Verapamil therapy in variant angina: assessment by high-fidelity frequency modulated ambulatory ECG.
Explore the source record for details and available documents.
Aged↗
SEARCH · Search PubMed
Results for “high-fidelity variants”
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.
Active-site arginines differentially control Cas12a DNA cleavage and specificity.
Cas12a is a CRISPR-Cas nuclease with biochemical features that make it useful for genome editing and nucleic acid diagnostics. However, its off-target and non-specific trans and CRISPR RNA-independent DNA cleavages can reduce the accuracy and limit applications requiring high fidelity. Here, we analyzed the role of two conserved arginine residues, R918 and R921, found in the RuvC active site pocket of Francisella novicida Cas12a. Through amino acid substitutions, biochemical assays, kinetic analysis, and computational study, we establish that a positive charge at 921 is required for CRISPR RNA-dependent DNA cleavage (cis cleavage), whereas R918 primarily enhances cleavage efficiency. Replacing R918 with lysine or alanine eliminates trans activity while retaining cis cleavage, whereas replacing R921 with lysine eliminates trans activity and replacing with alanine abolishes cis and trans cleavages. Furthermore, these changes significantly decrease RNA-independent cleavage and improve mismatch discrimination during cis cleavage, especially at PAM-distal sites. Structural analysis shows that R918 assists in the conversion of the lid covering the RuvC active site to an alpha helical form, while R921 stabilizes the DNA in the active site. Molecular dynamics simulations reveal that while R921 is critical in supporting the positioning of scissile phosphate, R918 is essential in maintaining catalytic-site organization through lid's conformational change as well as in positioning DNA through its role in stabilizing the active site framework. Together, our results highlight the importance of R918 and R921 in Cas12a's activity and the potential of modifying active pocket residues to reduce unwanted DNA cleavage while increasing on-target specificity.
CRISPR-Cas↗
Emerging techniques of CRISPR/Cas system in antiviral therapy and diagnostics: Applications, limitations, and translational perspectives.
The CRISPR/Cas (clustered regularly interspaced short palindromic repeats) system is a versatile technology for developing antiviral medicines and editing viral genomes in both diagnostics and vaccine synthesis. Emerging insights into class 2 effectors, such as Cas9, Cas12, and Cas13, which target viral DNA and RNA, have revolutionized vaccines against viruses such as HIV, HPV, HBV, and EBV. Innovative diagnostic techniques such as SHERLOCK, DETECTR, and FELUDA have demonstrated system's diversity and accuracy in detecting the virus markers, supporting clinical decision-making, indicating adaptability and precision of CRISPR. This review critically evaluates CRISPR's role in RNA editing, emphasizing its importance for functional genomics and development of recombinant vaccines. Translational challenges are critically discussed, including off-target effects, delivery limitations, and ethical issues, for which unique approaches such as high-fidelity Cas variants, non-viral delivery systems, and bioethical frameworks are evaluated to address these limitations. This review also covers other social implications, such as accessibility and biosecurity risks, associated with CRISPR technologies Collectively, these advances underscore the transformative potential of CRISPR technologies in shaping next-generation antiviral diagnostics and therapeutics.
CRISPR-Cas Systems↗
[Study on base insertion/deletion of CAG-rich region in insulin receptor substrate-1 5'-regulatory sequence].
To study the relationship of the polymorphism of the insulin receptor substrate-1 (IRS-1) gene 5'-flanking regulatory sequence and Type 2 diabetes, the IRS-1 gene 5'-flanking regulatory sequence was scanned by PCR-SSCP in 78 healthy control subjects and 76 Type 2 diabetic subjects. Applying PCR-denatured polyacrylamide gel electrophoresis and silver staining, the insertion/deletion polymorphism of the CAG-rich region was analyzed. The genome DNA of the normal and variant subjects was amplified with high-fidelity pfu DNA polymerase. The purified and digested target fragments were then subcloned into the pCAT Basic vector. Each allele was identified according to the mobility by the restrictive endonuclease digestion of the recombinant combined with denatured polyacrylamide gel electrophoresis and silver staining, and finally the constructive plasmids containing different alleles were analyzed by DNA sequencing. Firstly, we found several insertion/deletion variations in the CAG-rich region of IRS-1 gene. Secondly, 7 genotypes and 6 alleles(T1-T6) in this site were detected. Moreover, T5 and T6 were only observed in Type 2 diabetic group.
Adult↗
Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences.
