet to define clearly a pathway for the classical tumor promotion events associated with peroxisome proliferation. The findings presented here integrate a third member of the steroid receptor family into this process and suggest a novel autocrine loop and mechanism for creating both oxidative stress and tumor promotion. A central regulatory component in this pathway is farnesol which has recently been shown to induce transcription mediated by the steroid receptor family member, farnesoid X receptor (FXR). In this report, it is clearly demonstrated that farnesol can also upregulate the transcriptional events of PPAR, but most likely through a different farnesoid metabolite, resulting in the regulation of an entirely different set of genetic components. Deregulation of the activities of these receptors offers a provocative mechanism for explaining the hepatocarcinogenic effects of peroxisome proliferators in chronically treated rodents.

A model for farnesoid feedback control in the mevalonate pathway.

Mevalonate is the rate-limiting substrate leading to farnesyl pyrophosphate (FPP), the central intermediate for isoprenoids such as cholesterol, dolichols, ubiquinone, and carotenoids. One major challenge has been to identify the isoprenoid effector molecules and transcription factors mediating negative regulation in this metabolic pathway. A nuclear receptor called FXR has recently been characterized that is activated by farnesyl pyrophosphate metabolites such as farnesol, farnesal, farnesoic acid, and methyl farnesoate. FXR expression in isoprenoidogenic tissues suggests a hypothesis that these intracellular "farnesoids" may be signals for transcriptional feedback control of cholesterol biosynthesis.

Identification of a nuclear receptor that is activated by farnesol metabolites.

Nuclear hormone receptors comprise a superfamily of ligand-modulated transcription factors that mediate the transcriptional activities of steroids, retinoids, and thyroid hormones. A growing number of related proteins have been identified that possess the structural features of hormone receptors, but that lack known ligands. Known as orphan receptors, these proteins represent targets for novel signaling molecules. We have isolated a mammalian orphan receptor that forms a heterodimeric complex with the retinoid X receptor. A screen of candidate ligands identified farnesol and related metabolites as effective activators of this complex. Farnesol metabolites are generated intracellularly and are required for the synthesis of cholesterol, bile acids, steroids, retinoids, and farnesylated proteins. Intermediary metabolites have been recognized as transcriptional regulators in bacteria and yeast. Our results now suggest that metabolite-controlled intracellular signaling systems are utilized by higher organisms.

An adenoviral vector system for functional identification of nuclear receptor ligands.

A recombinant adenovirus system has been designed that confers glucocorticoid responsiveness upon infected cells in culture. Two mutually dependent viruses are required: a trans-activator virus containing the human glucocorticoid receptor transcription unit and a second receptor virus harboring a glucocorticoid response element linked to the firefly luciferase gene. Another reciprocal pair of viruses has been generated; one member expresses the rat thyroid hormone receptor alpha, while the other contains the luciferase gene regulated by a thyroid hormone-responsive DNA element. Corticosteroid- or thyroid hormone-induced transcription can be efficiently and accurately quantitated from cells coinfected with the appropriate complementary virus pair 20 h after infection in 96-well microtiter plates. This coinfection assay offers a convenient way to measure transcriptional activation by nuclear receptors and has certain key advantages over the commonly used cotransfection method. Its sensitivity and precision make it a practical approach to rapidly identify substances extracted from complex biological samples activating candidate "orphan" nuclear receptor molecules.

Differential expression of alpha and beta thyroid hormone receptor genes in rat brain and pituitary.

Multiple thyroid hormone receptor cDNAs have previously been identified in rat and are classified into alpha and beta subtypes. Alternative splicing of the alpha gene gives rise to the functional receptor, rTR alpha 1, and the non-thyroid hormone-binding isotype, rTR alpha 2. Recent evidence suggests the beta gene encodes two functional receptors, rTR beta 1, and the pituitary-specific receptor, rTR beta 2. By using synthetic DNA probes common to rTR beta transcripts and specific for rTR alpha 1 and rTR alpha 2 mRNAs, we mapped the expression of these transcripts in adult rat brain and pituitary by hybridization histochemistry. We also localized mRNAs encoding the putative nuclear receptor REV-ErbA alpha, a portion of which is derived from the opposite strand of the rTR alpha gene. rTR alpha 1 and rTR alpha 2 transcripts were widely distributed in a similar, if not identical, pattern. Highest levels of rTR alpha 1 and rTR alpha 2 transcripts were found in the olfactory bulb, hippocampus, and granular layer of the cerebellar cortex. REV-ErbA alpha and rTR beta mRNAs were found in more restricted patterns of expression distinct from those of rTR alpha 1 and rTR alpha 2. REV-ErbA alpha mRNA was highest in the neocortex. High levels of rTR beta transcripts in the anterior pituitary and the parvocellular part of the paraventricular hypothalamic nucleus suggest rTR beta gene products may mediate thyroid hormone feedback regulation of thyroid-stimulating hormone and thyrotropin-releasing hormone. Our results identify nuclei and structures in the mammalian central nervous system in which regulation of gene expression by specific thyroid hormone receptor subtypes may occur.

