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PubMedDate not supplied

Pragmatic principles--methodological pragmatism in the principle-based approach to bioethics.

In this paper it will be argued that Beauchamp and Childress' principle-based approach to bioethics has strongly pragmatic features. Drawing on the writings of William James, I first develop an understanding of methodological pragmatism as a method of justification. On the basis of Beauchamp's and Childress' most recent proposals concerning moral justification in the fifth edition of their Principles of Biomedical Ethics (2001), I then discuss different aspects that the principle-based approach and methodological pragmatism have in common.

Bioethics↗
PubMed1999

A cis-acting A-U sequence element induces kinetoplastid U-insertions.

A 34-nucleotide A-U sequence located immediately upstream of the editing sites of the Leishmania tarentolae cytochrome b mRNA induces a mitochondrial extract to insert U nucleotides independent of guide RNA. Insertions are localized to positions immediately 5' and 3' of the A-U sequence. When placed within an unedited mammalian transcript, the A-U sequence is sufficient to induce U-insertions. The sequence has a high degree of similarity with the templating nucleotides of a cytochrome b guide RNA and with a sequence adjacent to the editing sites in ND7 mRNA, the other characterized kinetoplastid mRNA supporting guide RNA-independent U-insertions. At least one protein specifically interacts with the A-U sequence. The reaction is consistent with a mechanism proposed for guide RNA-directed editing.

Animals↗
PubMed2003

The principles of writing the medical guide for ships.

The medical training and skills of seafarers are rather limited. In Finland, the master is responsible for medical care of his crew members, having only a 5-day training in medical matters which is refreshed every year. As medical incidents are rather rare events on board ship, he has not many opportunities to increase his knowledge in this field. Highly educated and experienced medical doctors have written medical guides for ships, describing diseases and advising on their treatment. This advice is based on diagnoses made on board ship by masters. They are often incorrect, therefore the advice on treatment may also be not correct. Authors of medical guides for ships should take into consideration the limited skills and medical knowledge of persons responsible for providing health services for crews at sea. This service is usually limited to giving first aid in accidents and sudden diseases, and care of the injured or sick seafarer until he can be transported to a medical facility on shore. Long lists of possible diagnoses in the text of such a guide only cause confusion in situations on board ship. In the new edition of the guide published in Finland in 2002, the advice on treatment is based on symptoms rather than on diagnoses.

Emergency Medicine↗
PubMed1995

RNA editing. An I for editing.

In vitro editing in mammalian nuclear extracts reveals adenosine-to-inosine conversions in glutamate receptor messenger RNAs.

Adenosine Deaminase↗
PubMed2004

Genetic dissection of lupus pathogenesis: Sle3/5 impacts IgH CDR3 sequences, somatic mutations, and receptor editing.

Sle3/5 is a lupus susceptibility locus identified on mouse chromosome 7 of the New Zealand Black/New Zealand White (NZB/NZW)-derived NZM2410 strain. Based on previous observations, this locus appears to contribute to lupus pathogenesis through its impact on diversification of immune responses. To understand how Sle3/5 affects somatic diversification of humoral responses, we analyzed IgH rearrangements preferentially encoding hapten-reactive IgG1 repertoires after immunization and assessed peripheral IgH VDJ recombination activities in C57BL/6 (B6) mice congenic for Sle3/5 (B6.Sle3/5). In addition to altered somatic V(H) mutation profiles, sequences from B6.Sle3/5 mice exhibited atypical IgH CDR3 structures characteristic of autoreactive B cells and consistent with peripheral B cells bearing putatively edited receptors. Significant expression of Rag genes and circular V(H)D gene excision products were detected in splenic mature B cells of B6.Sle3/5 but not B6 mice, showing that peripheral IgH rearrangements occurred beyond allelic exclusion. Taken together, on the nonautoimmune background, Sle3/5 affected V(H)DJ(H) junctional diversity and V(H) mutational diversity and led to recombinational activation of allelically excluded IgH genes in the periphery. Such impact on somatic IgH diversification may contribute to the development of autoreactive B cell repertoires. This is the first report to present evidence for significant association of a lupus susceptibility locus, which has been mapped to a chromosomal region in which no Ig genes have been identified, with somatic IgH sequence diversity and peripheral H chain receptor editing or revision without relying upon Ig transgene strategies.

Animals↗
PubMed2025

Cellular Inflammation-Induced Cleavage of Phosphorothioate DNA Locker Activates CRISPR/Cas9 Regulator for Gene Editing.

