SEARCH · Search PubMed

Results for “Base editing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,387 records · Page 77Linked to original sources

PubMed1991

RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria.

Amino Acid Sequence↗

PubMed2006

ChloroplastDB: the Chloroplast Genome Database.

The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and alignments (http://chloroplast.cbio.psu.edu/). With recent technical advances, the rate of generating new organelle genomes has increased dramatically. However, the established ontology for chloroplast genes and gene features has not been uniformly applied to all chloroplast genomes available in the sequence databases. For example, annotations for some published genome sequences have not evolved with gene naming conventions. ChloroplastDB provides unified annotations, gene name search, BLAST and download functions for chloroplast encoded genes and genomic sequences. A user can retrieve all orthologous sequences with one search regardless of gene names in GenBank. This feature alone greatly facilitates comparative research on sequence evolution including changes in gene content, codon usage, gene structure and post-transcriptional modifications such as RNA editing. Orthologous protein sets are classified by TribeMCL and each set is assigned a standard gene name. Over the next few years, as the number of sequenced chloroplast genomes increases rapidly, the tools available in ChloroplastDB will allow researchers to easily identify and compile target data for comparative analysis of chloroplast genes and genomes.

Chloroplasts↗

PubMedDate not supplied

Automated image registration: I. General methods and intrasubject, intramodality validation.

PURPOSE: We sought to describe and validate an automated image registration method (AIR 3.0) based on matching of voxel intensities. METHOD: Different cost functions, different minimization methods, and various sampling, smoothing, and editing strategies were compared. Internal consistency measures were used to place limits on registration accuracy for MRI data, and absolute accuracy was measured using a brain phantom for PET data. RESULTS: All strategies were consistent with subvoxel accuracy for intrasubject, intramodality registration. Estimated accuracy of registration of structural MRI images was in the 75 to 150 microns range. Sparse data sampling strategies reduced registration times to minutes with only modest loss of accuracy. CONCLUSION: The registration algorithm described is a robust and flexible tool that can be used to address a variety of image registration problems. Registration strategies can be tailored to meet different needs by optimizing tradeoffs between speed and accuracy.

Algorithms↗

PubMed2006

New possibilities of treatment for panic attacks in elderly patients: escitalopram versus citalopram.

PURPOSE: Panic attacks may represent additional therapeutic problems in the elderly. The utility of citalopram in panic attacks has been widely investigated. Here, we compare the efficacy and safety of citalopram, with its S-enantiomer escitalopram at half dosage as to citalopram, in elderly patients who have panic attacks. METHODS: This was an open community-based study. Forty patients who have panic attacks, according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria, were enrolled. Fifty percent of the patients were assigned for 8 weeks' treatment with escitalopram, and the remaining 50% were assigned to treatment with citalopram. The primary outcome measure was the weekly rate of panic attacks. The secondary outcome measures were the Hamilton scale for anxiety and depression and the Cooper Disability Scale. Analysis of variance by repeated measures was applied to calculate differences between groups. RESULTS: A similar decrease in weekly rate of panic attacks, in the scores of Hamilton Scale for anxiety and depression and in the Cooper Disability Scale scores, was observed in both groups after 8 weeks, but a significant variation of outcome measures from baseline was observed already after 2 weeks in the escitalopram group (P < 0.001) and only after 4 weeks in the citalopram group (P < 0.01). CONCLUSIONS: Escitalopram could be considered among the drugs of first choice in elderly patients with panic attacks because of its good efficacy and safety and for the advantage of reducing the total dose and of a more rapid onset of action as compared with citalopram, although further studies are needed to confirm these results.

Aged↗

PubMed2024

DNA-guided CRISPR/Cas12 for RNA targeting.

CRISPR-Cas nucleases are transforming genome editing, RNA editing, and diagnostics but have been limited to RNA-guided systems. We present ΨDNA, a DNA-based guide for Cas12 enzymes, engineered for specific and efficient RNA targeting. ΨDNA mimics a crRNA but with a reverse orientation, enabling stable Cas12-RNA assembly and activating trans-cleavage without RNA components. ΨDNAs are effective in sensing short and long RNAs and demonstrated 100% accuracy for detecting HCV RNA in clinical samples. We discovered that ΨDNAs can guide certain Cas12 enzymes for RNA targeting in cells, enhancing mRNA degradation via ribosome stalling and enabling multiplex knockdown of multiple RNA transcripts. This study establishes ΨDNA as a robust alternative to RNA guides, augmenting the potential of CRISPR-Cas12 for diagnostic applications and targeted RNA modulation in cellular environments.