Sets of genes improved by directed evolution can be recombined in vitro to produce further improvements in protein function. Recombination is particularly useful when improved sequences are available; costs of generating such sequences, however, must be weighed against the costs of further evolution by sequential random mutagenesis. Four genes encoding para-nitrobenzyl (pNB) esterase variants exhibiting enhanced activity were recombined in two cycles of high-fidelity DNA shuffling and screening. Genes encoding enzymes exhibiting further improvements in activity were analyzed in order to elucidate evolutionary processes at the DNA level and begin to provide an experimental basis for choosing in vitro evolution strategies and setting key parameters for recombination. DNA sequencing of improved variants from the two rounds of DNA shuffling confirmed important features of the recombination process: rapid fixation and accumulation of beneficial mutations from multiple parent sequences as well as removal of silent and deleterious mutations. The five to sixfold further enhancement of total activity towards the para-nitrophenyl (pNP) ester of loracarbef was obtained through recombination of mutations from several parent sequences as well as new point mutations. Computer simulations of recombination and screening illustrate the trade-offs between recombining fewer parent sequences (in order to reduce screening requirements) and lowering the potential for further evolution. Search strategies which may substantially reduce screening requirements in certain situations are described.
Carboxylic Ester Hydrolases↗
Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population.
An RNA virus population does not consist of a single genotype; rather, it is an ensemble of related sequences, termed quasispecies. Quasispecies arise from rapid genomic evolution powered by the high mutation rate of RNA viral replication. Although a high mutation rate is dangerous for a virus because it results in nonviable individuals, it has been hypothesized that high mutation rates create a 'cloud' of potentially beneficial mutations at the population level, which afford the viral quasispecies a greater probability to evolve and adapt to new environments and challenges during infection. Mathematical models predict that viral quasispecies are not simply a collection of diverse mutants but a group of interactive variants, which together contribute to the characteristics of the population. According to this view, viral populations, rather than individual variants, are the target of evolutionary selection. Here we test this hypothesis by examining the consequences of limiting genomic diversity on viral populations. We find that poliovirus carrying a high-fidelity polymerase replicates at wild-type levels but generates less genomic diversity and is unable to adapt to adverse growth conditions. In infected animals, the reduced viral diversity leads to loss of neurotropism and an attenuated pathogenic phenotype. Notably, using chemical mutagenesis to expand quasispecies diversity of the high-fidelity virus before infection restores neurotropism and pathogenesis. Analysis of viruses isolated from brain provides direct evidence for complementation between members in the quasispecies, indicating that selection indeed occurs at the population level rather than on individual variants. Our study provides direct evidence for a fundamental prediction of the quasispecies theory and establishes a link between mutation rate, population dynamics and pathogenesis.
Animals↗
High-fidelity perceptual long-term memory revisited--and confirmed.
Experiments on short-term perceptual memory for elemental visual attributes, such as contrast, motion, orientation, and spatial frequency, have relied on a delayed discrimination technique in which the subject compares two stimuli presented at different points in time and memory is indexed by discrimination thresholds measured for the different time intervals between reference and test. In a variant of this procedure, used in experiments on long-term memory, the presentation of a single reference is followed by a memory test that combines two-alternative forced-choice decisions with the method of constant stimuli With this procedure, it is impossible to distinguish the effects of criterion-setting processes and memory on performance, but this confound can be eliminated by testing many subjects and having each subject make a single decision. The resulting "group thresholds" are stable across time intervals of 24 hr, confirming previous findings of high-fidelity storage in the long-term memory range.
Humans↗
A real-time PCR-based method to independently sample single simian immunodeficiency virus genomes from macaques with a range of viral loads.
The generation of a diverse population of viral variants is a hallmark of simian immunodeficiency virus (SIV) infection. In order to address what role this diversity plays in disease progression, accurate sampling of the viral population is necessary. However, traditional PCR-based methods often rely on amplification of multiple genomes in one reaction, leading to resampling of viral genomes and potential errors in the estimations of viral diversity, especially when sequences from only one or a small number of PCRs are examined and/or viral copy number is low. Here we describe a method to amplify one viral envelope gene per PCR, thereby avoiding resampling. For this purpose we developed a highly accurate real-time PCR method to quantify SIV copy number, then used a single SIV template in a sensitive, high-fidelity full-length envelope PCR. Using this method, we have estimated the intra-animal viral diversity for a cohort of five pig-tailed macaques (Macaca nemestrina) infected with SIVMne variants, which displayed a broad range of viral loads at setpoint.
Amino Acid Sequence↗
One-pot Golden Gate Assembly of an avian infectious bronchitis virus reverse genetics system.