The CRISPR technology is a highly promising strategy for developing a versatile toolbox to engineer genetic circuits. However, achieving precise and specific control over the activity of the CRISPR/Cas9 system in response to intracellular processes remains a challenging endeavor. In this study, we present a cellular inflammation-induced activation of an engineered CRISPR/Cas9 regulator for gene regulation. A phosphorothioate (PS)-modified DNA sequence, referred as the "locker," is employed to deactivate single guide RNA (sgRNA), whose locker sequence complements the spacer region of sgRNA. In the presence of myeloperoxidase during cellular inflammation, a halogenation process is triggered, leading to the generation of HClO, specifically cleaving the PS site of locker and activating CRISPR/Cas9 for gene editing. The target GFP gene has been successfully edited, downregulating the GFP protein expression in HeLa cells. This study provides valuable insights into the CRISPR-based gene regulation through specific endogenous processes.

Humans↗
PubMed1992

Mitochondrial rps14 is a transcribed and edited pseudogene in Arabidopsis thaliana.

We have isolated and analysed a 2 kb region of the mitochondrial genome of Arabidopsis thaliana (Columbia) showing a high level of nucleotide identity with the mitochondrial (mt) rps14 small-subunit ribosomal protein gene from Oenothera berteriana and Vicia faba, as well as with an open reading frame (ORF) located upstream of the nad3 locus in O. berteriana. The rps14 locus is present as a single copy in the A. thaliana mt genome and has a translational stop codon located near the initiation codon, as well as a deletion of one nucleotide that disturbs the coding sequence. The cloning and sequencing of nine amplified mt rps14 cDNAs clearly demonstrated that this gene is transcribed and that the mRNA precursors are edited at three positions, all involving C-to-U conversions. No editing events changing the stop codon and restoring the correct coding sequence were witnessed within the 9 individual cDNA clones. Therefore, we conclude that the single rps14 sequence of the mitochondrial genome from A. thaliana is in fact a pseudogene that is transcribed and edited but not translated.

Amino Acid Sequence↗
PubMed1994

The apolipoprotein B messenger RNA editing enzyme.

The editing of apolipoprotein (apo)B messenger RNA (mRNA) involves a novel C to U modification, which creates an in-frame stop-translation codon, thereby generating the carboxyl-terminal of apoB48. The 27 kDa catalytic subunit of the editing enzyme has been cloned and established to be a zinc-containing cytidine deaminase. The catalytic subunit is guided to the editing site by a second targeting subunit or subunits. A candidate for the targeting subunit is a 60 kDa protein that can be UV crosslinked to the sequence UGAU, which is part of a motif downstream of the editing site that is essential for editing.

Amino Acid Sequence↗
PubMed1992

Uses of statistical editing of real-time ambulatory electrocardiographic recordings for quantitative ventricular ectopic beat counts.

Real-time ambulatory monitoring analyzes each heart beat, counts events, and stores ECG samples for later visual verification. Typically, a physician examines these to determine whether the computer algorithm accurately identified arrhythmias. Physician editing is performed using best clinical judgement. We developed a simple statistical editing procedure for adjusting false positive and false negative computer detections. In 20 subjects having 24-hr monitoring we compared statistically edited ventricular premature beat (VPB) counts and pair/run counts with the unedited monitor counts and with physician assessment using a visual counted gold standard. The agreement of the statistically edited count with the visual standard was 65% for total VPB, 85% for VPB pair/runs, and 90% for a risk score based on ventricular ectopy. Corresponding agreements for unedited monitor count were 15, 25, and 30%, respectively. Physician assessment was not sufficiently precise to allow quantitative count estimates. This study indicates a statistical editing procedure substantially increases the level of agreement between the visual standard and the monitor count of VPB frequency and complexity. Statistically edited data are suitable for quantitative counts of VPB and other arrhythmic events in research and in medical diagnosis and treatment. This editing procedure can be a useful adjunct to any ambulatory monitoring system.

Arrhythmias, Cardiac↗
PubMed1992

Three distinct RNA sequence elements are required for efficient apolipoprotein B (apoB) RNA editing in vitro.

Apolipoprotein B (apoB) mRNA is edited in rat liver and intestine to convert a CAA glutamine codon to a UAA translational stop codon by the direct conversion of cytidine to uridine at nucleotide 6666. We have proposed the 'mooring sequence' model for apoB RNA editing, in which editing complexes (editosomes) assemble on specific apoB mRNA flanking sequences to direct this site-specific editing event. One sequence element (approx. nts 6671-81, the presumed 'mooring sequence') has been previously identified as necessary for editing. We have identified two additional sequence elements which are necessary for efficient editing: (1) a 5' 'Regulator' region which modulates editing efficiency and (2) a 'Spacer' region between the editing site and the 3' mooring sequence, whose distance is critical for efficient editing. Utilizing this data, we have induced editing at a cryptic site and have defined a 22 nucleotide 'cassette' of specific apoB sequence which is sufficient to support wild-type levels of editing in vitro in a background of distal apoB RNA sequence.

