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Biomedical subjects

R Parker

Publications and source records attributed to R Parker.

At least 37 records · Page 2Linked to original sources
PubMed2001

Two related proteins, Edc1p and Edc2p, stimulate mRNA decapping in Saccharomyces cerevisiae.

The major mRNA decay pathway in Saccharomyces cerevisiae occurs through deadenylation, decapping, and 5' to 3' degradation of the mRNA. Decapping is a critical control point in this decay pathway. Two proteins, Dcp1p and Dcp2p, are required for mRNA decapping in vivo and for the production of active decapping enzyme. To understand the relationship between Dcp1p and Dcp2p, a combination of both genetic and biochemical approaches were used. First, we demonstrated that when Dcp1p is biochemically separated from Dcp2p, Dcp1p was active for decapping. This observation confirmed that Dcp1p is the decapping enzyme and indicated that Dcp2p functions to allow the production of active Dcp1p. We also identified two related proteins that stimulate decapping, Edc1p and Edc2p (Enhancer of mRNA DeCapping). Overexpression of the EDC1 and EDC2 genes suppressed conditional alleles of dcp1 and dcp2, respectively. Moreover, when mRNA decapping was compromised, deletion of the EDC1 and/or EDC2 genes caused significant mRNA decay defects. The Edc1p also co-immunoprecipitated with Dcp1p and Dcp2p. These results indicated that Edc1p and Edc2p interact with the decapping proteins and function to enhance the decapping rate.

Alleles↗
PubMed2001

The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3' termini from partial degradation.

A key aspect of understanding eukaryotic gene regulation will be the identification and analysis of proteins that bind mRNAs and control their function. Recently, a complex of seven Lsm proteins and the Pat1p have been shown to interact with yeast mRNAs and promote mRNA decapping. In this study we present several observations to indicate that the LsmI/Pat1 complex has a second distinct function in protecting the 3'-UTR of mRNAs from trimming. First, mutations in the LSM1 to LSM7, as well as PAT1, genes led to the accumulation of MFA2pG and PGK1pG transcripts that had been shortened by 10-20 nucleotides at their 3' ends (referred to as trimming). Second, the trimming of these mRNAs was more severe at the high temperature, correlating with the inability of these mutant strains to grow at high temperature. In contrast, trimming did not occur in a dcp1 Delta strain, wherein the decapping enzyme is lacking. This indicates that trimming is not simply a consequence of the inhibition of mRNA decapping. Third, the temperature-sensitive growth of lsm and pat1 mutants was suppressed by mutations in the exosome or the functionally related Ski proteins, which are required for efficient 3' to 5' mRNA degradation of mRNA. Moreover, in lsm ski double mutants, higher levels of the trimmed mRNAs accumulated, indicating that exosome function is not required for mRNA trimming but that the exosome does degrade the trimmed mRNAs. These results raise the possibility that the temperature-sensitive growth of the lsm1-7 and pat1 mutants is at least partially due to mRNA trimming, which either inactivates the function of the mRNAs or makes them available for premature 3' to 5' degradation by the exosome.

3' Untranslated Regions↗
PubMed2001

Identification of TFII-I as the endoplasmic reticulum stress response element binding factor ERSF: its autoregulation by stress and interaction with ATF6.

When mammalian cells are subjected to stress targeted to the endoplasmic reticulum (ER), such as depletion of the ER Ca(2+) store, the transcription of a family of glucose-regulated protein (GRP) genes encoding ER chaperones is induced. The GRP promoters contain multiple copies of the ER stress response element (ERSE), consisting of a unique tripartite structure, CCAAT(N(9))CCACG. Within a subset of mammalian ERSEs, N(9) represents a GC-rich sequence of 9 bp that is conserved across species. A novel complex (termed ERSF) exhibits enhanced binding to the ERSE of the grp78 and ERp72 promoters using HeLa nuclear extracts prepared from ER-stressed cells. Optimal binding of ERSF to ERSE and maximal ERSE-mediated stress inducibility require the conserved GGC motif within the 9-bp region. Through chromatographic purification and subsequent microsequencing, we have identified ERSF as TFII-I. Whereas TFII-I remains predominantly nuclear in both nontreated NIH 3T3 cells and cells treated with thapsigargin (Tg), a potent inducer of the GRP stress response through depletion of the ER Ca(2+) store, the level of TFII-I transcript was elevated in Tg-stressed cells, correlating with an increase in TFII-I protein level in the nuclei of Tg-stressed cells. Purified recombinant TFII-I isoforms bind directly to the ERSEs of grp78 and ERp72 promoters. The stimulation of ERSE-mediated transcription by TFII-I requires the consensus tyrosine phosphorylation site of TFII-I and the GGC sequence motif of the ERSE. We further discovered that TFII-I is an interactive protein partner of ATF6 and that optimal stimulation of ERSE by ATF6 requires TFII-I.

