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M J Berry

Publications and source records attributed to M J Berry.

At least 19 recordsLinked to original sources
PubMed2001

Interplay between termination and translation machinery in eukaryotic selenoprotein synthesis.

Termination of translation in eukaryotes is catalyzed by eRF1, the stop codon recognition factor, and eRF3, an eRF1 and ribosome-dependent GTPase. In selenoprotein mRNAs, UGA codons, which typically specify termination, serve an alternate function as sense codons. Selenocysteine incorporation involves a unique tRNA with an anticodon complementary to UGA, a unique elongation factor specific for this tRNA, and cis-acting secondary structures in selenoprotein mRNAs, termed SECIS elements. To gain insight into the interplay between the selenocysteine insertion and termination machinery, we investigated the effects of overexpressing eRF1 and eRF3, and of altering UGA codon context, on the efficiency of selenoprotein synthesis in a transient transfection system. Overexpression of eRF1 does not increase termination at naturally occurring selenocysteine codons. Surprisingly, selenocysteine incorporation is enhanced. Overexpression of eRF3 did not affect incorporation efficiency. Coexpression of both factors reproduced the effects with eRF1 alone. Finally, we show that the nucleotide context immediately upstream and downstream of the UGA codon significantly affects termination to incorporation ratios and the response to eRF overexpression. Implications for the mechanisms of selenocysteine incorporation and termination are discussed.

Base Sequence↗
PubMed2001

Selenocysteine incorporation directed from the 3'UTR: characterization of eukaryotic EFsec and mechanistic implications.

The mechanism of selenocysteine incorporation in eukaryotes has been assumed for almost a decade to be inherently different from that in prokaryotes, due to differences in the architecture of selenoprotein mRNAs in the two kingdoms. After extensive efforts in a number of laboratories spanning the same time frame, some of the essential differences between these mechanisms are finally being revealed, through identification of the factors catalyzing cotranslational selenocysteine insertion in eukaryotes. A single factor in prokaryotes recognizes both the selenoprotein mRNA, via sequences in the coding region, and the unique selenocysteyl-tRNA, via both its secondary structure and amino acid. The corresponding functions in eukaryotes are conferred by two distinct but interacting factors, one recognizing the mRNA, via structures in the 3' untranslated region, and the second recognizing the tRNA. Now, with these factors in hand, crucial questions about the mechanistic details and efficiency of this intriguing process can begin to be addressed.

3' Untranslated Regions↗
PubMed2001

Selenocysteine codons decrease polysome association on endogenous selenoprotein mRNAs.

BACKGROUND: Selenocysteine incorporation has been reported to be inefficient in all systems studied, including Escherichia coli, baculovirus-insect cell systems, rabbit reticulocyte in vitro translation systems, transiently transfected mammalian cells, and intact animals. Nonetheless, full-length selenoproteins containing up to 17 selenocysteine residues are produced in animals, indicating that the efficiency observed in manipulated systems might not accurately reflect the true efficiency of this process in nature. RESULTS: To begin to address this apparent discrepancy, we have examined the polysome profiles of endogenously expressed selenoprotein mRNAs in a mammalian cell line, and compared them with nonselenoprotein mRNAs. We report that three selenoprotein mRNAs, type 1 deiodinase, glutathione peroxidase and selenoprotein P, are under-loaded with ribosomes, based on their predicted open reading frame sizes. The average numbers of ribosomes per mRNA correspond to the sizes predicted by termination at the UGA selenocysteine codons. Appropriate loading on the type 1 deiodinase mRNA is seen following substitution of a cysteine codon for the selenocysteine codon, indicating that the UGA codon confers a translational penalty on the mRNA. Surprisingly, ribosomal loading is also increased by the expression of eukaryotic release factors eRF1 and eRF3. CONCLUSIONS: These results suggest that the presence of a selenocysteine codon confers a translational penalty on selenoprotein mRNAs, and that increased levels of release factors may alter the kinetics of termination.