Animals↗
PubMed1994

The glucose transporter of Escherichia coli. Overexpression, purification, and characterization of functional domains.

The glucose transporter of the bacterial phosphotransferase system couples vectorial translocation to phosphorylation of the transported sugar. It consists of a transmembrane subunit (IICBGlc) and a hydrophilic subunit (IIAGlc). The IICBGlc subunit consists of two domains. The NH2-terminal IIC domain (residues 1-386) spans the membrane eight times and contains the substrate binding site. The COOH-terminal hydrophilic IIB domain (residues 391-476) is accessible from the cytoplasmic side of the membrane. It contains the phosphorylation site (Cys421) and together with the IIC domain catalyzes the transfer of phosphoryl groups from the IIAGlc subunit to the transported solute. Starting from a plasmid vector containing ptsG under an inducible promoter, the IIB and the IIC domains have been subcloned separately, overexpressed in Escherichia coli, and purified by Ni2+ chelate affinity chromatography. Approximately 40 mg of IIBGlc-6H and 4 mg of IICGlc-6H could be purified from 1 liter of culture. Cells expressing IIBGlc-6H and IICGlc-6H separately have a three times longer generation time on glucose minimal medium than cells expressing wild-type IICBGlc. The rate of IIBGlc-6H phosphorylation determined in a nitrocellulose filter binding assay is indistinguishable from wild-type IICBGlc. The in vitro specific activity of IICGlc-6H in the presence of excess IIBGlc-6H is 2% of the control. IIBGlc-6H also complements the activity of a IICBGlc mutant with an inactive IIB domain (C421S) indicating that IIC and IIB are flexibly linked such that a free IIB domain can displace an inactive IIB domain from its contact site on the IIC domain. Based on this work, the secondary structure of the IIBGlc domain has been determined by isotope-edited NMR spectroscopy (Golic Grdadolnik, S., Eberstadt, M., Gemmecker, G., Kessler, H., Buhr, A., and Erni, B. (1994) Eur. J. Biochem. 219, 945-952).

Amino Acid Sequence↗
PubMed2004

The Child Report Form of the CHIP-Child Edition: reliability and validity.

BACKGROUND: There is increasing recognition of the importance of obtaining children's reports of their health, but significant challenges must be overcome to do so in a systematic, population-based manner. OBJECTIVE: The objective of this study was to present the initial tests of the Child Report Form of the Child Health and Illness Profile-Child Edition (CHIP-CE/CRF), a self-report health status instrument for children 6 to 11 years old. METHODS: Three studies iteratively evaluated revisions of the CHIP-CE/CRF in 4 geographic locations in the United States. Children (N=1708) whose families represent the low to middle socioeconomic strata and predominant U.S. racial/ethnic groups were involved. RESULTS: The final CHIP-CE/CRF includes 5 domains: Satisfaction (with self and health), Comfort (emotional and physical symptoms and limitations), Resilience (positive activities that promote health), Risk Avoidance (risky behaviors that influence future health), and Achievement (of social expectations in school and with peers). The internal consistency and test-retest reliability of the domains are good to excellent, with a definite age gradient such that younger children's responses are less reliable although still acceptable. Validity is supported through criterion and construct validity tests and structural analyses. Standard scores (mean, 50; standard deviation, 10) were established. CONCLUSIONS: Health status can be reliably and validly assessed directly from children 6 to 11 years old on the CHIP-CE/CRF. In combination with the CHIP-AE, self-reported health status can now be obtained from youth 6 to 18 years old using a consistent conceptual framework. This can greatly improve the precision and comparability of health assessments of youth, enhancing the validity of outcome research and longitudinal studies across childhood and adolescence.

Adaptation, Psychological↗
PubMed1992

[Reliability of bronchial tumor typing base on fibroscopically obtained biopsies].

