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At least 703 records · Page 39Linked to original sources
PubMed1995

RNA editing of the coI mRNA throughout the life cycle of Physarum polycephalum.

Editing of RNA via the insertion, deletion or substitution of genetic information affects gene expression in a variety of systems. Previous characterization of the Physarum polycephalum cytochrome c oxidase subunit I (coI) mRNA revealed that both nucleotide insertions and base substitutions occur during the maturation of this mitochondrial message. Both types of editing are known to be developmentally regulated in other systems, including mammals and trypanosomatids. Here we show that the coI mRNA present in Physarum mitochondria is edited via specific nucleotide insertions and C to U conversions at every stage of the life cycle. Primer extension sequencing of the RNA indicates that this editing is both accurate and efficient. Using a sensitive RT-PCR assay to monitor the extent of editing at individual sites of C insertion, we estimate that greater than 98% of the steady-state amount of coI mRNA is edited throughout the Physarum developmental cycle.

Animals↗
PubMed2005

Mitochondrial electroporation and in organello RNA editing of chimeric atp6 transcripts.

The Sorghum bicolor atp6-1 gene and chimeric atp6 genes with additional maize sequences were introduced into isolated maize mitochondria via electroporation. Transcripts isolated after in vitro incubation of the transformed organelles were then analysed for RNA editing. Transcripts of the S. bicolor atp6-1 gene, and the RNAs obtained from most of chimeric sorghum-maize atp6 gene constructs tested, were not edited. However, the transcript of one engineered chimeric gene comprising the 5'untranslated sequence and a segment of the N-terminal ORF of the maize atp6 combined with the sorghum atp6 core ORF and 3'untranslated sequence was found to be partially edited. We were able to exclude low RNA stability or insufficient editing capacity as the reason for failure to edit in the other instances. Instead, the data indicate that the maize sequence in the edited fusion transcript provides a structural motif or binding site for a transcript-specific editing factor.

Base Sequence↗
PubMed2025

A quick guide to evaluating prime editing efficiency in mammalian cells.

According to the Clinvar database, modeling the diseases associated with pathogenic mutations requires the installation of base substitutions, small insertions or deletions. Prime editor (PE) was recently developed to precisely install any base substitutions and/or small insertions/deletions (indels) in mammalian cells and animals without requiring DSBs or donor DNA templates. PE also offers greater editing and targeting flexibility compared to other precision CRISPR editing methods because the versatile editing information is encoded in the reverse-transcription template of its prime editing guide RNA. However, optimal PE system selection and experimental design can be complex, and there are various factors that can affect PE efficiency. This chapter serves as a rapid entry-level guideline for the application of PE, providing an experimental framework for using PE at a specific genomic locus. RUNX1 was selected as a representative target site to illustrate the detailed methodology for constructing PE plasmids and the process of transfecting these plasmids into 293FT cells. We further examined the efficiency of PE-mediated genome editing in mammalian cells by using next-generation sequencing.

Gene Editing↗
PubMed2026

Establishment of a CRISPR/Cas9-mediated system for targeted editing of the MFS gene in mint.

