In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications.

Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N 6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.

High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq).

RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states.

RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA.

Deoxyribozymes are emerging as modification-specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA-cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3-methylcytidine (m3 C), N4 -methylcytidine (m4 C), and 5-methylcytidine (m5 C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10- to 30-fold accelerated cleavage of their target m3 C-, m4 C- or m5 C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The mX C-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m3 C and m5 C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.

Evaluation of myocardial injury patterns and ST changes among critical and non-critical patients with coronavirus-19 disease.

Novel coronavirus disease (COVID-19) has led to a major public health crisis globally. Currently, myocardial damage is speculated to be associated with COVID-19, which can be seen as one of the main causes of death of patients with COVID-19. We therefore, aim to investigate the effects of COVID-19 disease on myocardial injury in hospitalized patients who have been tested positive for COVID-19 pneumonia in this study. A prospective study was conducted among 201 patients with COVID-19 in the Pakistan Military Hospital from April 1 to August 31, 2020, including non-critical cases and critical cases. COVID-19 patients were stratified as critical and non-critical according to the signs and symptoms severity; with those requiring intensive care and invasive mechanical ventilation as critical, and those did not requiring invasive mechanical ventilation as non-critical. A total of 201 COVID-19 patients with critical and non-critical categories presented with myocardial injury. All patients with myocardial injury had an elevation in CKMB and Troponin-I levels. Of these patients, 43.7% presented with new electrocardiography (ECG) changes, and ST depression was typically observed in 36.3% patients. In addition, 18.7% patients presented with abnormal echocardiography findings, with right ventricular dilatation and dysfunction commonly seen among critical group patients. Results analyzed by a logistic regression model showing COVID-19 direct contribution to myocardial injury in these patients. COVID-19 disease directly leads to cardiovascular damage among critical and non-critical patients. Myocardial injury is associated not only with abnormal ECG changes but also with myocardial dysfunction on echocardiography and more commonly observed among critical patients.

A Spotlight on the Underlying Activation Mechanisms of the NLRP3 Inflammasome and its Role in Atherosclerosis: A Review.

The world's number one cause of death is cardiovascular diseases. The pathogenesis of different disease entities in the cardiovascular disease spectrum is complicated and multifactorial. Inflammation in these complicated etiologies serves as a key position and is a significant cause of atherosclerosis, which contributes to the underlying pathology. Therefore, therapeutic targeting of inflammatory pathways in patients with cardiovascular diseases such as atherosclerosis enhances cardiovascular results. Inflammasomes are intracellular protein complexes engaged in atherosclerosis pathogenesis and activated by multiple danger signals. Emerging proof has revealed that Nod-like receptor protein 3 (NLRP3) inflammasome, which regulates caspase-1 activation and later pro-interleukin processing, triggers inflammatory reactions in the vascular wall and leads to atherosclerotic plaque formation. Inflammasome-mediated signaling interference could decrease inflammation and mitigate illness severity. In this section, we provide an overview of the present literature on the underlying mechanisms leading to the activation of NLRP3 inflammasome and the role of NLRP3 inflammasome in the progression of atherogenesis and highlight the possibility of therapeutic interventions due to mechanisms involved in the of inhibition of NLRP3 activation.

N6 -Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes.

RNA-cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site-specific endonuclease deoxyribozymes that selectively cleave post-transcriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. We report that the native tRNA modification N6 -isopentenyladenosine (i6 A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA-cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i6 A-modified RNA at least 2500-fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i6 A RNA modification. Together with deoxyribozymes that are strongly inhibited by i6 A, these results highlight that post-transcriptional RNA modifications modulate the catalytic activity of DNA in various intricate ways.

Effect of Quinolones Versus Cefixime on International Normalized Ratio Levels After Valve Replacement Surgery with Warfarin Therapy.

Background and Objectives: A dispute over interaction of warfarin with two quinolones-i.e., moxifloxacin and levofloxacin-leading to significant increase in international normalized ratio (INR) levels and coagulopathies is currently in debate. The study objective was to compare the INR values due to addition of quinolones and cefixime in warfarin treated patients after replacement of disease valves with metallic valves. Material and Methods: A prospective evaluation of patients who undergone valve replacement surgeries in the cardiology hospital setup in Pakistan during the period 2018-2019 was done, including all those subjects treated concurrently with levofloxacin, moxifloxacin, cefixime, and warfarin for the study. Data organized included demographic information, concurrent medications, and appropriate analytical parameters, especially INR values taken before and within seven days after prescribing three antibiotics in discharged patients who had undergone valve replacement surgeries. Patients for whom laboratory INR values were not given at the time of discharge and with deranged liver function, renal function, low albumin levels, and febrile patients were removed from study. Furthermore, patients were advised on possible food interactions and evaluated to examine if these factors have any possible influence on the interaction being studied. Results: Differences in INR were analyzed statistically by means of SPSS analysis before and after the possible interaction. Following the administration of levofloxacin and moxifloxacin to warfarin therapy, statistical analysis showed remarkable increase in INR (p < 0.001) and no significant change in INR was observed after cefixime treatment (p > 0.05). Conclusion: Results showed that, after adding levofloxacin and moxifloxacin in patients on warfarin, therapy contributed to remarkable increase in INR. However, addition of cefixime prevented frequent coagulopathies; therefore, close monitoring of INR and switching to a safe antibiotic such as cefixime is recommended.