Journal Article↗

PubMed1980

Chemical DNA synthesis and recombinant DNA studies.

Chemically synthesized DNA has been used in many recombinant DNA studies. These uses have included the total synthesis and cloning of functional genes, the cloning and expression of natural genes, and editing of changing genes by directed mutation.

Base Sequence↗

PubMed1991

Synthesis of leader RNA and editing of the P mRNA during transcription by purified measles virus.

A transcription system with detergent-disrupted purified measles virus was developed. Synthesis of authentic, full-length measles virus N, P, M, and F mRNAs by purified virus occurred as identified by dot-blot hybridization analysis of individual measles virus clones and gel electrophoresis. The relative abundance of the first five viral mRNAs synthesized in vitro decreased significantly with their distance from the 3' end. The addition of the soluble protein fraction from uninfected A549 cells stimulated overall viral RNA synthesis but did not alter the relative abundance of each of the mRNAs. Measles virus synthesized in vitro a leader RNA of approximately 55 nucleotides in length, suggesting that like other negative-strand viruses, transcription initiated only at the 3' end of the genome RNA. Purified measles virus also catalyzed RNA editing during the synthesis of the P mRNA as shown by modified primer extension analysis of the mRNA products and by translation of the modified RNA into the V protein in rabbit reticulocyte lysates. These data suggested that the RNA editing activity was virus encoded.

Animals↗

PubMed2005

Sal-Site: integrating new and existing ambystomatid salamander research and informational resources.

Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1) Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2) Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3) Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4) Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5) Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6) Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at http://www.ambystoma.org.

Animals↗

PubMed2025

DNA-guided CRISPR/Cas12 for RNA targeting.

CRISPR-Cas nucleases are transforming genome editing, RNA editing, and diagnostics but have been limited to RNA-guided systems. We present ΨDNA, a DNA-based guide for Cas12 enzymes, engineered for specific and efficient RNA targeting. ΨDNA mimics a crRNA but with a reverse orientation, enabling stable Cas12-RNA assembly and activating trans-cleavage without RNA components. ΨDNAs are effective in sensing short and long RNAs and demonstrated 100% accuracy for detecting HCV RNA in clinical samples. We discovered that ΨDNAs can guide certain Cas12 enzymes for RNA targeting in cells, enhancing mRNA degradation via ribosome stalling and enabling multiplex knockdown of multiple RNA transcripts. This study establishes ΨDNA as a robust alternative to RNA guides, augmenting CRISPR-Cas12's potential for diagnostic applications and for targeted RNA modulation in cellular environments.

Journal Article↗

PubMedDate not supplied

Panic plaques: panic disorder & coronary artery disease in patients with chest pain.

BACKGROUND: The purpose of this systematic review was to identify characteristics of the chest pain associated with the presence of panic disorder, to determine the strength of the association between panic disorder and coronary artery disease (CAD), and to determine the association between panic disorder and known cardiovascular risk factors. METHODS: Potential studies were identified via computerized search using MEDLINE and PSYCINFO databases, and review of bibliographies. MeSH headings used included "panic disorder" with "chest pain," "panic disorder" with "coronary disease or cardiovascular disorders or heart disorders," and "panic disorder" with "cholesterol or essential hypertension or tobacco smoking." Studies had to base their diagnosis of panic disorder on criteria from the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition, and objective criteria of CAD and risk factors had to be used. Only case-control and cohort studies were included. RESULTS: The relative risk of panic disorder in patients with nonanginal chest pain is 2.03 [confidence interval (CI), 1.41 to 2.92]. Concerning the relationship between panic disorder and CAD, studies conducted in emergency departments found a relative risk of 1.25 (CI, 0.87 to 1.80). However, there is an inverse relationship between the prevalence of CAD in the study and the prevalence of panic disorder among the patients with CAD (r = -.469, P =.086). Panic disorder has also been linked to cardiac risk factors. CONCLUSIONS: Panic disorder and CAD are correlated in noncardiology settings, and recurrent panic attacks may actually cause CAD. Recognition of either condition should lead the family physician to consider the other, resulting in increased vigilance and possible screening.

Chest Pain↗

PubMed2026

When Homing Endonuclease Meets Transposon: The OMEGA System.

