Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens.

ABSTRACT: The hammerhead, hairpin, HDV, VS and glmS ribozymes are the five known, naturally occurring catalytic RNAs classified as the "small ribozymes". They share common reaction chemistry in cleaving their own backbone by phosphodiester transfer, but are diverse in their secondary and tertiary structures, indicating that Nature has found at least five independent solutions to a common chemical task. Fluorescence resonance energy transfer (FRET) has been extensively used to detect conformational changes in these ribozymes and dissect their reaction pathways. Common and diverse features are beginning to emerge that, by extension, highlight general biophysical properties of non-protein coding RNAs.

SUBMITTER: Walter NG

PROVIDER: S-EPMC3142921 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens.

Walter Nils G NG Perumal Shiamalee S

Springer series in biophysics 20090101

The hammerhead, hairpin, HDV, VS and glmS ribozymes are the five known, naturally occurring catalytic RNAs classified as the "small ribozymes". They share common reaction chemistry in cleaving their own backbone by phosphodiester transfer, but are diverse in their secondary and tertiary structures, indicating that Nature has found at least five independent solutions to a common chemical task. Fluorescence resonance energy transfer (FRET) has been extensively used to detect conformational changes ...[more]

PMID: 21796234

Similar Datasets

Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes.

Project description:Ribozymes are catalytic RNAs present in modern genomes but regarded as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-LTR retrotransposons of the retrozyme class. These retroelements are expressed as abundant linear and circular RNAs of ∼170-400 nt in different animal tissues. Bioinformatic and in vitro analyses indicate an efficient self-cleavage of the HHRs harboured in most invertebrate retrozymes, whereas HHRs in retrozymes of vertebrates, such as the axolotl and other amphibians, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which opens the door for the development of new tools in the emerging field of study of circRNAs.

| S-EPMC7229834 | biostudies-literature

Ecosystem service lens reveals diverse community values of small-scale fisheries.

Project description:The ocean provides benefits to coastal communities around the world, however, the depth and complexity of people's interactions with marine ecosystems are not well represented in many marine management initiatives. Many fisheries are managed to maximize provisioning value, which is readily quantified, while ignoring cultural values. An ecosystem services approach that includes both provisioning and cultural services will enable managers to better account for the diverse values marine fisheries provide to coastal communities. In this study, we assess community values related to a top fished species, the Mexican chocolate clam, Megapitaria squalida, in Loreto, Baja California Sur, Mexico. We conducted an exploratory analysis based on 42 household surveys, and found that community members perceive multiple provisioning and cultural benefits from the clam, including community economic, historical, and identity values. Despite reporting infrequent harvest and consumption of clams, participants perceive the species as an important part of community identity, highlighting the role of Mexican chocolate clams as a cultural keystone species in the Loreto region. Fisheries management that recognizes the full range of ecosystem services a species contributes to coastal communities will be better equipped to sustain these diverse values into the future.

| S-EPMC7882666 | biostudies-literature

Thermo-Responsive Fluorescent Polymers with Diverse LCSTs for Ratiometric Temperature Sensing through FRET.

Project description:Temperature is a significant parameter to regulate biological reactions and functions inside cells. Sensing the intracellular temperature with a competent method is necessary to understand life science. In this work, an energy-transfer polymeric thermometer was designed for temperature sensing. The thermometer was prepared from two thermo-responsive polymers with different lower critical solution temperatures (LCSTs) of 31.1 °C and 48.6 °C, coupling with blue and red fluorescent molecules, respectively, developed for ratiometric temperature sensing based on the Förster resonance energy transfer (FRET) mechanism. The polymers were synthesized from two monomers, N-isopropylacrylamide (NIPA) and N-isopropylmethacrylamide (NIPmA), which provided different temperature responses. The fluorescent intensity of each polymer (peaked at 436 and 628 nm, respectively) decreased upon the heating of the polymer aqueous solution. While these two polymer aqueous solutions were mixed, the fluorescent intensity decrease at 436 nm and substantial fluorescence enhancement at 628 nm was observed with the increasing temperature due to FRET effect. The cell imaging of HeLa cells by these thermo-responsive polymers was explored. The difference of LCSTs resulting in ratiometric fluorescence change would have a potential impact on the various biomedical applications.

| S-EPMC6415166 | biostudies-literature

Immunotherapy through the Lens of Non-Small Cell Lung Cancer.

Project description:Immunotherapy has revolutionised anti-cancer treatment in solid organ malignancies. Specifically, the discovery of CTLA-4 followed by PD-1 in the early 2000s led to the practice-changing clinical development of immune checkpoint inhibitors (ICI). Patients with lung cancer, including both small cell (SCLC) and non-small cell lung cancer (NSCLC), benefit from the most commonly used form of immunotherapy in immune checkpoint inhibitors (ICI), resulting in increased survival and quality of life. In NSCLC, the benefit of ICIs has now extended from advanced NSCLC to earlier stages of disease, resulting in durable benefits and the even the emergence of the word 'cure' in long term responders. However, not all patients respond to immunotherapy, and few patients achieve long-term survival. Patients may also develop immune-related toxicity, a small percentage of which is associated with significant mortality and morbidity. This review article highlights the various types of immunotherapeutic strategies, their modes of action, and the practice-changing clinical trials that have led to the widespread use of immunotherapy, with a focus on ICIs in NSCLC and the current challenges associated with advancing the field of immunotherapy.

| S-EPMC10252117 | biostudies-literature

What Will You Protect? Redefining Professionalism Through the Lens of Diverse Personal Identities.