The key message of this study is that we established a CRISPR/Cas9-mediated genome-editing system for Mentha haplocalyx "738" by optimizing protoplast transient assay and screening effective regulatory elements. Targeted knockout of the MFS gene generated edited mint plants with reduced menthofuran content, offering a strategy for quality improvement of mint essential oil. The commercial value of mint (Mentha spp.) essential oil is often diminished by the presence of undesirable metabolites, notably menthofuran, which impairs flavor and raises safety concerns. This study aimed to develop a robust CRISPR/Cas9 gene editing system for mint 738 (Mentha haplocalyx "738") and apply it to disrupt the menthofuran synthase (MFS) gene, thereby redirecting metabolic flux to enhance oil quality. We established an optimized system for high-efficiency protoplast isolation and transient transformation from young mint leaves. Key parameters for enzymatic digestion (1.5% cellulase R10, 0.2% macerozyme R-10, 3 h) and PEG-mediated transformation (40% PEG6000, 0.4 M mannitol, 0.4 M CaCl₂) were systematically determined. Using this platform, we screened endogenous regulatory elements, identifying a truncated mint U6 promoter (HmU6.1-3P) and the tomato SlEF1α promoter as the most effective drivers for sgRNA and Cas9 expression, respectively. A CRISPR/Cas9 vector targeting the MFS gene was constructed and used for Agrobacterium-mediated stable transformation. The positive transgenic mint lines were obtained. Sequencing confirmed heritable mutations at the target sites within the MFS gene in multiple independent lines. The results revealed a substantial decrease in menthofuran content in the essential oil of the edited line #10 compared to the wild-type control, thereby demonstrating a viable strategy for improving mint essential oil quality through genome-editing.

CRISPR-Cas Systems↗
PubMed2002

Using 2-aminopurine fluorescence to detect base unstacking in the template strand during nucleotide incorporation by the bacteriophage T4 DNA polymerase.

The fluorescence of the base analogue 2-aminopurine (2AP) was used to detect physical changes in the template strand during nucleotide incorporation by the bacteriophage T4 DNA polymerase. Fluorescent enzyme-DNA complexes were formed with 2AP placed in the template strand opposite the primer terminus (the n position) and placed one template position 5' to the primer terminus (the n + 1 position). The fluorescence enhancement for 2AP at the n position was shown to be due to formation of the editing complex, which indicates that the 2AP-T terminal base pair is recognized primarily as a mismatch. 2AP fluorescence at the n + 1 position, however, was a reporter for DNA interactions in the polymerase active center that induce intrastrand base unstacking. T4 DNA polymerase produced base unstacking at the n + 1 position following formation of the phosphodiester bond. Thus, the increase in fluorescence intensity for 2AP at the n + 1 position could be used to measure the nucleotide incorporation rate in primer extension reactions in which 2AP was placed initially at the n + 2 position. Primer extension occurred at the rate of about 314 s(-1). The amount of base unstacking at the template n + 1 position was sensitive to the local DNA sequence. More base unstacking was detected for DNA substrates with an A-T base pair at the primer terminus compared to C-G or G-C base pairs. Since proofreading is also increased by A-T base pairs compared to G-C base pairs at the primer terminus, we propose that base unstacking may provide an opportunity for the DNA polymerase to reexamine the primer terminus.

2-Aminopurine↗
PubMed2026

CRISPR-Cas9-induced genetic mosaicism in three species of the microcrustacean Daphnia.

Genetic mosaicism can arise from in vivo CRISPR-Cas9 gene editing, especially in the embryos. This study evaluates the extent of genetic mosaicism resulted from CRISPR-Cas9-mediated knockout for 11 genes in the freshwater microcrustacean Daphnia magna, Daphnia pulex, and Daphnia sinensis. Based on extensive genotyping data of the asexually produced progenies of successfully edited females, we find strong evidence of mosaicism in 9 of these genes. The genotyping data also suggest that the gene editing activity can take place as early as the one-cell embryo stage and extends into the 32-cell and later stages. This study establishes genetic mosaicism as an important feature of Cas9-mediated gene editing in Daphnia.

Animals↗
PubMed1999

Mapping contacts between gRNA and mRNA in trypanosome RNA editing.

