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 217 records · Page 12Linked to original sources

[Current state and problem of collecting blood--from medical technologists standpoint].

Blood collection is indispensable, but discussion over proper blood collection methods became active after a problem occurred in both the collecting method and the blood collection tube itself, during vacuum blood collection. In Japan there has been no standard blood collection method until now, and it has been executed based on individual facilities, guidelines, or on individual experience. Regarding these points, the Japanese Committee on Clinical Laboratory Standards (JCCLS) created the 1st edition of guidelines based on National Committee on Clinical Laboratory Standards (NCCLS) in July 2004, and this has been used until now. Here I would like to describe current issues of collecting blood from the point of view of medical technologists.

Clinical Laboratory Techniques↗

RNA editing of a Drosophila sodium channel gene.

Extensive analysis of cDNAs from the para locus in D. melanogaster reveals posttranscriptional modifications indicative of adenosine-to-inosine RNA editing. Most of these edits occur in highly conserved regions of the Na+ channel, and they occur in distant relatives of D. melanogaster as well. Sequence comparison between species has identified putative cis-acting elements important for each RNA editing site. Double-stranded RNA secondary structures with striking similarity to known RNA editing sites were generated based on these data. In addition, the RNA editing sites appear to be developmentally regulated. We have cloned a potential RNA editase, DRED, with a high degree of homology to the mammalian RED1,2 genes. The DRED locus itself is highly regulated by transcription from alternative promoters and alternative splicings.

Adenosine Deaminase↗

Benign tumors of the jaws.

There are a variety of types of benign tumors of the jaws, ranging from tumors developed from the odontogenic tissues to regular osseous tumors and dysplasias. During the last 20 years, the World Health Organization classification on odontogenic tumors, neoplasms, and lesions related to bone has been used. This year, a revised edition will appear, and this review has been based on the revised edition. A number of good articles have been published during the period of review (late 1988 to early 1991). An attempt has been made to extract the essence of these papers.

Fibroma↗

Spectral editing in (13)C MAS NMR under moderately fast spinning conditions.

Novel procedures for the spectral assignment of peaks in high-resolution solid-state (13)C NMR are discussed and demonstrated. These methods are based on the observation that at moderate and already widely available rates of magic-angle spinning (10--14 kHz MAS), CH and CH(2) moieties behave to a large extent as if they were effectively isolated from the surrounding proton reservoir. Dipolar-based analogs of editing techniques that are commonly used in liquid-state NMR such as APT and INEPT can then be derived, while avoiding the need for periods of homonuclear (1)H--(1)H multipulse decoupling. The resulting experiments end up being very simple, essentially tuning-free, and capable of establishing unambiguous distinctions among CH, CH(2), and --C--/-CH(3) carbon sites. The principles underlying such sequences were explored using both numerical calculations and experimental measurements, and once validated their editing applications were illustrated on a number of compounds.

Journal Article↗

Base changes at positions 1014 and 578 of delta virus RNA in Greek isolates maintain base pair in rod conformation with efficient RNA editing.

Analysis of delta hepatitis virus (HDV) genomic RNA, derived from Greek patients from an area where HDV infection is associated with low pathogenicity, is described. In all isolates sequenced, which included 18/18 HDV cDNA clones derived from 6 different patients, irrespective of pathogenicity, a base change (T-->C) was found in position 1014. No significant differences in editing efficiency were found between isolates from inactive and active forms of the disease, although L-antigen was present in low to undetectable levels in the serum of 5/6 patients. An additional mutation was identified at position 578 (A-->G), which reestablishes the canonical base pair G/C with the mutated 1014 when the genome adopts the "rod-like" conformation. This finding supports the presence of this genome conformation in vivo and the requirement for the Watson-Crick base pair 1014/578. A mutation, found at amino acid position 170 (serine-->asparagine), appears to segregate with patients with inactive disease.

Amino Acid Sequence↗

Extent of RNA editing of glutamate receptor subunit GluR5 in different brain regions of the rat.