Animals↗
PubMed2001

Does intraductal breast cancer spread in a segmental distribution? An analysis of residual tumour burden following segmental mastectomy using tumour bed biopsies.

INTRODUCTION: Breast-conserving surgery for early breast cancer is now routinely used as an alternative to mastectomy. Despite post-operative radiotherapy, early local recurrence of tumour remains a concern. It has been reported that invasive and in-situ ductal carcinoma spread locally through the ductal tree in a segmental distribution, however, there is no consensus as to the best surgical method to maximize tumour clearance whilst leaving a good cosmetic result. AIM: We aimed to measure the effectiveness of segmental mastectomy (excision of tumour plus associated segmental ductal tissue) in the clearance of different tumour types. Bed biopsy of the excision cavity was employed to assess the rate of incomplete excision or the multifocality of certain breast cancers. METHODS: One hundred and one patients with breast cancers underwent segmental mastectomy and cavity bed biopsies. Specimens were assessed for tumour type and completeness of excision. An excision of the cancer was considered incomplete if the margins were involved or if any of the bed biopsies showed residual or multifocal tumour. RESULTS: A total of 24 patients had incomplete tumour excision. Invasive ductal carcinoma was more likely to be completely excised by segmental mastectomy than invasive lobular carcinoma (P<0.05). Incomplete excision was associated with multifocality and the presence of extensive DCIS. The report of clear pathological margins was significantly more likely to be accurate, as measured by negative bed biopsies, in invasive ductal carcinoma when compared to invasive lobular carcinoma (P<0.05). CONCLUSION: These results support the concept that ductal carcinomas spread locally in a segmental fashion. Patients with invasive ductal carcinomas are more likely to benefit from breast conserving surgery that is tailored to include the associated ductal tissue, in a segmental fashioned excision.

Adult↗
PubMed2001

In silico identification of novel selenoproteins in the Drosophila melanogaster genome.

In selenoproteins, incorporation of the amino acid selenocysteine is specified by the UGA codon, usually a stop signal. The alternative decoding of UGA is conferred by an mRNA structure, the SECIS element, located in the 3'-untranslated region of the selenoprotein mRNA. Because of the non-standard use of the UGA codon, current computational gene prediction methods are unable to identify selenoproteins in the sequence of the eukaryotic genomes. Here we describe a method to predict selenoproteins in genomic sequences, which relies on the prediction of SECIS elements in coordination with the prediction of genes in which the strong codon bias characteristic of protein coding regions extends beyond a TGA codon interrupting the open reading frame. We applied the method to the Drosophila melanogaster genome, and predicted four potential selenoprotein genes. One of them belongs to a known family of selenoproteins, and we have tested experimentally two other predictions with positive results. Finally, we have characterized the expression pattern of these two novel selenoprotein genes.

Amino Acid Sequence↗
PubMed2001

Selective inhibition of selenocysteine tRNA maturation and selenoprotein synthesis in transgenic mice expressing isopentenyladenosine-deficient selenocysteine tRNA.

