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At least 235 records · Page 13Linked to original sources
PubMed2006

Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes.

BACKGROUND: The duration of treatment for HCV infection is partly indicated by the genotype of the virus. For studies of disease transmission, vaccine design, and surveillance for novel variants, subtype-level classification is also needed. This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions. RESULTS: Different regions of the HCV genome yield inconsistent phylogenies, which can lead to erroneous conclusions about classification of a given infection. In particular, the highly conserved 5' untranslated region (UTR) yields phylogenetic trees with topologies that differ from the HCV polyprotein and complete genome phylogenies. Phylogenetic trees from the NS5B gene reliably cluster related subtypes, and yield topologies consistent with those of the whole genome and polyprotein. CONCLUSION: These results extend those from previous studies and indicate that, unlike the NS5B gene, the 5' UTR contains insufficient variation to resolve HCV classifications to the level of viral subtype, and fails to distinguish genotypes reliably. Use of the 5' UTR for clinical tests to characterize HCV infection should be replaced by a subtype-informative test.

5' Untranslated Regions↗
PubMed1985

Refining personality assessments by combining MCMI high point profiles and MMPI codes, Part I: MMPI code 28/82.

In this study it has been shown that the addition of MCMI high-point code types to the MMPI 28/82 code type clarifies contradictory MMPI descriptors and locates three distinct clinical clusters. These MMPI/MCMI clusters were defined as an interpersonally acting-in group, an emotionally acting-out group and an emotionally acting-in group to describe the levels on which they characteristically operate. The results of this study lend support to the utility of combining two objective assessment instruments for the purposes of identifying and discriminating subtleties among relevant personality disorders (DSM-III: Axis II) and clinical syndromes (DSM-III: Axis I).

Acting Out↗
PubMed1985

Refining personality assessments by combining MCMI high point profiles and MCMI codes. Part III. MMPI code 24/42.

In this study it has been shown that the addition of MCMI high point code data to the MMPI 24/42 code type serves to clarify contradictory MMPI descriptors and produces three distinct clusters. These MMPI/MCMI clusters comprise an interpersonally acting-out group, an interpersonally acting-in group, and an emotionally acting-out group. These groups were useful in determining different roles for the MMPI 2 and 4 scales insofar as they relate to both personality (Axis II) and its clinical consequences (Axis I). The results of this study also lend support to the utility of combining objective assessment instruments both for identifying and for discriminating among relevant personality disorders and clinical syndromes.

Adult↗
PubMed1987

Refining personality assessments by combining MCMI high-point profiles and MMPI codes, Part V: MMPI code 78/87.

The present investigation shows that the addition of Millon Clinical Multiaxial Inventory (MCMI) high-point code data to the Minnesota Multiphasic Personality Inventory (MMPI) 78/87 code type may be used to clarify contradictory MMPI descriptors and produces three distinct clusters. These MMPI/MCMI clusters were designated as an interpersonally acting-in group, an emotionally acting-out group, and an emotionally acting-in group. In addition to the identification and elaboration of these three subgroups, we outline several clinical uses of this objective test battery approach. The results of this study support the efficacy of combining two objective assessment inventories for the purpose of multiaxial diagnosis as prescribed by the DSM-III.

Acting Out↗
PubMed2005

The Da Vinci code dynamically de-coded.

The novel The Da Vinci Code, by Dan Brown has been on best-seller lists for over two years. An examination of Brown's previous novels reveals a well-designed plot line shared by all four novels that not only makes them good "thrillers" but also creates a mythological structure to the novels that draws on common unconscious fantasies in the same way that fairy tales do. One aspect of this mythological structure is the use of evil conspiracies (and benign ones as well) for the protagonist to overcome. In addition, The Da Vinci Code presents a religious theme involving legends about Mary Magdalene. This theme touches on the role of a feminine aspect to divinity in allowing for an erotic connection with the divine.

Humans↗
PubMed1992

Ethical codes and the health professions: looking at the ACHCA code.

Codes play an important role in both the development of professions as well as provide ethical guidance for their members. They should be recognized as an aggregate "best" effort to define the moral expectations and boundaries of professional behavior and practice. In addition, they cannot and should not be viewed as a means of policing professional standards given their lack of formal legal backing. Finally, they should be amended as needed. With respect to the ACHCA Code, while not attempting to be overly specific and allowing for reasonable professional interpretation, it is well designed and addresses most of the major attributes found in such formal statements. Coupled with parallel documents addressing "standards of practice" and a more detailed listing of "patients rights," long-term care professionals should be prepared to meet most of the difficult professional challenges facing them.

Ethics, Professional↗
PubMed1992

DNA methylation of coding and non-coding regions of the human H-RAS gene in normal and tumor tissues.