All guide RNAs (gRNAs) identified to date have defined 5' anchor sequences, guiding sequences and a non-encoded 3' uridylate tail. The 5' anchor is required for in vitro editing and is thought to be responsible for selection and binding to the pre-edited mRNA. Little is known, however, about how the gRNAs are used to direct RNA editing. Utilizing the photo-reactive crosslinking agent, azidophenacyl (APA), attached to the 5'- or 3'-terminus of the gRNA, we have begun to map the structural relationships between the different defined regions of the gRNA with the pre-edited mRNA. Analyses of crosslinked conjugates produced with a 5'-terminal APA group confirm that the anchor of the gRNA is correctly positioning the interacting molecules. 3' Crosslinks (X-linker placed at the 3'-end of a U10tail) have also been mapped for three different gRNA/mRNA pairs. In all cases, analyses indicate that the U-tail can interact with a range of nucleotides located upstream of the first edited site. It appears that the U-tail prefers purine-rich sites, close to the first few editing sites. These results suggest that the U-tail may act in concert with the anchor to melt out secondary structure in the mRNA in the immediate editing domain, possibly increasing the accessibility of the editing complex to the proper editing sites.

Animals↗
PubMed1993

Maternal mortality due to hemorrhage in Ghana.

OBJECTIVE: This hospital-based review of maternal mortality due to hemorrhage in Kumasi, Ghana was undertaken to determine the factors related to and influencing cases of fatal maternal hemorrhage. METHOD: The review was based on inpatient case notes, labor ward delivery notes, and operative records at the Maternity Block of the Komfo Anokye Teaching Hospital, Kumasi. The diagnoses were based on International Classification of Diseases (ICD) 9th and 10th editions. It covered the period 1981 to 1989. RESULT: It was observed that maternal hemorrhage accounted for over 40% of all obstetric complications admitted and also 27% of all maternal deaths in the period under review. However, the case fatality rate for maternal hemorrhage decreased from 1.34% in 1981 to 0.7% in 1989. The cesarean section rate increased from 6.7% in 1981 to 9.1% in 1989. The maternal mortality rate over the period was 1140 per 100,000 births. CONCLUSION: Based on this review and other related research, the following interventions have been planned for implementation in order to improve the situation: improving staff-patient relationship through training in interpersonal skills; ensuring 24-h availability of drugs, supplies and blood; establishment of a resuscitation unit at the casualty department so that first aid can be provided to patients with obstetric emergencies before transfer to the wards; establishment of a maternity care monitoring system to continually improve the quality of care; introduction of confidential enquiry into all maternal deaths in order to reduce their incidence. A monitoring and evaluation plan has been developed to assess regularly progress on implementation. Although, maternal deaths are due to multifactorial causes, it is hoped that these interventions, if successfully implemented, will contribute significantly towards the reduction of maternal deaths due to institutional factors, especially direct obstetric causes like maternal hemorrhage.

Female↗
PubMed2004

Use of relaxation-edited one-dimensional and two dimensional nuclear magnetic resonance spectroscopy to improve detection of small metabolites in blood plasma.

The 1H nuclear magnetic resonance (NMR) spectra of biological samples, such as blood plasma and tissues, are information rich but data complex owing to superposition of the resonances from a multitude of different chemical entities in multiple-phase compartments, hampering detection and subsequent resonance assignments. To overcome these problems, several spectral-editing NMR experiments are described here, combining spin-relaxation filters (based on T(1), T(rho), and T(2)) with both one-dimensional and two-dimensional (2D) NMR spectroscopy. These techniques enable the separation of NMR resonances based on their relaxation times and allow simplification of the complex spectra. In this paper, the approach is exemplified using a control human blood plasma, which is a complex mixture of proteins, lipoproteins, and small-molecule metabolites. In the case of T(1rho)- and T(2)-edited 2D NMR experiments, a "flip-back" pulse was introduced after the relaxation editing to make the phase cycling of the "relaxation filter" and the 2D NMR part independent, thus enabling easy implementation of the phase-sensitive 2D NMR experiments. These methods also permit much higher receiver gains to be used to reduce digitization error, in particular, for the small resonances, which are sometimes vitally important for metabonomics studies. Both pulse sequences and experimental results are discussed for T(1)-, T(1rho)-, and T(2)-filtered COSY, T(2)-filtered phase-sensitive DQF-COSY, and T(1), T(1rho)-, and T(2)-filtered TOCSY NMR.

