Search PubMed⌕ Search

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.

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

At least 325 records · Page 18Linked to original sources
PubMedDate not supplied

On-line analysis of neuromuscular bioelectric potentials.

A computer system is presented which provides for on-line data capture and analysis of evoked end-plate potentials and action potentials, and on-line data capture with off-line analysis of spontaneously occurring miniature end-plate potentials at the end-plate region of the neuromuscular junction. Sampling of evoked waveforms begins after an adjustable delay following the stimulus. Spontaneously occurring waveforms are captured by 'freezing' the contents of a circular buffer. The software provides MENU selectable support functions including storage and retrieval of data and calculated parameters, analog and digital display of waveforms, data calibration and gain modification, data editing, file management, and hardcopy output. Calculated parameters of the waveform are optionally placed in a data base file by the analysis programs. The data base may be used for editing, arithmetic operations, and subsetting of variables as well as statistical analysis and plotting of any selected variables.

Action Potentials↗
PubMed2000

Changing genetic information through RNA editing.

RNA editing, the post-transcriptional alteration of a gene-encoded sequence, is a widespread phenomenon in eukaryotes. As a consequence of RNA editing, functionally distinct proteins can be produced from a single gene. The molecular mechanisms involved include single or multiple base insertions or deletions as well as base substitutions. In mammals, one type of substitutional RNA editing, characterized by site-specific base-modification, was shown to modulate important physiological processes. The underlying reaction mechanism of substitutional RNA editing involves hydrolytic deamination of cytosine or adenosine bases to uracil or inosine, respectively. Protein factors have been characterized that are able to induce RNA editing in vitro. A supergene family of RNA-dependent deaminases has emerged with the recent addition of adenosine deaminases specific for tRNA. Here we review the developments that have substantially increased our understanding of base-modification RNA editing over the past few years, with an emphasis on mechanistic differences, evolutionary aspects and the first insights into the regulation of editing activity.

Animals↗
PubMed2005

Addressing the need for a simpler algorithm for the management of women with urinary incontinence.

AIMS: Urinary incontinence (UI) is a prevalent and bothersome condition for many women. However, few women convey the problem to primary care physicians (PCPs), and few PCPs proactively ask about it. One reason may be that available UI recommendations are too complex and difficult to implement. Simplification may encourage greater adaptation as long as a simplified algorithm does not compromise patient safety. I review the opportunity to develop a simpler UI algorithm based on the 3rd edition 2005 International Consultation of Incontinence (ICI) guidelines for the initial management of UI in women. METHODS: A literature search for scientific evidence supporting simplification was performed using PubMed, the Cochrane Database, the Agency for Health Care Policy and Research's (AHCPR) 1996 recommendations, and the ICI's 2005 Incontinence Book / CD-ROM. Each level in the ICI algorithm for initial assessment and treatment was evaluated to develop an updated and less complex management strategy. RESULTS: A simpler UI algorithm for PCPs should focus on considering reversible risk factors and identifying those who need specialized management. A short questionnaire may be sufficient to assess type and severity of UI, whereas a standard neurologic or comprehensive abdominal and pelvic examination seems unnecessary. Treatment should be restricted to a few evidence-based options. CONCLUSIONS: In conclusion, a simpler UI algorithm allows the initiation of evidence-based treatment after a simplified assessment in primary care.

Algorithms↗
PubMedDate not supplied

Comparative analysis of RNA editing sites in higher plant chloroplasts.

Transcripts of land plant chloroplast genomes undergo C-to-U RNA editing. Systematic search disclosed 31 editing sites in tobacco, 27 in maize, and 21 in rice. Based on these identified sites, potential editing sites have been predicted in the transcripts from four angiosperm chloroplast genomes which have been completely sequenced. Most RNA editing events occur in internal codons, which result in amino-acid substitutions. The initiation codon AUG was found to be created from ACG by RNA editing in the transcripts from rpl2, psbL, and ndhD genes. Comparison of editing patterns raises a possibility that many editing sites were acquired in the evolution of angiosperms.

Binding Sites↗
PubMed2005

ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs.