1. The structure and function of glutamate receptor subunits GluR2, GluR5, and GluR6 are changed by RNA editing. This reaction produces a base transition in the second transmembrane spanning region. The triplet CAG (coding for glutamine) is changed to CGG (coding for arginine). This transition has a pronounced effect on calcium fluxes through the respective ion channels, because calcium currents decrease with the rate of editing. 2. In the present study the extent of RNA editing of the glutamate receptor subunit GluR5 was studied in different brain regions of control rats using a newly developed analysis system. This system is based on restriction analysis of the polymerase chain reaction (PCR) product, derived from reverse-transcribed mRNA as template, with the enzyme Bbv1. Bbv1 recognizes the sequence of the nonedited receptor subunit around the edited base (sequence GCAGC) but not that of the edited subunit (sequence GCGGC; A edited to G). 3. Total RNA was isolated from the cerebral cortex, striatum, hippocampus, thalamus, hypothalamus, cerebellum, pons/medulla oblongata, and white matter and reverse transcribed into cDNA. The region across the edited sequence was amplified by PCR using GluR5-specific primers and the cDNA as template. PCR products were cleaned by ethanol precipitation, incubated with Bbv1, and electrophoresed on an agarose gel together with standards. Gels were photographed and the extent of GluR5 mRNA editing was quantified using an image analysis system. A calibration curve was obtained using PCR products amplified from plasmids with edited and nonedited GluR5 as inserts. 4. In the brain of control rats the extent of RNA editing of the GluR5 subunit amounted to 62 +/- 6.0% of total (cortex), 43 +/- 5.3% (striatum), 52 +/- 5.3% (hippocampus), 91 +/- 6.3% (thalamus), 85 +/- 10.2% (hypothalamus), 82 +/- 6.5% (cerebellum), 88 +/- 6.8% (pons/medulla oblongata), and 41 +/- 2.7% (white matter). 5. The extent of RNA editing varied, thus, considerably in different brain regions, being lowest in the white matter and striatum and highest in the thalamus and pons/medulla oblongate. RNA editing of glutamate receptor subunits may play an important role in the control of calcium fluxes through non-N-methyl-D-aspartate receptor channels in different physiological and/or pathological states of the brain.

Animals↗

A transportable interactive package for the statistical analysis and handling of sequence data.

A real-time, machine-independent software for the analysis and manipulation of sequence data is described. The implemented system allows users to read in sequence data from existing data bases, and to edit, manipulate, analyse and align them. It is easy to use and is suitable for routine investigations and to modify sequences in order to create a user customized data base.

Algorithms↗

RNA editing in higher plant plastids: oligoribonucleotide SSCP analysis allows the proof of base conversion directly at the RNA level.

Plastid RNA editing of a number of transcripts at specific sites changes genomically encoded cytidines to nucleosides, which act like uridines in RT-PCR analyses. To study plastid-editing directly at the RNA level, we established a single-strand conformational polymorphism assay for the discrimination of small RNA molecules. The electrophoretic mobility of a oligoribonucleotide resulting from a RNase T1-digested and edited plastid mRNA was shown to be identical with a control RNA molecule containing a uridine at the editing site, whereas the unedited RNA behaved like a RNA molecule containing a cytidine at the respective position.

Chromosome Mapping↗

[The names of drugs in the cassia-bark family in China prior to the 11th century--On the standardization as Guizhi by Ling Yi and other scholars of cassia-bark family drug names appearing in the medical works written by Zhongjing].

The Chinese medical classics Shangham Lun, Jingui Yaolue and Jingui Yuhanjing are regarded as having been written by Zahn Zhongjing in the early part of the third century A.d. However, all current editions of the three works are based on the northern Song edition revised by Lin Yi and other scholars that was first published in 1065 and 1066. Guizhi appears in prescriptions in all three books as an important medicine. Yet whereas in the Chinese Pharmacopoeia (C.P.) Guizhi is defined as the Cinnamomi Ramulus (the whole twig), in the Japanese Pharmacopoeia (J.P.) it is defined as the Cinnamomi Cortex (the bark). The reasons for this difference between China and Japan has not been studied before. The author conducted a historical analysis of the terms and materials used for cinnamomic medicine in China from the third century B.C. to the year 1066, and the following results were obtained. (1) Until the Han period, the drug name Gui was commonly used for products made from the bark (the cork from the bark being removed) of cinnamomic plant. Such products have been excavated from a tomb where they were interred in the second century B.C., and the drug name Guixin was commonly used for them until the Tang period. (2) The terms Gui, Qin, Mugui, Mugui, guirou, Rougui, Guixin, and Guizhi found in medical texts up to the tenth century were all used for the products made from the bark. The Tang government's pharmacopoeia of 659, the Xinxiu Bencao, designates their material plant as either C. cassia or C. obtusifolium. This product primarily corresponds to Cinnamomi cortex, being Keihi in J.P. or Rougui in C.P. (3) The term Jungui was used from the third century B.C. for products in the shape of a bamboo pipe which were made from the bark of cinnamomic plant twig that had been repeatedly rolled up, and which were used as dietary foods or spices. The Xinxiu Bencao designates the material plant as C. burmanni, and the product corresponds to the cinnamon sticks now in use. (4) As to use Guizhi as decoction, we cannot deny the possibility that in the original medical works of Zhongjing there was a prescription by the name of Guizhi Tang. However, there are no examples of the drug name Guizhi until the sixth century, and most prescriptions of Zhongjing that were used around the Tang period employ Guixin or Gui. Because of this, in some prescriptions there has arisen a contradiction in the terminology; for example in Guizhi Tang, Guizhi might be prescribed instead of Guixin. Further, there are also prescriptions named Guixin... Tang. On the other hand, no evidence has been found that the whole twig of cinnamomic plant was used as a drug prior to the eleventh century. Consequently, this indicates an extremely small likelihood that in the time of Zhongjing the drug name Gizhi was employed, or that the whole cinnamomic twig was employed as a drug. (5) In the Taiping Shenghifang which was published in the early part of northern Song period there is, among the prescriptions for Guizhi, and example drawn from the prescriptions of Zhonjing, of the use of a drug named Guizhi, which has the same meaning as Guixin. However, at the time Gixin was a commonly used term.