Selenocysteine (Sec) tRNA (tRNA([Ser]Sec)) serves as both the site of Sec biosynthesis and the adapter molecule for donation of this amino acid to protein. The consequences on selenoprotein biosynthesis of overexpressing either the wild type or a mutant tRNA([Ser]Sec) lacking the modified base, isopentenyladenosine, in its anticodon loop were examined by introducing multiple copies of the corresponding tRNA([Ser]Sec) genes into the mouse genome. Overexpression of wild-type tRNA([Ser]Sec) did not affect selenoprotein synthesis. In contrast, the levels of numerous selenoproteins decreased in mice expressing isopentenyladenosine-deficient (i(6)A(-)) tRNA([Ser]Sec) in a protein- and tissue-specific manner. Cytosolic glutathione peroxidase and mitochondrial thioredoxin reductase 3 were the most and least affected selenoproteins, while selenoprotein expression was most and least affected in the liver and testes, respectively. The defect in selenoprotein expression occurred at translation, since selenoprotein mRNA levels were largely unaffected. Analysis of the tRNA([Ser]Sec) population showed that expression of i(6)A(-) tRNA([Ser]Sec) altered the distribution of the two major isoforms, whereby the maturation of tRNA([Ser]Sec) by methylation of the nucleoside in the wobble position was repressed. The data suggest that the levels of i(6)A(-) tRNA([Ser]Sec) and wild-type tRNA([Ser]Sec) are regulated independently and that the amount of wild-type tRNA([Ser]Sec) is determined, at least in part, by a feedback mechanism governed by the level of the tRNA([Ser]Sec) population. This study marks the first example of transgenic mice engineered to contain functional tRNA transgenes and suggests that i(6)A(-) tRNA([Ser]Sec) transgenic mice will be useful in assessing the biological roles of selenoproteins.

Animals↗
PubMed2001

Metabolically efficient information processing.

Energy-efficient information transmission may be relevant to biological sensory signal processing as well as to low-power electronic devices. We explore its consequences in two different regimes. In an "immediate" regime, we argue that the information rate should be maximized subject to a power constraint, and in an "exploratory" regime, the transmission rate per power cost should be maximized. In the absence of noise, discrete inputs are optimally encoded into Boltzmann distributed output symbols. In the exploratory regime, the partition function of this distribution is numerically equal to 1. The structure of the optimal code is strongly affected by noise in the transmission channel. The Arimoto-Blahut algorithm, generalized for cost constraints, can be used to derive and interpret the distribution of symbols for optimal energy-efficient coding in the presence of noise. We outline the possibilities and problems in extending our results to information coding and transmission in neurobiological systems.

Action Potentials↗
PubMed2001

Gender moderates the effects of exercise therapy on health-related quality of life among COPD patients.

STUDY OBJECTIVES: To determine whether long-term treatment with exercise therapy results in more favorable, disease-specific, health-related quality of life (HRQL) compared with short-term treatment with exercise therapy; and to determine whether there are gender differences in disease-specific HRQL among individuals randomized into the two treatment groups. DESIGN: Randomized clinical trial. SETTING: Center-based exercise therapy unit at a university. PARTICIPANTS: One hundred forty patients with COPD; 118 completed trial. INTERVENTIONS: Short-term exercise therapy (3 months); long-term exercise therapy (18 months). MEASUREMENTS: Chronic Disease Respiratory Questionnaire (CRQ). RESULTS: After 3 months of treatment, there were significant improvements in all CRQ scores for men and women (p < 0.01), and for the total sample (p < 0.01). At 18 months, individuals randomized into the long-term group had significantly more favorable scores than the short-term group for dyspnea (p = 0.03), fatigue (p < 0.01), emotional function (p = 0.04), and mastery (p = 0.04). However, these effects were moderated by gender. That is, men in the long-term group reported significantly more favorable scores than men in the short-term group for dyspnea (0.04), fatigue (p < 0.001), emotional function (p = 0.02), and mastery (p = 0.02). At the 18-month assessment, there were no differences between long-term and short-term exercise therapy for women on any of the subscales of the CRQ. CONCLUSIONS: Taken collectively, the CRQ data demonstrate that long-term exercise therapy has little added benefit for women over short-term exercise therapy; however, men derive significant benefits from extended training.

Aged↗
PubMed2000

SECIS-SBP2 interactions dictate selenocysteine incorporation efficiency and selenoprotein hierarchy.