Posttranscriptional, site-specific adenosine to inosine (A-to-I) base conversions, designated as RNA editing, play significant roles in generating diversity of gene expression. However, little is known about how and in which cellular compartments RNA editing is controlled. Interestingly, the two enzymes that catalyze RNA editing, adenosine deaminases that act on RNA (ADAR) 1 and 2, have recently been demonstrated to dynamically associate with the nucleolus. Moreover, we have identified a brain-specific small RNA, termed MBII-52, which was predicted to function as a nucleolar C/D RNA, thereby targeting an A-to-I editing site (C-site) within the 5-HT2C serotonin receptor pre-mRNA for 2'-O-methylation. Through the subcellular targeting of minigenes that contain natural editing sites, we show that ADAR2- but not ADAR1-mediated RNA editing occurs in the nucleolus. We also demonstrate that MBII-52 forms a bona fide small nucleolar ribonucleoprotein particle that specifically decreases the efficiency of RNA editing by ADAR2 at the targeted C-site. Our data are consistent with a model in which C/D small nucleolar RNA might play a role in the regulation of RNA editing.

Adenosine Deaminase↗
PubMed1998

Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry.

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for calculation; 2) 18O-labeling of a peptide at the C terminus, a methodology which was developed to differentiate N-terminal from C-terminal ions, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups.

Algorithms↗
PubMed2026

Glycocalyx-edited mesenchymal stem/stromal cell therapy in advanced osteoporosis.

Mesenchymal stem/stromal cells (MSCs) are osteoregenerative; however, their therapeutic efficacy for skeletal conditions is hampered by poor bone-homing ("osteotropism"). In preclinical models, this deficit is correctable by MSC glycocalyx editing to enforce sialylated Lewis X (sLeX) expression, thereby programming osteotropism. We conducted a first-in-human clinical trial (ClinicalTrials.gov: NCT02566655) involving a single intravenous infusion of glycocalyx-edited autologous bone marrow-derived MSCs in ten women with advanced-stage osteoporosis. The protocol-mandated evaluation spanned 2 years and included clinical assessments, radiographic studies, and measurements of bone turnover markers (BTMs), bone tissue area (BTA), and bone mineral density (BMD). Thereafter, fracture and safety monitoring continued for >3 additional years for each patient. No serious adverse events occurred. Fragility fractures were markedly and durably reduced, amidst increased osteoanabolic BTM levels, BTA, and volumetric BMD. These findings indicate that glycocalyx editing effectuates MSC-based osteoporosis therapy and also refute notions that MSCs derived from older persons and/or diseased-tissue sites are biologically compromised.

E-selectin ligand↗
PubMed1993

RNA editing in plant mitochondria and chloroplasts.

In the mitochondria and chloroplasts of flowering plants (angiosperms), transcripts of protein-coding genes are altered after synthesis so that their final primary nucleotide sequence differs from that of the corresponding DNA sequence. This posttranscriptional mRNA editing consists almost exclusively of C-to-U substitutions. Editing occurs predominantly within coding regions, mostly at isolated C residues, and usually at first or second positions of codons, thereby almost always changing the amino acid from that specified by the unedited codon. Editing may also create initiation and termination codons. The net effect of C-to-U RNA editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonplant homologs. In a few cases, a strong argument can be made that specific C-to-U editing events are essential for the production of functional plant mitochondrial proteins. Although the phenomenon of RNA editing in plants is now well documented, fundamental questions remain to be answered: What determines the specificity of editing? What is the biochemical mechanism (deamination, base exchange, or nucleotide replacement)? How did the system evolve? RNA editing in plants, as in other organisms, challenges our traditional notions of genetic information transfer.

Amino Acid Sequence↗
PubMed1992

An algorithm for comparing RNA secondary structures and searching for similar substructures.

To access the functional informations carried by RNA molecules at the level of their secondary structure interactions, we propose a comparison method based on a tree edit algorithm which takes into account the tree structure of RNA foldings. Any secondary structure is translated into a tree involving all its elementary substructures; then a shorter condensed tree is built in which any unbranched helix interspersed with bulges and interior loops is taken as a single node. This method includes several parameters: a comparison matrix between structural units, gap penalties, and the scoring between nodes of the condensed trees. Their effects have been analysed using as a model a rapidly divergent domain of the large ribosomal RNA, for which structural variation during evolution is well known. This method allows one to recognize precisely, in large target molecules, definite substructures that present with the query molecules only a limited set of closely related secondary structure features; it is still efficient if intervening features, which can correspond to insertion/deletion of entire stem regions, separate such structural elements. When coupled with a hierarchical clustering algorithm, this method is suitable for classifying RNA molecules according to their secondary structure homologies.