Cassia↗

Spectral editing with adiabatic pulses.

Amplitude- and frequency-modulated pulses, known as adiabatic pulses, can induce uniform flip angles in the presence of extreme B1 inhomogeneity, which makes them advantageous for in vivo surface-coil studies. This paper describes the conversion of conventional (square pulse-based) spectral-editing sequences into their adiabatic counterparts. Eight adiabatic homo- and heteronuclear sequences are experimentally evaluated for lactate editing. For homonuclear lactate editing, gradient-enhanced multiple-quantum-coherence filtering provides the best overall performance (100% signal recovery with excellent water and lipid suppression in a single acquisition). For heteronuclear [3-(13)C]lactate editing, gradient-enhanced heteronuclear multiple-quantum-coherence filtering provides the best suppression of unwanted signals in a single acquisition, whereas J-modulated spin-echo sequences yield maximum sensitivity.

Animals↗

An edit script for taxonomic classifications.

BACKGROUND: The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. RESULTS: In this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels. CONCLUSION: These algorithms have been recently implemented, and the software is freely available for download from http://darwin.zoology.gla.ac.uk/~rpage/forest/.

Algorithms↗

Computational modeling of human genetic variants in mice.

Mouse models represent a powerful platform to study genes and variants associated with human diseases. While genome editing technologies have increased the rate and precision of model development, predicting and installing specific types of mutations in mice that mimic the native human genetic context is complicated. Computational tools can identify and align orthologous wild-type genetic sequences from different species; however, predictive modeling and engineering of equivalent mouse variants that mirror the nucleotide and/or polypeptide change effects of human variants remains challenging. Here, we present H2M (human-to-mouse), a computational pipeline to analyze human genetic variation data to systematically model and predict the functional consequences of equivalent mouse variants. We show that H2M can integrate mouse-to-human and paralog-to-paralog variant mapping analyses with precision genome editing pipelines to devise strategies tailored to model specific variants in mice. We leveraged these analyses to establish a database containing > 3 million human-mouse equivalent mutation pairs, as well as in silico-designed base and prime editing libraries to engineer 4,944 recurrent variant pairs. Using H2M, we also found that predicted pathogenicity and immunogenicity scores were highly correlated between human-mouse variant pairs, suggesting that variants with similar sequence change effects may also exhibit broad interspecies functional conservation. Overall, H2M fills a gap in the field by establishing a robust and versatile computational framework to identify and model homologous variants across species while providing key experimental resources to augment functional genetics and precision medicine applications. The H2M database (including software package and documentation) can be accessed at https://human2mouse.com.

Journal Article↗

A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs.

The prediction of translation initiation sites (TISs) in eukaryotic mRNAs has been a challenging problem in computational molecular biology. In this paper, we present a new algorithm to recognize TISs with a very high accuracy. Our algorithm includes two novel ideas. First, we introduce a class of new sequence-similarity kernels based on string editing, called edit kernels, for use with support vector machines (SVMs) in a discriminative approach to predict TISs. The edit kernels are simple and have significant biological and probabilistic interpretations. Although the edit kernels are not positive definite, it is easy to make the kernel matrix positive definite by adjusting the parameters. Second, we convert the region of an input mRNA sequence downstream to a putative TIS into an amino acid sequence before applying SVMs to avoid the high redundancy in the genetic code. The algorithm has been implemented and tested on previously published data. Our experimental results on real mRNA data show that both ideas improve the prediction accuracy greatly and that our method performs significantly better than those based on neural networks and SVMs with polynomial kernels or Salzberg kernels.

Algorithms↗

Engineered genomic attachment sites for site-specific recombinases enable high-efficiency integration in plants and human cells.

Here we developed a DNA-centric strategy for optimizing site-specific recombination by rationally engineering chimeric attachment sites. The high-activity att variants enhance Bxb1-mediated integration efficiency in human cells and plants. Among these att variants, the engineered attB(V111) site achieved 51.9% integration efficiency in HEK293T cells (1.7-fold versus wild-type attB) and 35.6% in rice protoplasts (4.4-fold versus wild-type attB). When paired with an engineered single protein mutant in the Bxb1 catalytic domain, the optimized system achieved targeted integration efficiencies of 31% for a CD19 chimeric antigen receptor cassette and 25% for an ornithine transcarbamylase expression cassette in human cells. In rice, these engineered variants enabled integration of a 5.8 kb herbicide-resistance cassette at a targeted genomic locus, with stable integration detected in 24% of regenerated plants. Oxford Nanopore-based long-read sequencing of edited plants reveals complete and precise insertion with high specificity. Propagation of edited seedlings to T1 plants confirms heritable editing to future generations. This approach provides a safe, broadly applicable approach for recombinase-based genome editing.

Journal Article↗