Selenocysteine incorporation at UGA codons requires cis-acting mRNA secondary structures and several specialized trans-acting factors. The latter include a selenocysteine-specific tRNA, an elongation factor specific for this tRNA and a SECIS-binding protein, SBP2, which recruits the elongation factor to the selenoprotein mRNA. Overexpression of selenoprotein mRNAs in transfected cells results in inefficient selenocysteine incorporation due to limitation of one or more of these factors. Using a transfection-based competition assay employing overexpression of selenoprotein mRNAs to compete for selenoprotein synthesis, we investigated the ability of the trans-acting factors to overcome competition and restore selenocysteine incorporation. We report that co-expression of SBP2 overcomes the limitation produced by selenoprotein mRNA overexpression, whereas selenocysteyl-tRNA and the selenocysteine-specific elongation factor do not. Competition studies indicate that once bound to SECIS elements, SBP2 does not readily exchange between them. Finally, we show that SBP2 preferentially stimulates incorporation directed by the seleno protein P and phospholipid hydroperoxide glutathione peroxidase SECIS elements over those of other selenoproteins. The mechanistic implications of these findings for the hierarchy of selenoprotein synthesis and nonsense-mediated decay are discussed.

Cell Line↗
PubMed2000

Structure-expression relationships of the 15-kDa selenoprotein gene. Possible role of the protein in cancer etiology.

Selenium has been implicated in cancer prevention, but the mechanism and possible involvement of selenoproteins in this process are not understood. To elucidate whether the 15-kDa selenoprotein may play a role in cancer etiology, the complete sequence of the human 15-kDa protein gene was determined, and various characteristics associated with expression of the protein were examined in normal and malignant cells and tissues. The 51-kilobase pair gene for the 15-kDa selenoprotein consisted of five exons and four introns and was localized on chromosome 1p31, a genetic locus commonly mutated or deleted in human cancers. Two stem-loop structures resembling selenocysteine insertion sequence elements were identified in the 3'-untranslated region of the gene, and only one of these was functional. Two alleles in the human 15-kDa protein gene were identified that differed by two single nucleotide polymorphic sites that occurred within the selenocysteine insertion sequence-like structures. These 3'-untranslated region polymorphisms resulted in changes in selenocysteine incorporation into protein and responded differently to selenium supplementation. Human and mouse 15-kDa selenoprotein genes manifested the highest level of expression in prostate, liver, kidney, testis, and brain, and the level of the selenoprotein was reduced substantially in a malignant prostate cell line and in hepatocarcinoma. The expression pattern of the 15-kDa protein in normal and malignant tissues, the occurrence of polymorphisms associated with protein expression, the role of selenium in differential regulation of polymorphisms, and the chromosomal location of the gene may be relevant to a role of this protein in cancer.

3' Untranslated Regions↗
PubMed2000

Inhibition of selenoprotein synthesis by selenocysteine tRNA[Ser]Sec lacking isopentenyladenosine.

A common posttranscriptional modification of tRNA is the isopentenylation of adenosine at position 37, creating isopentenyladenosine (i(6)A). The role of this modified nucleoside in protein synthesis of higher eukaryotes is not well understood. Selenocysteyl (Sec) tRNA (tRNA([Ser]Sec)) decodes specific UGA codons and contains i(6)A. To address the role of the modified nucleoside in this tRNA, we constructed a site-specific mutation, which eliminates the site of isopentenylation, in the Xenopus tRNA([Ser]Sec) gene. Transfection of the mutant tRNA([Ser]Sec) gene resulted in 80% and 95% reduction in the expression of co-transfected selenoprotein genes encoding type I and II iodothyronine deiodinases, respectively. A similar decrease in type I deiodinase synthesis was observed when transfected cells were treated with lovastatin, an inhibitor of the biosynthesis of the isopentenyl moiety. Neither co-transfection with the mutant tRNA gene nor lovastatin treatment reduced type I deiodinase mRNA levels. Also, mutant tRNA expression did not alter initiation of translation or degradation of the type I deiodinase protein. Furthermore, isopentenylation of tRNA([Ser]Sec) was not required for synthesis of Sec on the tRNA. We conclude that isopentenylation of tRNA([Ser]Sec) is required for efficient translational decoding of UGA and synthesis of selenoproteins.