Tight linkage between the syndrome of generalized thyroid hormone resistance and the human c-erbA beta gene.

Multiple cDNAs belonging to the c-erbA gene family encode proteins that bind T3 with high affinity. However, the biological functions of these multiple thyroid hormone receptors have not yet been clarified. Generalized thyroid hormone resistance (GTHR) refers to a human syndrome characterized by tissue refractoriness to the action of thyroid hormones; several studies have suggested quantitative or qualitative defects in T3 binding to nuclear receptors in certain kindreds. To investigate the biological functions of the c-erbA genes, c-erbA alpha and c-erbA beta, we tested the hypothesis that an abnormal c-erbA gene product is present in GTHR by examining these genes in members of one kindred. Restriction enzyme analysis failed to identify an abnormal pattern in affected individuals suggesting no rearrangements or large deletions. However, we demonstrated that the gene conferring the GTHR phenotype is tightly linked to the c-erbA beta locus on chromosome 3. This linkage strongly suggests that the c-erbA beta gene is important in man as a thyroid hormone receptor and identifies a putative c-erbA beta mutant phenotype with central nervous system, pituitary, liver, metabolic, and growth abnormalities.

Localization of human ERBA2 to the 3p22----3p24.1 region of chromosome 3 and variable deletion in small cell lung cancer.

Human genes homologous to the v-erbA oncogene of avian erythroblastosis virus have been mapped to at least two human chromosomes. Recently, the ERBA2 gene was shown to encode a thyroid hormone receptor and localized to chromosome 3 by using flow-sorted chromosomes. We now demonstrate that this gene is located at 3p22----3p24.1, using both somatic cell hybrids and in situ hybridization studies. Since this localization is close to the distal border of the small cell lung cancer (SCLC) 3p14----3p23 deletion, we undertook additional studies to examine the ERBA2 gene in SCLC. Using somatic cell hybrids constructed from the SCLC line NCI-H182 as well as matched patient tumor and control tissue samples, we found that ERBA2 is variably deleted. Therefore, ERBA2 defines at the molecular level the distal border of the SCLC deletion and further implies that the putative suppressor gene is located centromeric of this locus. We also determined that, at least in NCI-H182, the 3p14 breakpoint is proximal to the constitutive 3p14.2 fragile site. These studies would indicate that the mechanism or initiation site of chromosomal rearrangement in SCLC is different from that which occurs during induction of the 3p14 fragile site by aphidicolin.

A c-erb-A binding site in rat growth hormone gene mediates trans-activation by thyroid hormone.

The substance 3,5,3-triiodothyronine (T3) stimulates growth hormone gene transcription in rat pituitary tumour cells. This stimulation is thought to be mediated by the binding of nuclear T3 receptors to regulatory elements 5' to the transcriptional start site. Understanding of the mechanism by which thyroid hormone activates gene transcription has been limited by failure to purify nuclear T3 receptors because of their low abundance, and by the absence of defined T3 receptor-DNA binding sites affecting T3 regulation. Recently, human and avian c-erb-A gene products have been shown to bind thyroid hormone with high affinity and to have a molecular weight and nuclear association characteristic of the thyroid hormone receptor. In the present report, we describe the development of an avidin-biotin complex DNA-binding assay which can detect specific, high-affinity binding of rat pituitary cell T3 receptors to the sequence 5'CAGGGACGTGACCGCA3', located 164 base pairs 5' to the transcriptional start site of the rat growth hormone gene. An oligonucleotide containing this sequence transferred T3 regulation to the herpes simplex virus thymidine kinase promoter in transfected rat pituitary GC2 cells, and specifically bound an in vitro translation product of the human placental c-erb-A gene. The data provide supporting evidence that the human c-erb-A gene product mediates the transcriptional effects of T3 and also that GC2 cell nuclear extracts contain additional factors that modify the binding of pituitary T3 receptors to the rat growth hormone gene T3 response element.

Identification of a novel thyroid hormone receptor expressed in the mammalian central nervous system.

A complementary DNA clone derived from rat brain messenger RNA has been isolated on the basis of homology to the human thyroid hormone receptor gene. Expression of this complementary DNA produces a high-affinity binding protein for thyroid hormones. Sequence analysis and the mapping of this gene to a distinct human genetic locus indicate the existence of multiple human thyroid hormone receptors. Messenger RNA from this gene is expressed in a tissue-specific fashion with highest levels in the central nervous system.

Cloning of human mineralocorticoid receptor complementary DNA: structural and functional kinship with the glucocorticoid receptor.

Low-stringency hybridization with human glucocorticoid receptor (hGR) complementary DNA was used to isolate a new gene encoding a predicted 107-kilodalton polypeptide. Expression studies demonstrate its ability to bind aldosterone with high affinity and to activate gene transcription in response to aldosterone, thus establishing its identity as the human mineralocorticoid receptor (hMR). This molecule also shows high affinity for glucocorticoids and stimulates a glucocorticoid-responsive promoter. Together the hMR and hGR provide unexpected functional diversity in which hormone-binding properties, target gene interactions, and patterns of tissue-specific expression may be used in a combinatorial fashion to achieve complex physiologic control.