Avian infectious bronchitis is an acute respiratory disease of poultry of particular concern for global food security. Investigation of infectious bronchitis virus (IBV), the causative agent of avian infectious bronchitis, via reverse genetics enables deeper understanding of virus biology and a rapid response to emerging variants. Classic methods of reverse genetics for IBV can be time consuming, rely on recombination for the introduction of mutations, and, depending on the system, can be subject to genome instability and unreliable success rates. In this study, we have applied data-optimized Golden Gate Assembly design to create a rapidly executable, flexible, and faithful reverse genetics system for IBV. The IBV genome was divided into 12 fragments at high-fidelity fusion site breakpoints. All fragments were synthetically produced and propagated in E. coli plasmids, amenable to standard molecular biology techniques for DNA manipulation. The assembly can be carried out in a single reaction, with the products used directly in subsequent viral rescue steps. We demonstrate the use of this system for generation of point mutants and gene replacements. This Golden Gate Assembly-based reverse genetics system will enable rapid response to emerging variants of IBV, particularly important to vaccine development for controlling spread within poultry populations.
Infectious bronchitis virus↗
The role of iPSC research for insight into inherited arrhythmia conditions.
Human induced pluripotent stem cells (iPSCs) have emerged as a transformative platform for modeling inherited cardiac arrhythmia syndromes and uncovering human-specific disease mechanisms. However, the promise of iPSC-derived cardiomyocytes lies beyond the recapitulation of arrhythmogenic phenotypes and channelopathies. In this review, we explore recent works which have enabled mechanistic interrogation and therapeutic insight for inherited arrhythmia syndromes, beyond the capabilities of traditional animal models. Such studies have leveraged iPSCs to elucidate the role of splice variants, transcriptional regulation, and mitochondrial stress in arrhythmogenesis. Further, iPSC systems have proven important for reclassifying variants of uncertain significance and in modeling idiopathic arrhythmias where genotype-phenotype links are elusive. Advances in directed differentiation now permit chamber-specific cardiac cell generation, allowing for atrial and ventricular disease modeling and revealing critical cell-cell interactions. iPSCs also serve as high-fidelity precursor platforms for drug testing, offering predictive insight into mutation-specific responses to pharmacologic and genetic therapies. Though limitations in maturation and scalability persist, ongoing efforts for integration with tissue engineering, multi-cellular models, and computational frameworks are evolving to improve model reliability. iPSC-based systems now occupy a critical role in arrhythmia research, bridging basic discovery with translational applications, thereby contributing to personalizing care and advancing therapeutics in inherited and idiopathic arrhythmic syndromes.
Humans↗
Arrayed primer extension computing with variant mRNA splice forms. Multiple isoforms of CD44 in a human breast tumor.
The analysis of RNA splicing is important to understanding the diversity in protein sequences at specific disease loci, in the immune response, and across the proteome. The presence of each exon in a mature mRNA formed from a genomic sequence of n exons can be represented by a Boolean variable, enabling mRNA structure to be encoded by an n-bit binary number. The CD44 locus has been studied as an example of a variantly spliced RNA. Microarray methods can be used to address RNA splicing provided they exhibit high fidelity. Our previous work showed that the arrayed primer extension (APEX; single-nucleotide polymerase extension of microarrays of DNA primers) method gives high-fidelity, digital detection of nucleic acid sequences, and it has been used for the solution of Boolean computing problems. APEX was adapted to RNA analysis by the use of reverse transcriptase and arrays of primers specific to each exon in the CD44 locus. "Splicotypes" were readily assigned for a number of variant RNA templates. Because CD44 is known to be aberrantly spliced in a number of cancers, the RNA APEX method with a CD44 microarray was applied to samples from primary tumors of individual patients. Up to four different splicing forms of CD44 were detected, whereas there have been no previous reports of the presence of more than two CD44 isoforms within the same tissue.
Alternative Splicing↗
Design of a bacterial host for site-specific incorporation of p-bromophenylalanine into recombinant proteins.
Introduction of a yeast suppressor tRNA (ytRNA(Phe)(CUA)) and a mutant yeast phenylalanyl-tRNA synthetase (yPheRS (T415G)) into an Escherichia coli expression host allows in vivo incorporation of phenylalanine analogues into recombinant proteins in response to amber stop codons. However, high-fidelity incorporation of non-natural amino acids is precluded in this system by mischarging of ytRNA(Phe)(CUA) with tryptophan (Trp) and lysine (Lys). Here we show that ytRNA(Phe)(CUA) and yPheRS can be redesigned to achieve high-fidelity amber codon suppression through delivery of p-bromophenylalanine (pBrF). Two strategies were used to reduce misincorporation of Trp and Lys. First, Lys misincorporation was eliminated by disruption of a Watson-Crick base pair between nucleotides 30 and 40 in ytRNA(Phe)(CUA). Loss of this base pair reduces mischarging by the E. coli lysyl-tRNA synthetase. Second, the binding site of yPheRS was redesigned to enhance specificity for pBrF. Specifically, we used the T415A variant, which exhibits 5-fold higher activity toward pBrF as compared to Trp in ATP-PP(i) exchange assays. Combining mutant ytRNA(Phe)(CUA) and yPheRS (T415A) allowed incorporation of pBrF into murine dihydrofolate reductase in response to an amber codon with at least 98% fidelity.