Animals↗
PubMed2000

Selenoprotein P expression, purification, and immunochemical characterization.

Most selenoproteins contain a single selenocysteine residue per polypeptide chain, encoded by an in-frame UGA codon. Selenoprotein P is unique in that its mRNA encodes 10-12 selenocysteine residues, depending on species. In addition to the high number of selenocysteines, the protein is cysteine- and histidine-rich. The function of selenoprotein P has remained elusive, in part due to the inability to express the recombinant protein. This has been attributed to presumed inefficient translation through the selenocysteine/stop codons. Herein, we report for the first time the expression of recombinant rat selenoprotein P in a transiently transfected human epithelial kidney cell line, as well as the endogenously expressed protein from HepG2 and Chinese hamster ovary cells. The majority of the expressed protein migrates with the predicted 57-kDa size of full-length glycosylated selenoprotein P. Based on the histidine-rich nature of selenoprotein P, we have purified the recombinant and endogenously expressed proteins using nickel-agarose affinity chromatography. We show that the recombinant rat and endogenous human proteins react in Western blotting and immunoprecipitation assays with commercial anti-histidine antibodies. The ability to express, purify, and immunochemically detect the recombinant protein provides a foundation for investigating the functions and efficiency of expression of this intriguing protein.

Animals↗
PubMed2000

The influence of speed, grade and mass during simulated off road bicycling.

The purpose of this investigation was to examine the effects of bicycle mass, speed, and grade on oxygen consumption (VO2), heart rate (HR), and ratings of perceived exertion (RPE) during a simulated off-road riding paradigm. Nine adult subjects with mean +/- SD age, mass, and VO2 max of 26.1 +/- 5.6 years, 71.7 +/- 7.5 kg, 56.6 +/- 5.2 ml x kg(-1) x min(-1) respectively, were trained to ride a fully suspended Trek Y-22 mountain bike on a treadmill with a 3.8 cm bump affixed to the belt. Riders completed a maximum of nine separate trials encompassing three different bike masses (11.6, 12.6 and 13.6 kg), 3 speeds (2.7, 3.6 and 4.5 m x s(-1)), and 3 grades (0, 2.5, and 5%). Throughout a trial, bike mass and speed remained constant while riding grade was increased every 5 min. During simulated off-road riding on a fully suspended mountain bike, increases in speed and grade significantly increased VO2, heart rate, and RPE. Increases in bike mass had no significant effects on VO2, heart rate or RPE. In addition, speed and grade changes interacted to differentially affect VO2, heart rate, and RPE at all speeds and grades.

Adult↗
PubMed2000

Expression and characterization of nonmammalian selenoprotein P in the zebrafish, Danio rerio.

BACKGROUND: Selenoprotein P is a protein of considerable intrigue, due to its unusual composition and requirements for its biosynthesis. Whereas most selenoproteins contain a single selenocysteine residue, the human, bovine and rodent selenoprotein P genes encode proteins containing 10-12 selenocysteines. Selenoprotein P genes have, to date, only been reported in mammals, and the function of the protein remains elusive. RESULTS: Herein, we report the identification and characterization of nonmammalian selenoprotein P in the zebrafish Danio rerio. Sequencing of the cDNA revealed the presence of 17 selenocysteine codons, the highest number reported in any protein. Two histidine-rich regions present in the mammalian selenoprotein P sequences are conserved in the zebrafish protein, and two SECIS elements are present in the 3' untranslated region. Whole-mount in situ hybridization of zebrafish embryos revealed high levels of expression of selenoprotein P mRNA in fertilized eggs and in the yolk sac of developing embryos. Transient transfection of the cDNA in mammalian cells resulted in efficient expression of the full-length secreted selenoprotein. A single N-glycosylation site is predicted, and shown to be utilized. CONCLUSIONS: Discovery of selenoprotein P in the zebrafish opens a previously unavailable avenue for genetic investigation of the functions of this unusual protein.

