Biomedical subjects

C A Fox

Publications and source records attributed to C A Fox.

At least 19 recordsLinked to original sources

PubMed2001

Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation.

The roles of DNA and Mcm1p interactions in determining the overlapping and distinct functions of the yeast cell cycle regulatory transcription factors Fkh1p and Fkh2p were examined. Full-length recombinant Fkh1p and Fkh2p were purified and their binding to bona fide promoters examined in vitro. Each protein bound a variety of target promoters with similar specificity in vitro, consistent with the observation that these proteins bind common promoters in vivo. However, in vivo, the Fkh1p and Fkh2p occupied different target promoters to different extents, suggesting that each was primarily responsible for controlling a different set of genes. Additional in vitro studies provided a mechanistic explanation for this differential promoter-occupancy. Specifically, the Fkh2p, but not the Fkh1p, was capable of binding cooperatively with Mcm1p. The Mcm1p-Fkh2p cooperative binding was enhanced by, but did not require, the presence of a Mcm1p-binding site within a target promoter. Consistent with these data, Mcm1p was present at Fkh-controlled promoters in vivo regardless of whether they contained Mcm1p-binding sites, suggesting a role for Mcm1p at promoters not thought previously to be under Mcm1p control. Analysis of Fkh1p and Fkh2p binding to promoter targets in vivo by use of mutant strains indicated that the two proteins compete for promoter-occupancy at a number of target promoters. We postulate that Fkh1p and a stable Fkh2p/Mcm1p complex compete for binding to target promoters and that the levels and/or binding activity of Fkh1p, but not Fkh2p, are most limiting for promoter-occupancy in vivo. Interestingly, the in vitro DNA-binding assays, using a variety of promoter targets, revealed that bona fide Fkh target promoters contained two or more Fkh-binding sites that allowed the Fkh1p and Fkh2p proteins to form multiple protein-DNA complexes in vitro. Multiple Fkh-binding sites may be a distinguishing feature of bona fide Fkh promoters in yeast and other organisms.

Base Sequence↗

PubMed2001

Sir3-dependent assembly of supramolecular chromatin structures in vitro.

Baculovirus-expressed recombinant Sir3p (rSir3p) has been purified to near homogeneity, and its binding to naked DNA, mononucleosomes, and nucleosomal arrays has been characterized in vitro. At stoichiometric levels rSir3p interacts with intact nucleosomal arrays, mononucleosomes, and naked DNA, as evidenced by formation of supershifted species on native agarose gels. Proteolytic removal of the core histone tail domains inhibits but does not completely abolish rSir3p binding to nucleosomal arrays. The linker DNA in the supershifted complexes remains freely accessible to restriction endonuclease digestion, suggesting that both the tail domains and nucleosomal DNA contribute to rSir3p--chromatin interactions. Together these data indicate that rSir3p cross-links individual nucleosomal arrays into supramolecular assemblies whose physical properties transcend those of typical 10-nm and 30-nm fibers. Based on these data we hypothesize that Sir3p functions, at least in part, by mediating reorganization of the canonical chromatin fiber into functionally specialized higher order chromosomal domains.

Animals↗

PubMed2001

The Sir1 protein's association with a silenced chromosome domain.

Silencing of the cryptic mating-type locus HMR requires recognition of a small DNA sequence element, the HMR-E silencer, by the Sir1p, one of four Sir proteins required for the assembly of silenced chromatin domains in Saccharomyces cerevisiae. The Sir1p recognizes the silencer through interactions with the origin recognition complex (ORC), a protein complex that binds the silencer DNA directly. Sir1p was physically associated with HMR in chromatin, and this association required a Sir1p-ORC interaction, suggesting that it reflected the Sir1p silencer-recognition function required for silencing. Sir1p was not associated with nonsilencer replication origins that bind the ORC, indicating that a Sir1p-ORC interaction is confined to silencers. Significantly, the other SIR genes were required for Sir1p's association with HMR. Thus, multiple protein contacts required for and unique to silent chromatin may confine a Sir1p-ORC interaction to silencers. The Sir1p was present at extremely low concentrations in yeast cells yet was associated with HMR at all stages of the cell cycle examined. These data provide insights into the mechanisms that establish and restrict the assembly of silenced chromatin to only a few discrete chromosomal domains.

