A simple method of characterizing mitochondrial ribonucleic acid.
Ontology highlight
ABSTRACT:
SUBMITTER: Haldar D
PROVIDER: S-EPMC1165492 | biostudies-other | 1975 Jun
REPOSITORIES: biostudies-other
Similar Datasets
Project description:The E(280)/E(260) ratio was found to be suitable for following the ionization of cytosine residues of polynucleotides on the basis of studies with model compounds such as oligoguanylic acid, oligocytidylic acid, a complex formed between polyadenylic acid and polyuridylic acid, and a copolymer of guanylic acid and cytidylic acid, provided that changes in secondary structure were taken into account. The pK of cytosine residues of a polynucleotide in the amorphous form was found to be 4.70 at 25 degrees in 0.1m-sodium phosphate on the basis of titration at 75-85 degrees and on the assumption that the heat of ionization was the same as the value (5.2kcal./mole) found for CMP. In contrast, the pK of cytosine residues in the double-helical form of DNA was found to be about 3.25. These observations were utilized in estimating the fraction of cytosine residues in helical segments of ribosomal RNA, a copolymer of guanylic acid and cytidylic acid, and a copolymer of adenylic acid, guanylic acid, uridylic acid and cytidylic acid. The ionization of guanine and uracil residues was estimated from changes in the E(270)/E(260) ratio and E(230)/E(260) ratio respectively. In the amorphous form of RNA both residues had the same pK, whereas in the double-helical form ionization was suppressed. The fraction of guanine and uracil residues in amorphous segments may be estimated from the titration curves. The difference in the denaturation spectrum of adenine--uracil and guanine--cytosine base pairs at 280mmu was enhanced in acidic solutions whereas E(260) was hardly affected. Hence a comparison of the increments in E(280) and E(260) obtained on increasing the temperature at constant pH may be used to distinguish the melting ranges of helical domains differing in nucleotide composition. In alkaline solutions comparison of the increments in E(260) and E(270) yields similar information. In acidic solutions the fraction of cytosine residues involved in helical secondary structure, the degree of ionization of cytosine residues and the fraction of adenine--uracil base pairs denatured may be estimated from DeltaE(265) and DeltaE(280). In alkaline solutions the fractions of guanine and uracil residues involved in secondary structure and the degrees of ionization of these residues may be estimated from DeltaE(230), DeltaE(245), DeltaE(260) and DeltaE(280).
| S-EPMC1265105 | biostudies-other
Project description:Noncoding RNA (ncRNA) is a kind of RNA that plays an important role in many biological processes, diseases, and cancers, while cannot translate into proteins. With the development of next-generation sequence technology, thousands of novel RNAs with long open reading frames (ORFs, longest ORF length > 303 nt) and short ORFs (longest ORF length ? 303 nt) have been discovered in a short time. How to identify ncRNAs more precisely from novel unannotated RNAs is an important step for RNA functional analysis, RNA regulation, etc. However, most previous methods only utilize the information of sequence features. Meanwhile, most of them have focused on long-ORF RNA sequences, but not adapted to short-ORF RNA sequences. In this paper, we propose a new reliable method called NCResNet. NCResNet employs 57 hybrid features of four categories as inputs, including sequence, protein, RNA structure, and RNA physicochemical properties, and introduces feature enhancement and deep feature learning policies in a neural net model to adapt to this problem. The experiments on benchmark datasets of 8 species shows NCResNet has higher accuracy and higher Matthews correlation coefficient (MCC) compared with other state-of-the-art methods. Particularly, on four short-ORF RNA sequence datasets, specifically mouse, Saccharomyces cerevisiae, zebrafish, and cow, NCResNet achieves greater than 10 and 15% improvements over other state-of-the-art methods in terms of accuracy and MCC. Meanwhile, for long-ORF RNA sequence datasets, NCResNet also has better accuracy and MCC than other state-of-the-art methods on most test datasets. Codes and data are available at https://github.com/abcair/NCResNet.
| S-EPMC7059790 | biostudies-literature
Project description:A highly stable and magnetized citric acid (CA)-functionalized iron oxide aqueous colloidal solution (Fe3O4@CA) was synthesized by using a simple and rapid method of one-step co-participation via a chemical reaction between Fe3+ and Fe2+ in a NaOH solution at 65 °C, followed by CA addition to functionalize the Fe3O4 surface in 25 min. The NPs were synthesized at lower temperatures and shortened time compared with conventional methods. Surface functionalization is highly suggested because bare Fe3O4 nanoparticles (Fe3O4 NPs) are frequently deficient due to their low stability and hydrophilicity. Hence, 19 nm-sized Fe3O4 NPs coated with CA (Fe3O4@CA) were synthesized, and their microstructure, morphology, and magnetic properties were characterized using X-ray diffraction, transmission electron microscopy, Zeta potential, Fourier transform infrared spectroscopy, and vibrating sample magnetometer. CA successfully modified the Fe3O4 surface to obtain a stabilized (homogeneous and well dispersed) aqueous colloidal solution. The Zeta potential value of the as-prepared Fe3O4@CA increases from - 31 to - 45 mV. These CA-functionalized NPs with high magnetic saturation (54.8 emu/g) show promising biomedical applications.
| S-EPMC7330025 | biostudies-literature
Project description:D-Amino acid oxidase (DAO) plays important roles in regulating D-amino acid neurotransmitters and was recently identified as a key enzyme integral to hydrogen sulfide production from D-Cys. We report here the development of a simple biocompatible, bioluminescent method for measuring DAO activity based on the highly selective condensation of D-Cys with 6-hydroxy-2-cyanobenzothiazole (CBT-OH) to form D-luciferin.