3T3 Cells↗
PubMed2001

A survey of problematic sexualized behaviors of children in the New York City Child Welfare System:estimates of problem, impact on services, and need for training.

Forty-eight of 52 (92%) agencies contracted with the New York City Administration for Children's Services (ACS) responded to a survey about problematic sexualized behaviors (PSB) of children in different levels of care within the child welfare system. Results revealed that almost all agencies reported PSB within their foster boarding home and residential treatment centers. A majority of agencies perceived PSB to be a significant problem for which staff and families were not sufficiently trained. These findings highlight many avenues for advocacy, clinical intervention, and staff development.

Child↗
PubMed2000

Effect of molecular structure and water content on the dielectric relaxation behaviour of amorphous low molecular weight carbohydrates above and below their glass transition.

The dielectric relaxation behaviour of several amorphous low molecular weight carbohydrates and their 10% w/w water mixtures has been studied in the supercooled liquid and glassy regions in the frequency range 100 Hz to 100 kHz. The dry carbohydrates show a primary alpha-relaxation (activation energy 250-405 kJ mol(-1)) at temperatures above the calorimetric glass transition temperature, Tg, and, in most cases, a secondary beta-relaxation (activation energy 42-55 kJ mol(-1)) at sub-Tg temperatures. Whilst D-mannose showed a beta-relaxation similar in strength to D-glucose, its deoxy sugar, L-rhamnose showed a relatively weak beta-relaxation. This indicates that the hydroxymethyl group influences relaxation in carbohydrate glasses. Addition of water shifted the alpha-relaxations to lower temperatures and increased the strength of the beta-relaxations. In glucitol this resulted in a merging of the alpha- and beta-relaxations. The beta-relaxation increased in strength and decreased in temperature for the series of water mixtures: D-glucose, maltose, and maltotriose.

Calorimetry, Differential Scanning↗
PubMed2000

The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast.

Eukaryotic post-transcriptional regulation is often specified by control elements within mRNA 3'- untranslated regions (3'-UTRs). In order to identify proteins that regulate specific mRNA decay rates in Saccharomyces cerevisae, we analyzed the role of five members of the Puf family present in the yeast genome (referred to as JSN1/PUF1, PUF2, PUF3, PUF4 and MPT5/PUF5). Yeast strains lacking all five Puf proteins showed differential expression of numerous yeast mRNAs. Examination of COX17 mRNA indicates that Puf3p specifically promotes decay of this mRNA by enhancing the rate of deadenylation and subsequent turnover. Puf3p also binds to the COX17 mRNA 3'-UTR in vitro. This indicates that the function of Puf proteins as specific regulators of mRNA deadenylation has been conserved throughout eukaryotes. In contrast to the case in Caenorhabditis elegans and Drosophila, yeast Puf3p does not affect translation of COX17 mRNA. These observations indicate that Puf proteins are likely to play a role in the control of transcript-specific rates of degradation in yeast by interacting directly with the mRNA turnover machinery.

3' Untranslated Regions↗
PubMed2000

A multivariate analysis of factors associated with depression: evaluating the role of health literacy as a potential contributor.

BACKGROUND: High rates of low health literacy among elderly populations along with a high prevalence of chronic conditions may lead to increased levels of depression symptomatology. We sought to determine whether older adults with inadequate health literacy were more likely to report depressive symptoms and whether health literacy was an independent predictor of depression symptomatology. METHODS: A total of 3260 new Medicare enrollees 65 years or older were interviewed in person between June and December 1997 from 4 managed care plans (853 in Cleveland, Ohio, 498 in Houston, Tex, 975 in South Florida, and 934 in Tampa, Fla). Depression symptoms were measured by the Geriatric Depression Scale. RESULTS: Overall, 13% of respondents were classified as depressed. Individuals with inadequate health literacy had 2.7 times the odds (95% confidence interval, 2.2-3.4) of being depressed compared with individuals with adequate health literacy skills. However, after controlling for health status with multiple logistic regression, individuals with inadequate health literacy were not more likely to be depressed (adjusted odds ratio, 1.2; 95% confidence interval, 0.9-1.7). Individuals who had less social support, exercised less than twice a week, drank alcohol heavily, or had poor health status (at least 3 health conditions, physical limitations, or fair or poor self-rated health) had significantly higher odds of depression symptomatology. CONCLUSIONS: Although individuals with inadequate health literacy were more than twice as likely to report depressive symptoms, this was mostly explained by their worse health status. The strong relation between depression symptoms and poor health status suggests the need to research interventions to improve mental and physical health concurrently. The influence of particular interventions on depression, such as referral to community support contacts and recommendations for an exercise program, needs to be further evaluated. Arch Intern Med. 2000;160:3307-3314.