Sequence-specific DNA endonucleases have made significant contributions to biology, biotechnology, and medicine; restriction enzymes and homing endonucleases are among classic examples. The demonstration of programmable genome editing using Cas9 in the CRISPR-Cas system, in which the target DNA sequence is recognized by base pairing with a guide RNA, revolutionized the field of genome engineering, making target selection more flexible and convenient. The OMEGA (Obligate Mobile Element-Guided Activity) system, considered a precursor to Cas12, and likely to Cas9, in the CRISPR-Cas system, is an RNA-guided DNA endonuclease composed of a TnpB, IscB, IsrB, or Fanzor protein, and a structural RNA designated reRNA or ωRNA. The OMEGA system is present in the three domains of life as an auxiliary component of transposons. The OMEGA system cuts DNA in an allele from which a transposon is excised and triggers recombination to reinstate the transposon at the same position. This "transposon restorative homing" redefines the OMEGA system as a homing endonuclease. In this review, the selfish aspects of the OMEGA system are discussed in the historical context of homing endonuclease research.

Cas12↗

PubMed2004

Towards a Belgian consensus for prevention of perinatal group B streptococcal disease.

BACKGROUND & OBJECTIVES: In Belgium, as in many other countries, group B Streptococcus (GBS) is still the leading cause of sepsis and meningitis in neonates. In 2001, though no Belgian guidelines for their prevention were available, in some hospitals, obstetrical programmes included a GBS prevention policy. With an aim to reach a Belgian consensus for the prevention of perinatal group B streptococcal disease, a national consensum meeting was organized in 2001. We report here our experience and findings of this meeting. METHODS: In November 2001, obstetricians, neonatologists, microbiologists and infectious diseases specialists were invited to participate in a GBS symposium. International and Belgian speakers presented epidemiological aspects, argued comparative cost-effectiveness of different approaches for prevention and debated technical and practical problems. Management of neonates with risk factors for GBS disease and progress in GBS vaccines were also included in the programme. Further results about Belgian obstetricians' practice and compliance to a policy for prevention of neonatal GBS diseases, as answered in two mail surveys, were commented and discussed. In an interactive session at the end, each participant was asked to vote on the key points related to the different steps of the ideal prevention strategy to recommend. RESULTS: For the main questions, 94 per cent of participants choose a screening-based approach and 94 per cent shifted from the current use of ampicillin to penicillin as first choice for antimicrobial prophylaxis. Further, 79 per cent voted for an approach with integrated neonatal prophylaxis for selected neonates at high risk for GBS disease and 47 per cent voted for a strategy based on an intrapartum rapid screening-based approach. INTERPRETATION & CONCLUSION: The state of the question by different speakers, the data from Belgian epidemiology, and the debate about cost-effectiveness of different approaches led to a massive vote in favour of the universal screening-based approach. Based on these results, a working group has been appointed by the Ministry of Health to draft and edit Belgian recommendations for the prevention of perinatal GBS disease.

Belgium↗

PubMed2002

An integrated knowledge management system for the clinical laboratories: an initial application of an architectural model.

eLABook is a web-distributed knowledge management system designed to support the needs of clinicians and laboratory staff in the selection and interpretation of investigations in laboratory medicine. Access can be by hyperlinks at any point through the request-report cycle, by browsing down a hierarchy, and by various search approaches. The information describes service issues, which are predominantly locally determined, and clinical implications, which may be local, national, governmental and international. The application has been implemented across the Oxford Clinical Intranet to support secondary care in the four hospital sites of the Oxford Radcliffe Hospitals and by general practitioners in Oxfordshire. The knowledge base is capable of rapid changes in response to input from both developers and users. It supports authoring, editing and a full audit trail of changes. The selected architecture allows very large scale hierarchical structures and is designed to accommodate future needs for an object-distributed processing deployment.

Artificial Intelligence↗

PubMed2004

[A 30-year history of the change in package insert for Japanese pharmaceutical medicines].

Package inserts are very important in the medical field. They are full of useful and fundamental information. We have edited two books, named 'Drugs in Japan - Ethical Drugs' and 'Drugs in Japan - Over-the-Counter Drugs' based on the review of package inserts provided for pharmaceutical medicine for more 30 years. We tried to analyze the change in package insert contents; in particular, information quality and quantity.The quality of the information provided in package inserts has improved year by year, with drastic improvements being seen three times. The information quantity has also increased in proportion to the improvement in quality. We created a graph based on package inserts, Warfarin; Eisai, chronologically. It shows that improvement in information quality is supported by the amount of text in the package insert.

Drug Labeling↗

PubMed1994

Productive re-arrangement at both alleles of the T-cell receptor beta-chain locus in CD4 T-cell clones specific for influenza haemagglutinin.