Base Sequence↗

PubMed2000

Dysphagia in children with a 22q11.2 deletion: unusual pattern found on modified barium swallow.

OBJECTIVES: To delineate feeding dysfunction in a population of children with a 22q11.2 deletion and report the associated findings noted during the modified barium swallow (MBS). STUDY DESIGN: Seventy-five children with a chromosome 22q11.2 deletion and history of persistent feeding difficulty received a feeding evaluation, including an MBS for those children for whom there was concern about airway penetration. RESULTS: A consistent pattern of feeding difficulty, independent of palatal or cardiac involvement, emerged from the evaluations. This group typically has trouble coordinating the suck/swallow/breath pattern, resulting in slow nipple feedings interrupted by gagging or regurgitation. Recurrent vomiting and constipation are common. With advancement to chewable table foods, gagging or refusal develops, related to an immature oral transport pattern. The MBS studies demonstrate pharyngeal hypercontractility, cricopharyngeal prominence, and/or diverticula. CONCLUSIONS: Because of the consistency of dysphagic symptoms and MBS findings, we propose that dysmotility, especially through the pharyngoesophageal segment, is central to the dysphagia affecting this group. Dysphagia related to dysmotility may be underdiagnosed in this population or erroneously attributed to cardiac disease. Therefore attention to feeding status and investigation with MBS and gastrointestinal studies as warranted are recommended for all patients with a 22q11.2 deletion and feeding problems.

Abnormalities, Multiple↗

PubMed2000

Forkhead genes in transcriptional silencing, cell morphology and the cell cycle. Overlapping and distinct functions for FKH1 and FKH2 in Saccharomyces cerevisiae.

The SIR1 gene is one of four specialized genes in Saccharomyces cerevisiae required for repressing transcription at the silent mating-type cassettes, HMLalpha and HMRa, by a mechanism known as silencing. Silencing requires the assembly of a specialized chromatin structure analogous to heterochromatin. FKH1 was isolated as a gene that, when expressed in multiple copies, could substitute for the function of SIR1 in silencing HMRa. FKH1 (Forkhead Homologue One) was named for its homology to the forkhead family of eukaryotic transcription factors classified on the basis of a conserved DNA binding domain. Deletion of FKH1 caused a defect in silencing HMRa, indicating that FKH1 has a positive role in silencing. Significantly, deletion of both FKH1 and its closest homologue in yeast, FKH2, caused a form of yeast pseudohyphal growth, indicating that the two genes have redundant functions in controlling yeast cell morphology. By several criteria, fkh1Delta fkh2Delta-induced pseudohyphal growth was distinct from the nutritionally induced form of pseudohyphal growth observed in some strains of S. cerevisiae. Although FKH2 is redundant with FKH1 in controlling pseudohyphal growth, the two genes have different functions in silencing HMRa. High-copy expression of CLB2, a G2/M-phase cyclin, prevented fkh1Delta fkh2Delta-induced pseudohyphal growth and modulated some of the fkhDelta-induced silencing phenotypes. Interestingly, deletions in either FKH1 or FKH2 alone caused subtle but opposite effects on cell-cycle progression and CLB2 mRNA expression, consistent with a role for each of these genes in modulating the cell cycle and having opposing effects on silencing. The differences between Fkh1p and Fkh2p in vivo were not attributable to differences in their DNA binding domains.

Cell Cycle↗

PubMed1999

A role for a replicator dominance mechanism in silencing.