Activities of Daily Living↗
PubMed2000

Diffusion of short chain alcohols from amorphous maltose-water mixtures above and below their glass transition temperature.

The apparent diffusion coefficient for short chain alcohols in undercooled maltose-water mixtures close to the calorimetric glass transition temperature, Tg, was measured by following desorption using headspace gas chromatography. The plasticising effect of the alcohols on Tg was characterised using differential scanning calorimetry. The initial appearance of alcohol in the headspace showed a linear dependence on the square root of time, allowing it to be modelled as a Fickian diffusive process. The diffusion coefficient decreased with increasing molecular size of alcohol and proximity to Tg. Close to the glass transition the variation of diffusion coefficient with temperature and composition does not follow that of viscosity and, for ethanol, divergence was observed at Tg/T> 0.88.

Alcohols↗
PubMed2000

Y-receptor-like genes GPR72 and GPR73: molecular cloning, genomic organisation and assignment to human chromosome 11q21.1 and 2p14 and mouse chromosome 9 and 6.

Two novel G-protein-coupled receptors, one from human, GPR72, and one from mouse, GPR73 have been isolated, sequenced and their genomic organisation determined. Non-isotopic in situ hybridisation and radiation hybrid mapping have identified GPR72 to be localised on human chromosome 11q21.1, and GPR73 on human chromosome 2p14. Interspecific mouse backcross mapping has localised the genes to mouse chromosomes 9 and 6, respectively. Northern analysis reveals GPR72 mRNA expression only in brain tissue. However, GPR73 mRNA can be found in heart, skeletal muscle and pancreas. Both receptors are closely related with 36 and 33% overall amino acid identity, respectively, to the Y-receptor family. However, although successful cell surface expression in a heterologous expression system can be achieved no specific binding to this ligand family can be detected, indicating that perhaps additional factors are required for binding.

Animals↗
PubMed2000

Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae.

Understanding the regulation of gene expression requires the identification of cis -acting control elements that modulate gene function. The recent availability of complete genome sequences and profiles of mRNA expression has facilitated the development and utilization of computational methods to identify discrete regulatory elements. We have developed an oligomer counting method that identifies sequences that occur significantly more often in a group of interest relative to other genes in the genome. The use of a second parameter, which measures the frequency of oligomers within the group of interest, allows the detection of false positive signals caused by very infrequent oligomers that would otherwise appear as significant. Applying this method to gene groups that have a common expression pattern or shared function should identify oligomers that comprise cis -acting control elements. As a test of this method, we applied this approach to a set of intron-containing yeast genes, where we easily identified the known splicing signals as control elements. We have used this training set to examine how this method is affected by the length of the oligomer examined, as well as the size and composition of the gene group. These simulations allowed us to identify rules for selecting groups of genes to analyze. Finally, application of this method to nuclear genes encoding proteins targeted to the mitochondria identified a new putative cis -acting sequence in the 3'-untranslated region of this family of genes, which may play a role in mRNA localization or the regulation of mRNA stability or translation.

3' Untranslated Regions↗
PubMed2000

Yeast Sm-like proteins function in mRNA decapping and decay.

One of the main mechanisms of messenger RNA degradation in eukaryotes occurs by deadenylation-dependent decapping which leads to 5'-to-3' decay. A family of Sm-like (Lsm) proteins has been identified, members of which contain the 'Sm' sequence motif, form a complex with U6 small nuclear RNA and are required for pre-mRNA splicing. Here we show that mutations in seven yeast Lsm proteins (Lsm1-Lsm7) also lead to inhibition of mRNA decapping. In addition, the Lsm1-Lsm7 proteins co-immunoprecipitate with the mRNA decapping enzyme (Dcp1), a decapping activator (Pat1/Mrt1) and with mRNA. This indicates that the Lsm proteins may promote decapping by interactions with the mRNA and the decapping machinery. In addition, the Lsm complex that functions in mRNA decay appears to be distinct from the U6-associated Lsm complex, indicating that Lsm proteins form specific complexes that affect different aspects of mRNA metabolism.

Autoantigens↗
PubMed2000

Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast.