T-cell receptor (TcR) beta-chain usage, and VDJ junctional region sequences thereof in a panel of CD4+ T-cell clones Ad-, or Ak- or Ek-restricted for major antigenic sites of influenza haemagglutinin (H3 subtype), were investigated. Direct sequencing of cDNA, obtained by polymerase chain reaction, revealed that the majority of T-cell clones contained both productive and non-productive rearranged transcripts. Moreover, T-cell clones specific for p206-227 (Ad) or p245-265 (AK) contained double-productive re-arranged transcripts (V beta 6 J beta 2.6, V beta 4, J beta 1.2) and (V beta 6 J beta 1.3, V beta 8.2, J beta 1.5) respectively. However, FACS analysis with V beta-specific monoclonal antibodies established that, for each of these T-cell clones, only a single beta-chain was expressed at the cell surface, thereby indicating post-transcriptional editing.

Alleles↗

PubMed1995

Automata-theoretic models of mutation and alignment.

Finite-state automata called transducers, which have both input and output, can be used to model simple mechanisms of biological mutation. We present a methodology whereby numerically-weighted versions of such specifications can be mechanically adapted to create string edit machines that are essentially equivalent to recurrence relations of the sort that characterize dynamic programming alignment algorithms. Based on this, we have developed a visual programming system for designing new alignment algorithms in a rapid-prototyping fashion.

Algorithms↗

PubMed1996

Determinants involved in regulating the proportion of edited apolipoprotein B RNAs.

Editing the apolipoprotein B (apoB) RNA involves deamination of cytidine by the catalytic subunit, APOBEC-1, as a component of an editosome. A tripartite sequence (editing motif) is essential for editosome assembly and site-specific editing. Current theory for the regulation of apoB RNA editing proposes that APOBEC-1 is rate limiting in cells and determines the proportion of edited apoB mRNAs. An evaluation of how the overexpression of APOBEC-1 increased the proportion of edited RNAs has led to the discovery of a paradox. McArdle cells edit a constant proportion of apoB RNA regardless of the total number of apoB RNAs expressed. Despite virtually identical editing motifs, apoB RNA transcripts from the endogenous gene and transfected, exogenous cDNA were edited with characteristic, but different efficiencies. This suggested that these RNAs were interacting with the editing machinery as distinct and noncompeting populations. We evaluated whether the presence of introns in the endogenous transcript may have distinguished it as a distinct population having reduced editing efficiency. The editing efficiency of chimeric splicing-editing RNA substrates was highest on fully processed RNA. Increased exon length improved utilization of the editing motif in these chimeric constructs. Taken together, the data suggest that the close proximity of introns can reduce apoB RNA editing efficiency. A population "gating" hypothesis is proposed wherein the proportion of edited RNAs in a population is determined my multiple cis- and trans-acting factors as RNAs pass through a nuclear restriction point.

APOBEC-1 Deaminase↗

PubMed1997

The World Wide Web--a new tool for biomedical engineering education.

An ever-increasing variety of materials (text, images, videos, and sound) are available through the World Wide Web (WWW). While textbooks, which are often outdated by the time they are published, are usually limited to black and white text and images, many supplemental materials can be found on the WWW. The WWW also provides many resources for student projects. In BAE 465: Biomedical Engineering Applications, student teams developed WWW-based term projects on biomedical topics, e.g. biomaterials, MRI, and medical ultrasound. After the projects were completed and edited by the instructor, they were placed on-line for world-wide access if permission for this had been granted by the student authors. Projects from three classes have been used to form the basis for an electronic textbook which is available at http:@www.eos.ncsu.edu/bae/research/blanchard /www/465/textbook/. This electronic textbook also includes instructional objectives and sample tests for specific topic areas. Student projects have been linked to the appropriate topic areas within the electronic textbook. Links to relevant sites have been included within the electronic textbook as well as within the individual projects. Students were required to link to images and other materials they wanted to include in their project in order to avoid copyright issues. The drawback to this approach to copyright protection is that addresses can change making links unavailable. In BAE 465 and in BAE 235: Engineering Biology, the WWW has also been used to distribute instructional objectives, the syllabi and class policies, homework problems, and abbreviated lecture notes. This has made maintaining course-related material easier and has reduced the amount of paper used by both the students and the instructor. Goals for the electronic textbook include the addition of instructional simulation programs that can be run from remote sites. In the future, biomedical engineering may be taught in a virtual classroom with participation by an instructor and students from many different parts of the world.

Biomedical Engineering↗