The role of the natural HMR-E silencer in modulating replication initiation and silencing by the origin recognition complex (ORC) was examined. When natural HMR-E was the only silencer controlling HMR, the silencer's ORC-binding site (ACS) was dispensable for replication initiation but essential for silencing, indicating that a non-silencer chromosomal replicator(s) existed in close proximity to the silencer. Further analysis revealed that regions flanking both sides of HMR-E contained replicators. In contrast to replication initiation by the intact silencer, initiation by the non-silencer replicator(s) was abolished in an orc2-1 mutant, indicating that these replicators were extremely sensitive to defects in ORC. Remarkably, the activity of one of the non-silencer replicators correlated with reduced silencing; inactivation of these replicators caused by either the orc2-1 mutation or the deletion of flanking sequences enhanced silencing. These data were consistent with a role for the ORC bound to the HMR-E silencer ACS in suppressing the function of neighboring ORC molecules capable of inhibiting silencing, and indicated that differences in ORC-binding sites within HMR itself had profound effects on ORC function. Moreover, replication initiation by natural HMR-E was inefficient, suggesting that closely spaced replicators within HMR contributed to an inhibition of replication initiation.

Alleles↗

PubMed1999

A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in saccharomyces cerevisiae.

Silencing of the cryptic mating-type loci HMR and HML requires the recognition of DNA sequence elements called silencers by the Sir1p, one of four proteins dedicated to the assembly of silenced chromatin in Saccharomyces cerevisiae. The Sir1p is thought to recognize silencers indirectly through interactions with proteins that bind the silencer DNA directly, such as the origin recognition complex (ORC). Eight recessive alleles of SIR1 were discovered that encode mutant Sir1 proteins specifically defective in their ability to recognize the HMR-E silencer. The eight missense mutations all map within a 17-amino-acid segment of Sir1p, and this segment was also required for Sir1p's interaction with Orc1p. The mutant Sir1 proteins could function in silencing if tethered to a silencer directly through a heterologous DNA-binding domain. Thus the amino acids identified are required for Sir1 protein's recognition of the HMR-E silencer and interaction with Orc1p, but not for its ability to function in silencing per se. The approach used to find these mutations may be applicable to defining interaction surfaces on proteins involved in other processes that require the assembly of macromolecular complexes.

Alleles↗

PubMed1998

Möbius syndrome with oculomotor nerve paralysis without abducens paralysis.

Möbius syndrome is typified by bilateral facial nerve palsies, usually with abducens palsies. We examined an infant with Möbius syndrome who had bifacial weakness and third nerve palsies, but intact abduction of both eyes. Lower cranial nerve involvement, leading to respiratory, swallowing, and cardiac difficulties, was also present. Pathologic examination of the brainstem showed absent or hypoplastic third, seventh, tenth, and twelfth nerve nuclei. The fourth, fifth, sixth, and eighth nerve nuclei were intact. In Möbius syndrome with ocular motor palsies, rarely the sixth nerve may be spared.

Abducens Nerve↗

PubMed1997

The origin recognition complex, SIR1, and the S phase requirement for silencing.

Silencing of transcription in Saccharomyces cerevisiae has several links to DNA replication, including a role for the origin recognition complex (ORC), the DNA replication initiator, in both processes. In addition, the establishment of silencing at the HML and HMR loci requires cells to pass through the S phase of the cell cycle. Passage through S phase was required for silencing of HMR even under conditions in which ORC itself was no longer required. The requirement for ORC in silencing of HMR could be bypassed by tethering the Sir1 protein to the HMR-E silencer. However, ORC had a Sir1-independent role in transcriptional silencing at telomeres. Thus, the role of ORC in silencing was separable from its role in initiation, and the role of S phase in silencing was independent of replication initiation at the silencers.

Aldose-Ketose Isomerases↗

PubMed1996

Influences of the cell cycle on silencing.

Silencing in Saccharomyces cerevisiae is a form of transcriptional repression that involves the assembly of a specialized and heritable structure of chromatin. The HML and HMR loci, which contain copies of the genes found at the yeast mating-type locus, are silenced, as are telomeres. These examples share several features which are also found in position-effect variegation in flies and X-chromosome inactivation and genomic imprinting in mammals. Silenced chromatin is confined to a few special domains of the yeast genome, and active genes inserted into these domains become silenced. Molecular and genetic evidence has suggested that the establishment of silenced chromatin requires some S phase specific function. Recent experiments indicate that the assembly and maintenance of silenced chromatin can also be influenced at other phases of the cell cycle.