To study a possible role of DNA methylation in the regulation of expression of the human H-RAS gene in vivo, 41 samples of different normal tissues and 33 tumors of various histotypes were analysed for DNA methylation. In a subset of normal tissues the RNA expression was also examined. The promoter region of the gene showed the features of a CpG island being CpG rich and unmethylated in all the normal tissues and tumors. The coding region displayed an intermediate level of methylation in the majority of normal and tumor tissues. Among the normal tissues only thymus DNA was found to be hypermethylated, while testes and sperm cells DNAs were hypomethylated. The 3' region was found to be completely methylated only in sperm cells and was never completely demethylated. The majority of the tissues showed an intermediate level of methylation, and a certain tissue specificity emerged by comparing tissues of the same and different histotypes. However, the overall methylation of both coding and 3' regions did not correlate with the levels of tissue-specific RNA expression. In heterozygous individuals, allelic methylation of the 3' region showed either perfectly balanced or slightly unbalanced methylation of the two alleles in normal tissues, while an allele-specific methylation was found in 5 out of 12 fresh tumor samples.

Alleles↗
PubMed1991

Medical ethics reflected in codes of ethics: the Hippocratic Oath and the 1980 AMA code compared.

The Hippocratic Oath and 1980 Code of Ethics of the American Medical Association (AMA) are compared to evaluate the nature of the relationship between students and teachers of medicine and the ethical injunctions that guide practice and make up the essence of the Hippocratic Oath. Such injunctions include the need to take care that harm is not done, to maintain confidentiality, and to avoid acts leading to death. The AMA code is analyzed from the perspective of its injunctions to give competent and compassionate care, to follow the law, to be responsible for guarding patients against incompetent physicians, and to assure that patient care is based on principles of compassion and skill. The centrality of trust in the relationship between patient and doctor as a crucial value in defining a profession is emphasized.

American Medical Association↗
PubMed1995

c-fos mRNA instability determinants present within both the coding and the 3' non coding region link the degradation of this mRNA to its translation.

The instability of oncogenic mRNA such as c-fos mRNA is controlled in cis by sequences present in both the coding and the 3' untranslated regions (3'UTR). The latter contains AU-rich elements (ARE) which, depending on the cellular context, mediate either their rapid degradation or inhibit their translation. These observations, along with the known increase of the life spans of many unstable mRNA promoted by inhibitors of protein synthesis, raise the possibility that both processes are linked. To investigate further the putative involvement of translation in both coding region and ARE-mediated rapid decay of c-fos mRNA, we designed an expression vector based on the use of the ferritin mRNA iron regulatory element (IRE). The latter structure links translation to intracellular iron concentration when inserted at the proper location within the 5'UTR. Rapid degradation of a beta-globin/c-fos 3'UTR construct was prevented by Desferrioxamine, an iron chelator, and facilitated by ferric ammonium citrate or hemin, while stability of other mRNAs not containing the IRE or the ARE were unchanged. The same conclusion was reached when the stability of a c-fos mRNA devoid of ARE was assessed in function of iron availability.

Adenine↗
PubMed1976

[Visual processing of 12,000 electrocardiograms according to the USPHS code and comparison of visual and automatic processing of about 6,000 electrocardiograms in accordance with the USPHS code].

Multistage screening in Hesse (W. Germany) and the visual processing of about 12,000 ECG's in accordance with the USPHS (Riedel programme) are reported. A good fit was found with data obtained from a similar study in another part of the country. Comparison is then made with the visual and computerised processing of about 6,000 ECG's in accordance with the same code, using four classes: "normal", "conditionally within the limits of normal", "suspect" and "definitely pathological". The encouraging result on comparison between "normal" and "pathological" in the 6.3% consisting of false negatives (only 2.1% definitely pathological) suggests that "normal" and "conditionally normal" ratings by the computer can be accepted, whereas considerable possibilities for cardiological diagnosis would remain in the case of pathological traces, which would always be accepted, where as considerable possibilities recognised standards set down by the USPHS code are considered reliable. They can be used under hospital or screening conditions. On the other hand, the "scale of values" programme offered as a model requires further checking. Notes on future development are also offered.

Coronary Disease↗
PubMed1996

The efficacy of SNOMED, Read Codes, and UMLS in coding ambulatory family practice clinical records.

This study was initially developed as a traditional quantitative study to determine the level of match of identified clinical terms in three (3) clinical vocabularies. To address concerns raised by a review of the literature and our own experience, a supplemental study to collect qualitative data was added. Dictated progress notes from a stratified sample of patient visits over a period of four (4) years were used to obtain a representative sample of terms. A total of 144 progress notes were selected taking into consideration the usual demographics plus additional variables. From the 144 clinical notes, 864 terms were extracted and evaluated by level of match. The within-term effect was highly significant (F = 58.69, p < or = .001), indicating significant differences in the mean level of match for the three coding systems. Qualitative findings suggest that this and other published studies may not answer questions about the "efficacy of available clinical vocabularies in coding ambulatory family practice clinical records", and additional studies are needed which must be carefully structured and utilize a standardized procedure.

Family Practice↗
PubMed2005

Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes.