This study is based on the bronchial tumors biopsied and later examined between 1971 and 1986 at the Institute of Pathology, Lausanne. In each case the diagnosis based on the initial biopsy material is compared with the final surgical or autopsy diagnosis (Reference: Histological typing of lung tumours, second edition, WHO, 1981, 2). The series studied is constituted by 163 cases: 144 men (88.3%) and 19 women (11.7%). In 136 cases (83.4%), the biopsy diagnoses are identical to the diagnoses based upon surgical or autopsy material; in 27 cases (16.6%) these diagnoses differ. The positive predictive value of bronchial biopsy appears to be excellent (100%) for small cell and epidermoid carcinoma (CA). It is satisfactory for adenocarcinoma (85.7%) but insufficient for large cell CA (42.3%) and the tumors grouped under "others" (50%). The diagnosis of large cell CA, in situ CA, papillary tumor, undifferentiated CA, or carcinomatous lymphangitis should be considered with caution and in some cases it is advisable to repeat the biopsy. The discrepancies between the initial and final diagnoses can, in all cases, be attributed either to the biopsy specimen being too small and therefore nonrepresentative or, less frequently, to crushing and necrosis of the tissues.

Autopsy↗
PubMed2006

RNA editing and alternative splicing: the importance of co-transcriptional coordination.

The carboxy-terminal domain (CTD) of the large subunit of RNA polymerase II (pol II) is essential for several co-transcriptional pre-messenger RNA processing events, including capping, 3'-end processing and splicing. We investigated the role of the CTD of RNA pol II in the coordination of A to I editing and splicing of the ADAR2 (ADAR: adenosine deaminases that act on RNA) pre-mRNA. The auto-editing of Adar2 intron 4 by the ADAR2 adenosine deaminase is tightly coupled to splicing, as the modification of the dinucleotide AA to AI creates a new 3' splice site. Unlike other introns, the CTD is not required for efficient splicing of intron 4 at either the normal 3' splice site or the alternative site created by editing. However, the CTD is required for efficient co-transcriptional auto-editing of ADAR2 intron 4. Our results implicate the CTD in site-selective RNA editing by ADAR2 and in coordination of editing with alternative splicing.

Adenosine Deaminase↗
PubMed2003

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle.

The further understanding of the mechanisms of gene regulatory networks requires comprehensive tools for both the representation of complicated signal transduction pathways and the in silico identification of genomic signals that govern the regulation of gene expression. Consequently, sophisticated notation must be developed to represent the signal transduction pathways in a form that can be readily processed by both computers and humans. We propose the regulator-reaction equations combined with detailed attributes including the associated cellular component, molecular function, and biological process and present the simulation-directed graphical notation that is derived from modification of Kohn's method. We have developed the software suite, CADLIVE (Computer-Aided Design of LIVing systEms), which features a graphical user interface (GUI) to edit large-scale maps of complicated signal transduction pathways using a conventional XML-based representation. The regulator-reaction equations represent not only mechanistic reactions, but also semantic models containing ambiguous and incomplete processes. In order to demonstrate the feasibility of CADLIVE, we constructed a detailed map of the budding yeast cell cycle, which consists of 184 molecules and 152 reactions, in a really compact space. CADLIVE enables one to look at the whole view of a large-scale map, to integrate postgenomic data into the map, and to computationally simulate the signal transduction pathways, which greatly facilitates exploring novel or unexpected interactions.

Cell Cycle↗
PubMed2005

How well do clinic-based blood pressure measurements agree with the mercury standard?

BACKGROUND: Obtaining accurate blood pressure (BP) readings is a challenge faced by health professionals. Clinical trials implement strict protocols, whereas clinical practices and studies that assess quality of care utilize a less rigorous protocol for BP measurement. OBJECTIVE: To examine agreement between real-time clinic-based assessment of BP and the standard mercury assessment of BP. DESIGN: Prospective reliability study. PATIENTS: One hundred patients with an International Classification of Diseases-9th edition code for hypertension were enrolled. MEASURES: Two BP measurements were obtained with the Hawksley random-zero mercury sphygmomanometer and averaged. The clinic-based BP was extracted from the computerized medical records. RESULTS: Agreement between the mercury and clinic-based systolic blood pressure (SBP) was good, intraclass correlation coefficient (ICC)=0.91 (95% confidence interval (CI): 0.83 to 0.94); the agreement for the mercury and clinic-based diastolic blood pressure (DBP) was satisfactory, ICC=0.77 (95% CI: 0.62 to 0.86). Overall, clinic-based readings overestimated the mercury readings, with a mean overestimation of 8.3 mmHg for SBP and 7.1 mmHg for DBP. Based on the clinic-based measure, 21% of patients were misdiagnosed with uncontrolled hypertension. CONCLUSIONS: Health professionals should be aware of this potential difference when utilizing clinic-based BP values for making treatment decisions and/or assessing quality of care.

Academic Medical Centers↗