Animals↗

PubMed1996

EcoCELLs: tools for mesocosm scale measurements of gas exchange.

We describe the use of a unique plant growth facility, which has as its centerpiece four 'EcoCELLs', or 5x7 m mesocosms designed as open-flow, mass-balance systems for the measurement of carbon, water and trace gas fluxes. This system is unique in that it was conceived specifically to bridge the gap between measurement scales during long-term experiments examining the function and development of model ecosystems. There are several advantages to using EcoCELLs, including (i) the same theory of operation as leaf level gas exchange systems, but with continuous operation at a much larger scale; (ii) the ability to independently evaluate canopy-level and ecosystem models; (iii) simultaneous manipulation of environmental factors and measurement of system-level responses, and (iv) maximum access to, and manipulation of, a large rooting volume. In addition to discussing the theory, construction and relative merits of EcoCELLs, we describe the calibration and use of the EcoCELLs during a 'proof of concept' experiment. This experiment involved growing soybeans under two ambient CO2 concentrations (approximately 360 and 710 micromoles mol-1). During this experiment, we asked 'How accurate is the simplest model that can be used to scale from leaf-level to canopy-level responses?' in order to illustrate the utility of the EcoCELLs in validating canopy-scale models.

Calibration↗

PubMed1995

Primary astroglial cultures derived from several rat brain regions differentially express mu, delta and kappa opioid receptor mRNA.

The existence of opioid receptors within glial cell membranes has been proposed by several laboratories based on biochemical and radioligand binding data. The recent cloning of the mu, delta and kappa receptors has enabled us to directly examine the issue of opioid receptor expression in rat brain astroglia by using solution hybridization/ribonuclease protection assays to analyze the total RNA obtained from primary cultures of cortical, striatal, cerebellar, hippocampal and hypothalamic astrocytes. The results indicate that all five glial cultures expressed mu, delta and kappa receptor mRNA. The rank order of receptor mRNA abundance, expressed collectively across all five cultures, was determined to be delta > or = kappa >> mu. An analysis of the glial distribution profile for each receptor type revealed that mu receptor mRNA levels were the most abundantly expressed in cortical cultures, while the greatest levels of delta receptor mRNA were found in the cortical and hypothalamic cultures, and significant kappa receptor mRNA levels were produced by the cortical, hypothalamic and cerebellar cultures. Furthermore, the five glial cultures each expressed different levels of total opioid receptor (mu + delta + kappa) mRNA. The rank order of total opioid receptor mRNA expression across different astroglial cultures was found to be cortex > hypothalamus > cerebellum = hippocampus > striatum. An analysis of the relative expression profiles for mu, delta and kappa receptor mRNA within each culture revealed that all cultures manifested relatively high levels of delta and kappa receptor mRNA, but relatively low levels of mu receptor mRNA. Generally, cortical, hippocampal and hypothalamic cultures were characterized by comparable levels of delta and kappa receptor mRNA, and little, if any, mu receptor mRNA. However, striatal cultures were characterized by a high level of delta receptor mRNA which was approximately twice and four times that of the kappa and mu receptor mRNA, respectively. In contrast, cerebellar cultures expressed predominantly kappa receptor mRNA at a level which was almost twice that of the delta receptor mRNA, and expressed very little mu receptor mRNA. These data show that primary astroglial cultures not only express mu, delta and kappa receptor mRNAs, but they do so in a manner dependent upon receptor type and brain region. This suggests a regional heterogeneity of astrocytes with respect to opioid receptor expression, a characteristic previously described only for neurons. Furthermore, it suggests the existence of an additional anatomical component in CNS opioid systems.

Animals↗

PubMed1995

The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication.