The localization of RNA within a cell or embryo is crucial for proper cellular function or development. There is evidence that the cytoskeleton and RNA may function in the anchoring of localized RNAs at the vegetal cortex of Xenopus laevis oocytes. We found that the organization of the cytokeratin filaments but not the actin cytoskeleton depends on the presence of intact VegT mRNA and a noncoding RNA, Xlsirts. Destruction of either of these transcripts results in disruption of the cytokeratin cytoskeleton in a transcript-specific manner and interferes with proper formation of the germinal granules and subsequent development of the germline. Analysis of the distribution of endogenous VegT and Xlsirts in live oocytes using molecular beacons showed that these RNAs are integrated into the cytokeratin cytoskeleton. These results demonstrate a novel structural role of coding and noncoding RNAs in the organization of the vegetal cortex of Xenopus oocytes.

Actins↗
PubMed2004

Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs.

The largest transcriptome reported so far comprises 60,770 mouse full-length cDNA clones, and is an effective reference data set for comparative transcriptomics. The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. This is largely because of extensive alternative splicing and the presence of many non-coding RNAs (ncRNAs), which are difficult to predict from genomic sequences. Notably, ncRNAs are a major component of the transcriptomes of higher organisms, and many sense-antisense pairs have been identified. The ncRNAs function in a range of regulatory mechanisms for gene expression and other biological processes. They might also have contributed to the increased functional diversification of genomes during evolution. In this review, we discuss aspects of the transcriptome of various organisms in relation to the mouse data, in order to shed light on the regulatory mechanisms and physiological significance of these abundant RNAs.

Alternative Splicing↗
PubMed2007

The end1 gene of Schizosaccharomyces pombe coding for a DNase is identical with the pnu1 gene coding for an RNase.

The DNA nuclease activity encoded by the end1 gene, and its inactivation by mutation, was described in connection with the characterization of DNA topoisomerases in the fission yeast Schizosaccharomyces pombe (Uemura and Yanagida, 1984). Subsequently, end1 mutant strains were used for the preparation of cell extracts for the study of enzymes and intermediates involved in DNA metabolism. The molecular identification of the end1 gene and its identity with the pnu1 gene is presented. The end1-458 mutation alters glycine to glutamate in the conserved motif TGPYLP. The pnu1 gene codes for an RNase that is induced by nitrogen starvation (Nakashima et al., 2002b). Thus, the End1/Pnu1 protein, like related mitochondrial proteins in other organisms, is an example of a sugar-non-specific nuclease. The analysis of strains carrying a pnu1 deletion revealed no defects in meiotic recombination and spore viability.

Amino Acid Sequence↗
PubMed1994

The nucleotide sequence of the 5'non-coding and capsid coding genome regions of two bovine enterovirus strains.

The sequence of cDNA clones representing the 5' non-coding regions (NCR) and capsid regions of two bovine enteroviruses (strains PS-87 and RM-2; serotype two viruses) have been determined and compared with that obtained from a serotype one strain (VG-5-27). All three strains showed a longer 5' NCR compared to human enteroviruses and rhinoviruses due in part to a hundred residue insertion approximately at a hundred residues in from the 5' end. However, another domain occurring at nucleotide 187-222 in poliovirus is absent in each bovine enterovirus. Comparisons of the predicted structural protein amino acid sequences indicate that PS-87 shares most sequence identity with RM-2 and then with VG-5-27 in that order. The VP1 protein of PS-87 and RM-2 are shorter than the equivalent VP1 of VG-5-27 due in part to a truncation at their C-terminii. VP3 is only slightly smaller than VP2 in each virus.

Amino Acid Sequence↗
PubMed2006

Rate code and temporal code for frequency of whisker stimulation in rat primary and secondary somatic sensory cortex.

We recorded responses to frequencies of whisker stimulation from 479 neurons in primary (S1) and secondary (S2) somatic sensory cortex of 26 urethane-anesthetized rats. Five whiskers on the right side of the snout were deflected with air puffs at seven frequencies between 1 and 18/s. In left S1 (barrels and septa) and S2, subsets of neurons (5%) responded to whisker stimulation across the entire range of frequencies with > or = 1 electrical discharges/ten stimuli (full responders). In contrast, 60% of the recorded cells responded above threshold only at stimulus frequencies below 6/s and 35% remained subthreshold at all frequencies tested. Thus, the full responders are unique in that they were always responsive and appeared particularly suited to facilitate a dynamic, broadband processing of stimulus frequency. Full responders were most responsive at 1 stimulus/s, and showed greatest synchrony with whisker motion at 18 stimuli/s. The barrel cells responded with the greatest temporal accuracy between 3 and 15 stimuli/s. The septum cells responded less accurately, but maintained their accuracy at all frequencies. Only septum cells continued to increase their discharge rate with increasing stimulus frequency. The S2 cells discharged with lowest temporal accuracy modulated only by stimulus frequencies < or = 6/s and exhibited the steepest decrease in discharge/stimulus with increasing stimulus frequency. Our observations suggest that full responders in the septa are well suited to encode high frequencies of whisker stimulation in timing and rate of discharge. The barrel cells, in contrast, showed the strongest temporal coding at stimulus frequencies in the middle range, and S2 cells were most sensitive to differences in low frequencies. The ubiquitous decline in discharge/stimulus in S1 and S2 may explain the decrease in blood flow observed at increasing stimulus frequency with functional imaging.

Action Potentials↗
PubMed2005

Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.

In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG1 only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5' HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together.

Animals↗