Acylation↗
Analysis of primary structural determinants that distinguish the centromere-specific function of histone variant Cse4p from histone H3.
Cse4p is a variant of histone H3 that has an essential role in chromosome segregation and centromere chromatin structure in budding yeast. Cse4p has a unique 135-amino-acid N terminus and a C-terminal histone-fold domain that is more than 60% identical to histone H3 and the mammalian centromere protein CENP-A. Cse4p and CENP-A have biochemical properties similar to H3 and probably replace H3 in centromere-specific nucleosomes in yeasts and mammals, respectively. In order to identify regions of Cse4p that distinguish it from H3 and confer centromere function, a systematic site-directed mutational analysis was performed. Nested deletions of the Cse4p N terminus showed that this region of the protein contains at least one essential domain. The C-terminal histone-fold domain of Cse4p was analyzed by changing Cse4p amino acids that differ between Cse4p and H3 to the analogous H3 residues. Extensive substitution of contiguous Cse4p residues with H3 counterparts resulted in cell lethality. However, all large lethal substitution alleles could be subdivided into smaller viable alleles, many of which caused elevated rates of mitotic chromosome loss. The results indicate that residues critical for wild-type Cse4p function and high-fidelity chromosome transmission are distributed across the entire histone-fold domain. Our findings are discussed in the context of the known structure of H3 within the nucleosome and compared with previous results reported for CENP-A.
Amino Acid Sequence↗
Assessment of the intrinsic contractile status of the heart during sepsis by myocardial pressure-dimension analysis.
The effect of sepsis on the intrinsic contractile status of the myocardium is best examined in the awake, closed-chest animal with intact circulation because anesthesia, open thoracotomy, and circulatory support are all known to affect hemodynamics. To fulfill these criteria, 18 adult dogs were chronically studied in the awake state after instrumentation with left ventricular high-fidelity pressure catheters and ultrasonic dimension transducers to measure left ventricular transmural pressure and minor axis dimension. This allowed computer assessment of the left ventricular end-systolic pressure-dimension relationship in the control state and at intervals following cecal ligation in one group of dogs. A second group of control animals was studied over variable time intervals without cecal ligation to evaluate the temporal stability and reproducibility of the animal model and the end-systolic pressure-dimension relationship. Evaluation of contractility by use of the end-systolic pressure-dimension relationship was essential because this relationship is a sensitive indicator of the intrinsic myocardial contractile state while remaining insensitive to the wide swings in preload and after load that are commonly seen in sepsis. In the control group of dogs, the temporal consistency and stability of the end-systolic pressure-dimension relationship in this model was confirmed; no significant changes in the slope and dimension-axis intercept were demonstrated over the study interval. In the septic group of dogs, however, the intrinsic myocardial contractility significantly deteriorated as the mean slope of the end-systolic pressure-dimension relationship (mmHg/mm) decreased from 16.87 +/- 0.85 to 12.79 +/- 1.67 over 120 hours following cecal ligation. Intrinsic contractility of the heart during sepsis was therefore isolated for the first time from the widely variant loading conditions seen during sepsis by pressure-dimension analyses in the chronically instrumented, awake, closed-chest canine with intact circulation.
Animals↗
Multiplex-PCR-based recombination as a novel high-fidelity method for directed evolution.
A new and convenient method for the in vitro recombination of single point mutations is presented. This method efficiently reduces the introduction of novel point mutations, which usually occur during recombination processes. A multiplex polymerase chain reaction (multiplex-PCR) generates gene fragments that contain preformed point mutations. These fragments are subsequently assembled into full-length genes by a recombination-PCR step. The process of multiplex-PCR-based recombination (MUPREC) does not require DNase I digestion for gene-fragmentation and is therefore easy to perform, even with small amounts of target DNA. The protocol yields high frequencies of recombination without creating a wild-type background. Furthermore, the low error rate results in high-quality variant libraries of true recombinants, thereby minimizing the screening efforts and saving time and money. The MUPREC method was used in the directed evolution of a Bacillus subtilis lipase that can catalyse the enantioselective hydrolysis of a model meso-compound. Thereby, the method was proved to be useful in producing a reliable second-generation library of true recombinants from which better performing variants were identified by using a high-throughput electrospray ionization mass spectrometry (ESI-MS) screening system.