The biogenesis of a number of RNA species in eukaryotic cells requires 3' processing. To determine the enzymes responsible for these trimming events, we created yeast strains lacking specific 3' to 5' exonucleases. In this work, we describe the analysis of three members of the RNase D family of exonucleases (Rex1p, Rex2p and Rex3p). This work led to three important conclusions. First, each of these exonucleases is required for the processing of distinct RNAs. Specifically, Rex1p, Rex2p and Rex3p are required for 5S rRNA, U4 snRNA and MRP RNA trimming, respectively. Secondly, some 3' exonucleases are redundant with other exonucleases. Specifically, Rex1p and Rex2p function redundantly in 5.8S rRNA maturation, Rex1p, Rex2p and Rex3p are redundant for the processing of U5 snRNA and RNase P RNA, and Rex1p and the exonuclease Rrp6p have an unknown redundant essential function. Thirdly, the demonstration that the Rex proteins can affect reactions that have been attributed previously to the exosome complex indicates that an apparently simple processing step can be surprisingly complex with multiple exonucleases working sequentially in the same pathway.

Conserved Sequence↗
PubMed2000

An adult formulation of a five-component acellular pertussis vaccine combined with diphtheria and tetanus toxoids is safe and immunogenic in adolescents and adults.

Pertussis is increasingly being recognized as an important cause of cough illness in adolescents and adults. To evaluate the safety and immunogenicity of an adult formulation of a five-component (pertussis toxoid, filamentous hemagglutinin, pertactin, fimbriae 2 and 3) acellular pertussis vaccine combined with diphtheria and tetanus toxoids, we randomly allocated 749 healthy adolescents and adults from 12-54 years of age recruited from five Canadian communities to receive either tetanus-diphtheria vaccine (Td), acellular pertussis vaccine (aP) or combined diphtheria-tetanus-acellular pertussis vaccine (TdaP). Subjects and personnel were unaware of the vaccine allocation. Antibody levels were measured before and one month postimmunization; adverse events were collected at 24 and 72 h and 8 to 10 days. Adverse events were reported in similar frequency amongst the three vaccine groups. Moderate pain at the injection site was reported less frequently in the aP group than the TdaP group (10.7% compared to 19.4%; relative risk 0.6, 95% confidence interval 0.3-0.9). Chills were reported less frequently after Td (5.3%) than after TdaP (12.5%; relative risk 0.4, 95% confidence interval 0.2-0.9). There were no statistically significant differences between recipients of Td and TdaP in tetanus and diphtheria antitoxin levels achieved. Antibody response against Bordetella pertussis antigens was vigorous in all groups although recipients of aP alone had higher levels of antibody levels against pertussis toxoid, fimbriae, and agglutinins and lower antibody levels against pertactin than did TdaP recipients. We conclude that this adult formulation 5-component acellular pertussis vaccine is safe and immunogenic in adolescents and adults and is a candidate vaccine for adolescent and adult immunization programs.

Adolescent↗
PubMed2000

The effects of intrapleural polyclonal anti-tumor necrosis factor alpha (TNF alpha) Fab fragments on pleurodesis in rabbits.

The mechanism by which various agents produce a pleurodesis is unknown. The purpose of this project was to determine whether the pleurodesis that results from the intrapleural administration of talc or doxycycline depends on tumor necrosis factor alpha (TNF alpha). In a randomized, blinded, placebo-controlled study, 34 New Zealand white rabbits were given 400 mg talc or 10 mg/kg doxycycline intrapleurally as a sclerosant through a chest tube. Half the rabbits in each group were also given 2,000 units of ovine, polyclonal affinity purified anti-TNF alpha Fab, or saline as placebo immediately after and 12 h after the injection of the sclerosant. Chest tubes were aspirated at 12-h intervals until their removal at 4 days. Rabbits were killed at 28 days. The pleural fluid volume, cell counts, lactate dehydrogenase (LDH) and pleurodesis scores were compared among groups. Both talc and doxycycline produced an exudative pleural effusion. The pleural fluid volume and the pleural fluid LDH levels were significantly (p < 0.05) greater in the group given doxycycline. The administration of anti-TNF alpha Fab had no significant effect on pleural fluid volume or leukocyte count in either group. However, the administration of anti-TNF alpha Fab resulted in a significant decrease (p = 0.004) in the pleurodesis score for the animals given talc (3.2 +/- 0.8 without Fab and 1.8 +/- 0.9 with Fab). In contrast, the pleurodesis score was virtually identical in the doxycycline group with (3.5 +/- 0.5) and without (3.4 +/- 0.7) Fab. The administration of anti-TNF alpha Fab diminishes the pleurodesis induced by talc but not that resulting from doxycycline. These findings suggest that different mechanisms are involved with the two different sclerosants.

Animals↗
PubMed2000

Functions of Lsm proteins in mRNA degradation and splicing.

Recent results have identified a family of Lsm (Like Sm) proteins that are related to the Sm protein family. Seven Lsm proteins form a complex, which interacts with the U6 snRNA and functions in splicing. In addition, a different complex of Lsm proteins interacts with cytoplasmic mRNA and promotes its turnover. These diverse functions of Lsm proteins suggest that they are important modulators of RNA biogenesis and function.

Humans↗