| S-EPMC4365669 | biostudies-literature
Project description:Sputum from 105 cases of pulmonary tuberculosis were studied. Direct and post concentration smears were stained by Ziehl - Neelsen (ZN) and cold staining methods. The cold staining method is simple, because it eliminates heatingof stain. For direct smear, the correlations of cold staining procedure with conventional ZN method was 93% and for post concentration smear it was 100%.
| S-EPMC5529720 | biostudies-other
Project description:Bacterial transcriptomics is widely used to investigate gene regulation, bacterial susceptibility to antibiotics, host-pathogen interactions, and pathogenesis. Transcriptomics is crucially dependent on suitable methods to isolate and detect bacterial RNA. Microfluidics offer ways of creating integrated point-of-care systems, analysing a sample from preparation, and RNA isolation to detection. A critical requirement for on-chip diagnostics to deliver on their promise is that mRNA expression is not altered via microfluidic sample processing. This article investigates the impact of the use of microfluidics upon RNA expression of bacteria isolated from blood, a key step towards proving the suitability of such systems for further development.
| S-EPMC4449352 | biostudies-literature
Project description:BackgroundVirus infections result in a range of clinical outcomes for the host, from asymptomatic to severe or even lethal disease. Despite global efforts to prevent and treat virus infections to limit morbidity and mortality, the continued emergence and re-emergence of new outbreaks as well as common infections such as influenza persist as a health threat. Challenges to the prevention of severe disease after virus infection include both a paucity of protective vaccines as well as the early identification of individuals with the highest risk that may require supportive treatment.MethodsWe completed a screen of mice from the Collaborative Cross (CC) that we infected with influenza, severe acute respiratory syndrome-coronavirus, and West Nile virus.ResultsThe CC mice exhibited a range of disease manifestations upon infections, and we used this natural variation to identify strains with mortality after infection and strains exhibiting no mortality. We then used comprehensive preinfection immunophenotyping to identify global baseline immune correlates of protection from mortality to virus infection.ConclusionsThese data suggest that immune phenotypes might be leveraged to identify humans at highest risk of adverse clinical outcomes upon infection, who may most benefit from intensive clinical interventions, in addition to providing insight for rational vaccine design.
| S-EPMC7107456 | biostudies-literature
Project description:The biological understanding of RNA has evolved since the discovery of catalytic RNAs in the early 1980s and the establishment of RNA interference (RNAi) in the 1990s. RNA is no longer seen as the simple mid-product between transcription and translation but as potential molecules to be developed as RNA therapeutic drugs. RNA-based therapeutic drugs have gained recognition because of their ability to regulate gene expression and perform cellular functions. Various nucleobase, backbone, and sugar-modified oligonucleotides have been synthesized, as natural oligonucleotides have some limitations such as poor low nuclease resistance, binding affinity, poor cellular uptake, and toxicity, which affect their use as RNA therapeutic drugs. In this review, we briefly discuss different RNA therapeutic drugs and their internal connections, including antisense oligonucleotides, small interfering RNAs (siRNAs) and microRNAs (miRNAs), aptamers, small activating RNAs (saRNAs), and RNA vaccines. We also discuss the important roles of RNA vaccines and their use in the fight against COVID-19. In addition, various chemical modifications and delivery systems used to improve the performance of RNA therapeutic drugs and overcome their limitations are discussed.
| S-EPMC8437697 | biostudies-literature
Project description:Acidification of 5-formyltetrahydropteroylglutamic acid, followed by reduction at pH7.0, provided a simple method of preparing 5-methyltetrahydropteroylglutamic acid.
| S-EPMC1198355 | biostudies-other
Project description:Hookworm infection is one of the most common neglected tropical diseases and is mainly found in tropical and subtropical areas. Two species of human hookworm are distributed in China, i.e., Ancylostoma duodenale (AD) and Necator americanus (NA).BackgroundTraditional microscopic technology such as the Kato-Katz method is not suitable for hookworm diagnosis due to the rapid degeneration of fragile hookworm eggs or for species identification of hookworm infection. The aim of the present study was to establish and evaluate a novel nucleic acid detection method based on recombinase-aided isothermal amplification (RAA) for the detection of hookworm infections and species identification.MethodsBased on the specific target gene sequences of hookworms (5.8S rRNA for AD and ITS2 for NA, respectively), we designed and synthesized amplification primers and fluorescence probes referring to the principle of the fluorescence recombinase-aided amplification (RAA) technique.ResultsEach assay provided specific amplification of larval DNA from AD and NA by fluorescence RAA, and the detection limits in plasmids reached 102 copies and 10 copies, respectively. Genomic DNA of two hookworm species was successfully detected at a concentration of 0.1 pg/μL, revealing a high detection sensitivity. No positive amplification occurred for genomic DNA from crossed hookworm species and genomic DNA from Cryptosporidium, Giardia lamblia, Strongyloides stercoralis, Schistosoma japonicum, Ascaris lumbricoides, and Clonorchis sinensis, revealing a satisfactory specificity. Fecal sample detection results demonstrated a similar efficacy to the Kato-Katz method; however, it had a greater sensitivity than the larvae culture method.ConclusionA simple and rapid nucleic acid method was successfully established based on RAA, which improved the detection efficacy and species identification for human hookworm infections.
| S-EPMC10142964 | biostudies-literature