Blood Chemical Analysis↗
PubMed2026

Virus-induced gene editing of stomatal regulators in Nicotiana benthamiana enables rapid functional genomics.

Virus-induced gene editing (VIGE) holds promise as a rapid and scalable approach for functional genomics in plants. Here, we apply a tobacco rattle virus (TRV)-based single-guide RNA (sgRNA) delivery system to target key regulators of stomatal development in Nicotiana benthamiana using transgenic Cas9-expressing lines. sgRNAs fused to a mobile RNA element and co-delivered with TRV enabled both somatic and heritable genome editing across orthologs of STOMAGEN, EPF2, YODA, and SPEECHLESS. Somatic editing frequencies reached up to 95%, and heritable tetra-allelic mutations were recovered in multiple target genes. Mutants exhibited significant, gene-specific changes in stomatal density, with corresponding effects on leaf temperature indicative of altered evaporative cooling. Additionally, sgRNAs fused to an AmCyan reporter enabled visualization of virus-infected tissues, allowing stomatal phenotyping in edited M0 sectors. This TRV-based platform facilitates functional assessment of genes influencing stomatal patterning and offers a powerful tool for dissecting gene function in a developmentally and physiologically relevant context.

Nicotiana↗
PubMed2004

Understanding sterol-membrane interactions, part II: complete 1H and 13C assignments by solid-state NMR spectroscopy and determination of the hydrogen-bonding partners of cholesterol in a lipid bilayer.

The complete assignment of cholesterol 1H and 13C NMR resonances in a lipid bilayer environment (Lalpha-dimyristoylphosphatidylcholine/cholesterol 2:1) has been obtained by a combination of 1D and 2D MAS NMR experiments: 13C spectral editing, ge-HSQC, dipolar HETCOR and J-based HETCOR. Specific chemical shift variations have been observed for the C1-C6 atoms of cholesterol measured in CCl4 solution and in the membrane. Based on previous work (F. Jolibois, O. Soubias, V. Reat, A. Milon, Chem. Eur. J. 2004, 10, preceding paper in this issue: DOI: 10.1002/chem.200400245) these variations were attributed to local changes around the cholesterol hydroxy group, such as the three major rotameric states of the C3-O3 bond and different hydrogen bonding partners (water molecules, carboxy and phosphodiester groups of phosphatidylcholine). Comparison of the experimental and theoretical chemical shifts obtained from quantum-chemistry calculations of various transient molecular complexes has allowed the distributions of hydrogen bonding partners and hydroxy rotameric states to be determined. This is the first time that the probability of hydrogen bonding occurring between cholesterol's hydroxy group and phosphatidylcholine's phosphodiester has been determined experimentally.

Carbon Isotopes↗
PubMed1989

The unequivocal determination of lactic acid using a one-dimensional zero-quantum coherence-transfer technique.

A method based on zero-quantum coherence transfer for spectral editing of metabolites in aqueous solution in a one-dimensional experiment is described. Water suppression factors of approximately 8000 were achieved by the use of pulsed B0 field gradients and excellent editing was obtained in a single acquisition. The methyl resonances of both lactate and acetaldehyde were readily observed in a mouse brain homogenate by generating zero-quantum coherence using Gaussian pulses for selective excitation of the respective CH resonances.

Aldehydes↗
PubMed2000

B48 is preferentially translated over B100 in cells with increased endogenous apo B mRNA.

We recently demonstrated that expression of BHMT in McArdle RH-7777 (McA-BHMT) cells increases apo B mRNA abundance, leading to parallel increases in apo B secretion. The ratio of unedited to edited apo B mRNA was unchanged by BHMT expression. Based on the observation that secretion of B48 is increased relative to B100 in McA-BHMT cells, current studies now include comparison of B48 and B100 synthesis and intracellular degradation. Minor differences in co- and posttranslational degradation were unable to account for relative increase in B48 secretion, and the disappearance kinetics of B48 were similar in McA-BHMT and control cells. Consistent with the increase in endogenous apo B mRNA in McA-BHMT cells, B48 synthesis is increased significantly. In contrast, synthesis of B100 was not significantly increased. We conclude that B48 is preferentially translated compared to B100 when endogenous apo B mRNA is increased.