Amino Acid Sequence↗
Neonatal gene therapy with AAV2/8-LSPhGAA improves hypertrophic cardiomyopathy in the Gaac.1826dupA knock-in murine model.
Pompe disease (PD) results from lysosomal acid α-glucosidase (GAA) deficiency, causing lysosomal glycogen accumulation in cardiac and skeletal muscles. We previously characterized a murine model carrying the orthologous human infantile-onset PD (IOPD) pathogenic variant, c.1826dupA (p.Y609*), introduced into the mouse Gaa gene. Compared to wild-type (WT; C57BL/6NJ) controls, Gaac.1826dupA mice exhibit reduced GAA activity and develop early-onset hypertrophic cardiomyopathy-evidenced by increased left ventricular wall thickness and left ventricular mass index (LVMI)- as well as impaired grip strength and gait abnormalities. To benchmark the model's disease fidelity and assess its responsiveness to established therapeutic intervention, Gaac.1826dupA mice received a single retro-orbital dose of AAV2/8-LSPhGAA (2 × 109 vg/g body weight) at postnatal day 12-14. Twelve weeks post-treatment, mice exhibited supraphysiological GAA enzymatic activity in the heart (550% of WT) and liver (400% of WT) with a 93% reduction in cardiac glycogen. No sex-dependent differences in therapeutic efficacy were observed. Echocardiography revealed robust reversal of cardiac pathology, with wall thicknesses and LVMI values approaching WT levels. In contrast to this profound cardiac rescue, skeletal muscle improvements were modest; while forelimb grip strength remained unchanged, automated gait analysis showed benefit limited to hind paw base of support. These findings demonstrate that the Gaac.1826dupA model mirrors the critical cardiomyopathy characteristic of IOPD. While systemic AAV treatment yields definitive cardiac correction, the partial skeletal muscle response highlights a clear need for optimization. Consequently, the Gaac.1826dupA mouse serves as a high-fidelity platform for evaluating next-generation genomic correction strategies targeting both cardiac and refractory neuromuscular manifestations of PD.
Acid α-glucosidase↗
Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR.
Random mutagenesis constitutes an important approach for identifying critical regions of proteins, studying structure-function relations and developing novel proteins with desired properties. Perhaps, the most popular method is the error-prone PCR, in which mistakes are introduced into a gene, and hence a protein, during DNA polymerase-catalysed amplification cycles. Unfortunately, the relatively high fidelities of the thermostable DNA polymerases commonly used for PCR result in too few mistakes in the amplified DNA for efficient mutagenesis. In this paper, we describe mutants of the family B DNA polymerase from Pyrococcus furiosus (Pfu-Pol), with superb performance in error-prone PCR. The key amino acid changes occur in a short loop linking two long alpha-helices that comprise the 'fingers' sub-domain of the protein. This region is responsible for binding the incoming dNTPs and ensuring that only correct bases are inserted opposite the complementary base in the template strand. Mutations in the short loop, when combined with an additional mutation that abolishes the 3'-5' proof-reading exonuclease activity, convert the extremely accurate wild-type polymerase into a variant with low fidelity. The mutant Pfu-Pols can be applied in error-prone PCR, under exactly the same conditions used for standard, high-fidelity PCR with the wild-type enzyme. Large quantities of amplified product, with a high frequency of nearly indiscriminate mutations, are produced. It is anticipated that the Pfu-Pol variants will be extremely useful for the randomization of gene, and hence protein, sequences.
Amino Acid Sequence↗
Hypertonic upper esophageal sphincter in the oculopharyngeal syndrome.
The oculopharyngeal syndrome (OPS) is a rare variant of muscular dystrophy characterized by progressive ptosis and dysphagia. Previous esophageal motility studies in OPS have yielded conflicting results because of low-fidelity esophageal recording systems. Although cricopharyngeal myotomy improves symptoms, accurate postoperative manometric findings have not been reported. Using a low-compliance, high-fidelity system and a radially oriented esophageal motility catheter in an OPS patient we found a hypertonic upper esophageal sphincter (UES), a hypotonic proximal esophagus, and elevated pressures in the distal two-thirds with prolonged duration of contraction. Clinical improvement followed myotomy. We also found a similar manometric pattern but a normotensive UES in an asymptomatic sibling.
Blepharoptosis↗