The role of the origin recognition complex (ORC) was investigated in replication initiation and in silencing. Temperature-sensitive mutations in ORC genes caused defects in replication initiation at chromosomal origins of replication, as measured by two-dimensional (2-D) origin-mapping gels, fork migration analysis, and plasmid replication studies. These data were consistent with ORC functioning as a eukaryotic replication initiator. Some origins displayed greater replication initiation deficiencies in orc mutants than did others, revealing functional differences between origins. Alleles of ORC5 were isolated that were defective for silencing but not replication, indicating that ORC's role in silencing could be separated from its role in replication. In temperature-sensitive orc mutants arrested in mitosis, temperature-shift experiments caused a loss of silencing, indicating both that ORC had functions outside of the S phase of the cell cycle and that ORC was required for the maintenance of the silenced state.

Cell Cycle↗

PubMed1995

Opioid-receptor mRNA expression in the rat CNS: anatomical and functional implications.

The cloning of the opioid receptors has profoundly affected our understanding of opioid-receptor expression, regulation and function. This review focuses on the impact that cloning has had on our understanding of opioid-receptor anatomy, and provides broad anatomical maps of the three opioid-receptor mRNAs in relation to their binding sites. In addition, three model anatomical systems, the nigrostriatal and mesolimbic dopamine systems, the hypothalamic neuroendocrine axes, and the ascending and descending pain pathways, have been highlighted to discuss issues of receptor transport, trafficking and pre- versus postsynaptic localization.

Animals↗

PubMed1995

Immunohistochemical localization of the cloned mu opioid receptor in the rat CNS.

Three opioid receptor types have recently been cloned that correspond to the pharmacologically defined mu, delta and kappa 1 receptors. In situ hybridization studies suggest that the opioid receptor mRNAs that encode these receptors have distinct distributions in the central nervous system that correlate well with their known functions. In the present study polyclonal antibodies were generated to the C terminal 63 amino acids of the cloned mu receptor (335-398) to examine the distribution of the mu receptor-like protein with immunohistochemical techniques. mu receptor-like immunoreactivity is widely distributed in the rat central nervous system with immunoreactive fibers and/or perikarya in such regions as the neocortex, the striatal patches and subcallosal streak, nucleus accumbens, lateral and medial septum, endopiriform nucleus, globus pallidus and ventral pallidum, amygdala, hippocampus, presubiculum, thalamic and hypothalamic nuclei, superior and inferior colliculi, central grey, substantia nigra, ventral tegmental area, interpeduncular nucleus, medial terminal nucleus of the accessory optic tract, raphe nuclei, nucleus of the solitary tract, spinal trigeminal nucleus, dorsal motor nucleus of vagus, the spinal cord and dorsal root ganglia. In addition, two major neuronal pathways, the fasciculus retroflexus and the stria terminalis, exhibit densely stained axonal fibers. While this distribution is in excellent agreement with the known mu receptor binding localization, a few regions, such as neocortex and cingulate cortex, basolateral amygdala, medial geniculate nucleus and the medial preoptic area fail to show a good correspondence. Several explanations are provided to interpret these results, and the anatomical and functional implications of these findings are discussed.

Amino Acid Sequence↗

PubMed1995

The origin recognition complex in silencing, cell cycle progression, and DNA replication.

This report describes the isolation of ORC5, the gene encoding the fifth largest subunit of the origin recognition complex, and the properties of mutants with a defective allele of ORC5. The orc5-1 mutation caused temperature-sensitive growth and, at the restrictive temperature, caused cell cycle arrest. At the permissive temperature, the orc5-1 mutation caused an elevated plasmid loss rate that could be suppressed by additional tandem origins of DNA replication. The sequence of ORC5 revealed a potential ATP binding site, making Orc5p a candidate for a subunit that mediates the ATP-dependent binding of ORC to origins. Genetic interactions among orc2-1 and orc5-1 and other cell cycle genes provided further evidence for a role for the origin recognition complex (ORC) in DNA replication. The silencing defect caused by orc5-1 strengthened previous connections between ORC and silencing, and combined with the phenotypes caused by orc2 mutations, suggested that the complex itself functions in both processes.