Algorithms↗
PubMed1992

[RNA editing].

Explore the source record for details and available documents.

Animals↗
PubMed2006

Concurrent chemoradiation therapy with low-dose CDDP and UFT for glottic carcinomas: evaluation using the sixth edition of the UICC TNM staging system.

We evaluated whether low-dose chemotherapy could improve effects of radiation therapy for glottic carcinoma with different prognostic factor based on the UICC 6th edition. Fifty-one patients with T2N0 glottic carcinoma classified by the UICC 5th edition underwent chemoradiation therapy with low-dose CDDP (4 mg/m(2)) and oral UFT (450 mg of tegafur) continuing for four weeks (CRT group). The historical control consisted of 49 patients treated with radiation therapy alone (RT group). Forty-six tumors with the adjacent sign, i.e. tumors located adjacent to the thyroid cartilage on radiological examinations, were classified as T3 according to the 6(th) edition. The 5-year local control and laryngeal preservation rates of the T2 (n=54) vs. T3 (n=46) lesions were 87% vs. 50% (p<0.0001) and 94% vs. 61% (p<0.0001), respectively. Among the T3 lesions, CRT (n=24) yielded significantly higher laryngeal preservation rates than did RT alone (n=22) (83% vs. 40%, p=0.0063), and the local control rates were higher in the CRT- than the RT group (62% vs. 36%, p=0.0882). While such benefits of CRT were not observed in patients with T2 lesions.

Adult↗
PubMed1997

Writing and evaluating computer-based training programs.

Publishers are preparing for the hitech future and authors and editors need to also. Publishers know that book sales may be down in the future, while computer program sales are expected to increase. Most book publishers have added media divisions to position themselves for the future. Authors and editors can also shift from writing or editing books to developing computer-based training programs. This author tells you how to write, edit, or evaluate the new computer-based training programs.

Authorship↗
PubMed1996

The international classification of childhood cancer.

The International Classification of Childhood Cancer (ICCC) updates the widely used Birch and Marsden classification scheme. ICCC is based on the second edition of the International Classification of Diseases for Oncology (ICD-O-2). The purpose of the new classification is to accommodate important changes in recognition of different types of neoplasms, while preserving continuity with the original classification. The grouping of neoplasms into 12 main diagnostic groups is maintained. The major changes are: (1) intracranial and intraspinal germ-cell tumours now constitute a separate subgroup within germ-cell tumours; (2) histiocytosis X (Langerhans-cell histiocytosis) is excluded from ICCC; (3) Kaposi's sarcoma is a separate subgroup within soft-tissue sarcomas; (4) skin carcinoma is a separate subgroup within epithelial neoplasms; (5) "other specified" and "unspecified" neoplasms are now usually separate sub-categories within the main diagnostic groups. Draft copies of the ICCC were distributed to some 200 professionals with interest and expertise in the field and their comments are considered in this final version. This classification will be used for presentation of data in the second volume of the IARC Scientific Publication "International Incidence of Childhood Cancer." A computer programme for automated classification of childhood tumours coded according to ICD-O-1 or ICD-O-2 is now available from IARC.

Bone Neoplasms↗
PubMed2026

Molecular Bases and Genetic Design of Rice Disease Resistance for Optimized Yield and Sustainable Agriculture.