Amino Acid Sequence↗
PubMed2000

Decoding apparatus for eukaryotic selenocysteine insertion.

Decoding UGA as selenocysteine requires a unique tRNA, a specialized elongation factor, and specific secondary structures in the mRNA, termed SECIS elements. Eukaryotic SECIS elements are found in the 3' untranslated region of selenoprotein mRNAs while those in prokaryotes occur immediately downstream of UGA. Consequently, a single eukaryotic SECIS element can serve multiple UGA codons, whereas prokaryotic SECIS elements only function for the adjacent UGA, suggesting distinct mechanisms for recoding in the two kingdoms. We have identified and characterized the first eukaryotic selenocysteyl-tRNA-specific elongation factor. This factor forms a complex with mammalian SECIS binding protein 2, and these two components function together in selenocysteine incorporation in mammalian cells. Expression of the two functional domains of the bacterial elongation factor-SECIS binding protein as two separate proteins in eukaryotes suggests a mechanism for rapid exchange of charged for uncharged selenocysteyl-tRNA-elongation factor complex, allowing a single SECIS element to serve multiple UGA codons.

3' Untranslated Regions↗
PubMed2000

The relationship between %HRpeak and %VO2peak in patients with chronic obstructive pulmonary disease.

PURPOSE: The relationship between the percent peak oxygen consumption (%VO2peak) and percent peak heart rate (%HRpeak) has been suggested as a method for exercise prescription. According to the American College of Sports Medicine (ACSM), 50, 60, 80, and 85% of VO2peak represent 62, 70, 85, and 90% of HRpeak, respectively. Recent research with young healthy adults has shown that this relationship is not as ACSM suggests. Furthermore, it has been suggested that this relationship be examined in populations with low functional capacity. METHODS: The present study evaluated the relationship between %HRpeak and %VO2peak in 125 patients with chronic obstructive pulmonary disease before and then after 3 months of exercise intervention. RESULTS: The mean percentages of HRpeak for the COPD patients at baseline were 70, 76, 87, and 90% at 50, 60, 80, and 85% of VO2peak. Percentages of HRpeak at 50, 60, and 80% of VO2peak were significantly different from those suggested by ACSM. The mean percentages of HRpeak after the 3-month exercise intervention were 71, 77, 87, and 90% at 50, 60, 80, and 85% of VO2peak. Percentages of HRpeak at 50, 60, and 80% of VO2peak were significantly different from those suggested by ACSM. There were no significant differences between the slopes and the intercepts of the two equations used to describe the relationship between %HRpeak and %VO2peak. Therefore, we pooled the data from the pre- and post-intervention tests to form the following equation to describe the relationship between %HRpeak and %VO2peak for COPD patients: %HRpeak = 0.55 (+/- 0.01)%VO2peak + 43.2 (+/- 1.4). CONCLUSION: In conclusion, the relationship between %HRpeak and %VO2peak described by ACSM is not applicable to patients with COPD. Furthermore, this relationship does not change with exercise training and can be described by a single equation.

Aged↗
PubMed2000

Cost-effectiveness analysis methods for the REACT Study.

The Reconditioning Exercise and Chronic Obstructive Pulmonary Disease Trial (REACT) is a two-arm randomized clinical trial designed to compare short-term versus long-term exercise intervention in terms of physical function, acute exacerbation of chronic obstructive pulmonary disease, health-related quality of life, and cost-effectiveness. Clinical trials such as REACT are now routinely paired with economic analyses, and nurses can expect to play a growing role in the conduct of these studies. This article describes a model that is useful for structuring economic evaluations of health care interventions, and illustrates a cost-effectiveness analysis that is being conducted in conjunction with the REACT study. An in-depth description of collection methods and procedures is provided, as well as a summary of recruitment and retention experience to date.

Aged↗