Amino Acid Sequence↗

PubMed1995

Differential expression of protein phosphatase 1 isoforms in mammalian brain.

Rat cDNAs encoding neuronal isoforms of protein phosphatase 1 (PP1) were isolated and their primary structures elucidated. The derived amino acid sequences allowed us to design synthetic C-terminal peptides that were used to raise antibodies. Isoform-specific anti-peptide antibodies against PP1 alpha and PP1 gamma 1 were used to investigate the tissue distribution of PP1 isoforms by immunoblotting. Both isoforms were ubiquitously expressed in mammalian tissues, with the highest levels being observed in brain. Of all neuronal tissues examined, PP1 alpha and PP1 gamma 1 were found to be most abundantly expressed in the striatum. Lesion experiments with kainic acid indicated that both the alpha and the gamma 1 isoforms of protein phosphatase 1 were relatively enriched in the medium-size spiny neurons of the striatum. "In situ" hybridization to rat brain slices using highly sensitive riboprobes also showed PP1 alpha, PP1 beta, and PP1 gamma 1 to be widely expressed in mammalian brain. However, some interesting differences were observed. For example, PP1 alpha and PP1 gamma 1 were found to be expressed in the striatum, where DARPP-32 (dopamine- and cAMP-regulated phosphoprotein, M(r) = 32,000 Da) is also known to be highly expressed. PP1 beta appeared to be relatively less abundant in the same cells, as judged both by "in situ" hybridization and by the apparent absence of PP1 beta clones from the striatal cDNA libraries used.

Amino Acid Sequence↗

PubMed1994

Mu, delta, and kappa opioid receptor mRNA expression in the rat CNS: an in situ hybridization study.

The mu, delta, and kappa opioid receptors are the three main types of opioid receptors found in the central nervous system (CNS) and periphery. These receptors and the peptides with which they interact are important in a number of physiological functions, including analgesia, respiration, and hormonal regulation. This study examines the expression of mu, delta, and kappa receptor mRNAs in the rat brain and spinal cord using in situ hybridization techniques. Tissue sections were hybridized with 35S-labeled cRNA probes to the rat mu (744-1,064 b), delta (304-1,287 b), and kappa (1,351-2,124 b) receptors. Each mRNA demonstrates a distinct anatomical distribution that corresponds well to known receptor binding distributions. Cells expressing mu receptor mRNA are localized in such regions as the olfactory bulb, caudate-putamen, nucleus accumbens, lateral and medial septum, diagonal band of Broca, bed nucleus of the stria terminalis, most thalamic nuclei, hippocampus, amygdala, medial preoptic area, superior and inferior colliculi, central gray, dorsal and median raphe, raphe magnus, locus coeruleus, parabrachial nucleus, pontine and medullary reticular nuclei, nucleus ambiguus, nucleus of the solitary tract, nucleus gracilis and cuneatus, dorsal motor nucleus of vagus, spinal cord, and dorsal root ganglia. Cellular localization of delta receptor mRNA varied from mu or kappa, with expression in such regions as the olfactory bulb, allo- and neocortex, caudate-putamen, nucleus accumbens, olfactory tubercle, ventromedial hypothalamus, hippocampus, amygdala, red nucleus, pontine nuclei, reticulotegmental nucleus, motor and spinal trigeminal, linear nucleus of the medulla, lateral reticular nucleus, spinal cord, and dorsal root ganglia. Cells expressing kappa receptor mRNA demonstrate a third pattern of expression, with cells localized in regions such as the claustrum, endopiriform nucleus, nucleus accumbens, olfactory tubercle, medial preoptic area, bed nucleus of the stria terminalis, amygdala, most hypothalamic nuclei, median eminence, infundibulum, substantia nigra, ventral tegmental area, raphe nuclei, paratrigeminal and spinal trigeminal, nucleus of the solitary tract, spinal cord, and dorsal root ganglia. These findings are discussed in relation to the physiological functions associated with the opioid receptors.

Animals↗