Animals↗
PubMed1999

The importance of internal loops within RNA substrates of ADAR1.

Adenosine deaminases that act on RNA (ADARs) are a family of RNA editing enzymes that convert adenosines to inosines within double-stranded RNA (dsRNA). Although ADARs deaminate perfectly base-paired dsRNA promiscuously, deamination is limited to a few, selected adenosines within dsRNA containing mismatches, bulges and internal loops. As a first step in understanding how RNA structural features promote selectivity, we investigated the role of internal loops within ADAR substrates. We observed that a dsRNA helix is deaminated at the same sites whether it exists as a free molecule or is flanked by internal loops. Thus, internal loops delineate helix ends for ADAR1. Since ADAR1 deaminates short RNAs at fewer adenosines than long RNAs, loops decrease the number of deaminations within an RNA by dividing a long RNA into shorter substrates. For a series of symmetric internal loops related in sequence, larger loops (>/=six nucleotides) acted as helix ends, whereas smaller loops (</=four nucleotides) did not. Our work provides the first information about how secondary structure within ADAR substrates dictates selectivity, and suggests a rational approach for delineating minimal substrates for RNAs deaminated by ADARs in vivo.

Adenosine Deaminase↗
PubMed1987

A new mutator strain of Bacillus subtilis.

Bacillus subtilis strain SB1207, widely used in our laboratory, was found to be highly temperature-sensitive and to exhibit a strong SOS-independent mutator phenotype at elevated temperatures. Both chromosomal and plasmid-borne genes were affected by the mutator. Lethality and mutator phenotype could not be attributed to a replication shut off or to thymine starvation. Due to the high frequency of base misincorporation, the mutator phenotype probably results from an editing defect rather than from a post-replication defect (mismatch repair).

Bacillus subtilis↗
PubMed1996

The annual guide to "America's best hospitals". Evidence of influence among health care leaders.

To determine health care leaders' opinions about a prominent guide to hospital quality, we surveyed 82 chief executive officers (CEOs) and 80 chiefs of staff of hospitals listed in the 1994 edition of the guide and 50 directors of employer based coalitions. Most of the CEOs (87%) and chiefs of staff (86%) said the guide was used in advertising. More than three quarters of the CEOs, chiefs of staff, and coalition directors who were familiar with the guide thought it was accurate, and most indicated that key constituencies (e.g., physicians, corporate managers) were aware of the guide. Our results demonstrate the likely influence of one prominent guide to health care quality and highlight the need for formal independent assessment of such guides.

Attitude of Health Personnel↗
PubMed1992

A comparison of quantitative EEG frequency analysis and conventional EEG in patients with focal brain lesions.

The sensitivity and specificity of quantified EEG frequency analysis (EEGFA) were assessed in a group of patients with CT or MRI verified unilateral cerebral lesions and compared with the results of conventional EEG interpretations. Digital EEG recordings were obtained in 25 patients and 25 normal control subjects during performance of an alerting task. Recording artifacts were carefully eliminated. The results of EEGFA were then statistically compared with those of 75 additional normal subjects in the same age range. Complete conventional EEGs were blindly interpreted by two independent electroencephalographers using a structured reporting procedure. We observed similar overall sensitivities for the two methods. Optimal yield for EEGFA was associated with the use of longer edited EEG lengths, longitudinal bipolar montage, and normative data based on total EEG power. In those recordings with normal or mildly abnormal EEG backgrounds the two techniques were to an extent complimentary, each detecting abnormalities missed by the other. In such circumstances EEGFA may be useful as an extension of conventional EEG interpretation.

Adult↗