Rice diseases continue to undermine yield stability and threaten the sustainability of rice production. The central challenge is therefore not simply to maximize immune activation, but to identify genetic interventions that remain effective across diverse pathogen races and environmental conditions without imposing excessive penalties on growth or yield. Here, we synthesize the molecular basis of rice immunity from a design-oriented perspective. We first examine cell-surface pattern-recognition receptors and intracellular nucleotide-binding leucine-rich repeat receptors, and then assess the shared signaling hubs and defence outputs that connect pathogen perception to antimicrobial responses. Rather than treating these components as equivalent breeding targets, we compare their translational potential according to resistance spectrum, anticipated durability, tunability, pleiotropic risk, and the strength of field evidence. We further discuss breeding strategies based on receptor engineering, editing of susceptibility genes and cis-regulatory elements, post-translational motif engineering, pathogen-inducible and upstream open reading frame-mediated regulation, resistance-gene stacking and artificial intelligence-assisted prediction. We argue that rational resistance design in rice should move beyond constitutive immune activation toward allele-specific, quantitative, spatially restricted and infection-responsive regulation. Integrating mechanistic insights with precision genome editing, accelerated breeding and responsible deployment offers a practical route to durable, yield-compatible disease resistance while reducing dependence on chemical control.

breeding strategy↗
PubMed2005

Crocus sativus L. in the treatment of mild to moderate depression: a double-blind, randomized and placebo-controlled trial.

Depression is a serious disorder in today's society, with estimates of lifetime prevalence as high as 21% of the general population in some developed countries. As a therapeutic plant, saffron is considered excellent for stomach ailments and as an antispasmodic, to help digestion and to increase appetite. It is also used for depression in Persian traditional medicine. Our objective was to assess the efficacy of the stigmas of Crocus sativus (saffron) in the treatment of mild to moderate depression in a 6-week double-blind, placebo-controlled and randomized trial. Forty adult outpatients who met the Diagnostic and Statistical Manual of Mental Disorders, 4th edition for major depression based on the structured clinical interview for DSM IV participated in the trial. Patients had a baseline Hamilton rating scale for depression score of at least 18. In this double-blind, placebo-controlled, single-centre and randomized trial, patients were randomly assigned to receive a capsule of saffron 30 mg[sol ]day (BD) (Group 1) or a capsule of placebo (BD) (Group 2) for a 6-week study. At 6 weeks, Crocus sativus produced a significantly better outcome on the Hamilton depression rating scale than the placebo (d.f. = 1, F = 18.89, p < 0.001). There were no significant differences in the two groups in terms of the observed side effects. The results of this study indicate the efficacy of Crocus sativus in the treatment of mild to moderate depression. A large-scale trial is justified.

Adult↗
PubMed1991

RNA editing of sorghum mitochondrial atp6 transcripts changes 15 amino acids and generates a carboxy-terminus identical to yeast.

Sequencing of sorghum mitochondrial atp6 cDNA clones revealed 19 C-to-U transcript editing events within a 756 bp-conserved core gene; three were silent and 16 resulted in 15 amino acid changes. Only one edit, which was silent, was found in the 381 bp amino-extension to the core gene. Eleven of the 15 changed amino acids were identical with or else represented conservative changes compared to yeast atp6. Editing of a CAA codon to TAA truncates the carboxy-terminus to a position identical to that of yeast. The frequency of editing at sites which change amino acids was very high in contrast to partial editing at silent, third base, sites.

Base Sequence↗
PubMed2004

TNM and Japanese staging systems for gastric cancer: how do they coexist?

Two staging systems for gastric cancer, International Union Against Cancer (UICC)/TNM and the Japanese classification, have been used widely for clinical practice and research. The two systems started independently in the 1960s, and underwent several revisions and amendments in order to approach each other, but have become more divergent in the latest editions because of characteristics based on different philosophies. The TNM system adopted a number-based system for N-staging that provides easy and accurate prognostic stratification. Comparative studies have shown that the TNM system has greater prognostic power than the Japanese classification. It contains, however, no treatment guidance and should primarily be used as a guide to prognosis. In contrast, the Japanese classification has been designed as a comprehensive guide to treatment, originally for surgeons and pathologists, and today for oncologists and endoscopists as well. Its anatomical-based N-staging was established based on analysis of lymphadenectomy effectiveness, and naturally provides direct surgical guidance. Clinicians should understand the roles of each system and must not mix the systems or terminology when they report their study results.

Humans↗
PubMed2005

Introduction to the new International Classification of Headache Disorders.

Based on the first edition of the classification (already validated), the ICHD-II is intended for not only the researcher and clinician but also the neurologist and general practitioner. All the headaches are classified into groups and subgroups to provide the level of diagnosis necessary for each user.

Headache Disorders↗