Project description:IntroductionProfessional identity formation (PIF) encapsulates the process of incorporating a physician's professional identity into existing personal identity. Medical schools shape PIF by reinforcing professional norms defined by a historical physician phenotype. Increasingly, medical students who are underrepresented in medicine must confront the apparent contradictions between personal identities and the often-subjective definitions of professionalism endorsed by faculty, patients, and peers. The lack of a framework for negotiating these conflicts can create barriers to achieving full academic and professional potential.MethodsWe designed a 2-hour professionalism module during the first-year medical student orientation at one medical school. Participating students listened to a physician discuss a defining career moment that required reconciliation of personal and professional identities. Afterwards, students broke into small groups and discussed vignettes illustrating personal identities challenged by professionalism norms. Students then anonymously wrote a reflection about one aspect of their identity they intended to protect during their PIF process. An overwhelming majority of students posted their anonymous reflections on a wall for other students, staff, and faculty to view.ResultsWe analyzed the written reflective responses to the module. Several broad-ranging themes, including Mission, Identity, and Relationships, were identified. Both participant and facilitator evaluations were analyzed to determine the module's success.DiscussionThis module provides a framework for faculty and administrators to create other curricular and pericurricular experiences that positively shape PIF. The session format utilized may generate greater interest in proactively supporting medical students as they navigate formation of their professional identities.

| S-EPMC8636300 | biostudies-literature

Morphologic Features of Crystalline Lens in Patients with Primary Angle Closure Disease Observed by CASIA 2 Optical Coherence Tomography.

Project description:Purpose:To investigate the morphologic features of crystalline lens in primary angle closure disease (PACD) by the swept-source anterior segment optical coherence tomography. Methods:This cross-sectional observational study included 125 consecutive eyes from 125 patients who underwent anterior segment optical coherence tomography (CASIA 2, Tomey, Nagoya, Japan) examination, including 38 eyes of normal controls, 57 eyes of PAC suspects (PACS), and 30 eyes with PAC or PAC glaucoma (PACG). Crystalline lens parameters were compared among the three groups. Spearman correlation analysis and multiple linear regression models were performed to evaluate the relationships between the lens parameters and related factors. Results:Significant differences were found for anterior chamber depth, axial length, iridotrabecular contact index, lens vault, lens thickness (all P < 0.001), the anterior radius curvature of lens (normal vs PACS vs PAC/PACG: 9.35 ± 1.29 mm vs 8.40 ± 0.62 mm vs 8.12 ± 0.54 mm; P < 0.001), lens decentration (normal vs PACS vs PAC/PACG: 0.14 ± 0.07 mm vs 0.19 ± 0.09 mm vs 0.22 ± 0.12 mm; P = 0.004), and tilt (normal vs PACS vs PAC/PACG: 4.9 ± 1.0° vs 5.3 ± 1.2° vs 5.8 ± 1.8°; P = 0.033) among the three groups. The multivariate regression analysis found that both iridotrabecular contact index and the stage of the PACD were negatively correlated with the anterior radius curvature of lens, positively correlated with lens thickness and decentration after adjustment for age, sex, and axial length (all P < 0.05). Conclusions:Steep anterior curvature and decentration of the crystalline lens may be another anatomic characteristic of eyes with PACD. These findings support that the crystalline lens morphologic features may have great contribution to the development of PACD.

| S-EPMC7405781 | biostudies-literature

In vitro evolution of distinct self-cleaving ribozymes in diverse environments.

Project description:In vitro evolution experiments have long been used to evaluate the roles of RNA in both modern and ancient biology, and as a tool for biotechnology applications. The conditions under which these experiments have been conducted, however, do not reflect the range of cellular environments in modern biology or our understanding of chemical environments on the early earth, when the atmosphere and oceans were largely anoxic and soluble Fe(2+) was abundant. To test the impact of environmental factors relevant to RNA's potential role in the earliest forms of life, we evolved populations of self-cleaving ribozymes in an anoxic atmosphere with varying pH in the presence of either Fe(2+) or Mg(2+). Populations evolved under these different conditions are dominated by different sequences and secondary structures, demonstrating global differences in the underlying fitness landscapes. Comparisons between evolutionary outcomes and catalytic activities also indicate that Mg(2+) can readily take the place of Fe(2+) in supporting the catalysis of RNA cleavage at neutral pH, but not at lower pH. These results highlight the importance of considering the specific environments in which functional biopolymers evolve when evaluating their potential roles in the origin of life, extant biology, or biotechnology.

| S-EPMC4538833 | biostudies-literature

Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.

Project description:Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.

| S-EPMC9826390 | biostudies-literature

RNA ligase ribozymes with a small catalytic core.

Project description:Catalytic RNAs, or ribozymes, catalyze diverse chemical reactions that could have sustained primordial life in the hypothetical RNA world. Many natural ribozymes and laboratory evolved ribozymes exhibit efficient catalysis mediated by elaborate catalytic cores within complex tertiary structures. However, such complex RNA structures and sequences are unlikely to have emerged by chance during the earliest phase of chemical evolution. Here, we explored simple and small ribozyme motifs capable of ligating two RNA fragments in a template-directed fashion (ligase ribozymes). One-round selection of small ligase ribozymes followed by deep sequencing revealed a ligase ribozyme motif comprising a three-nucleotide loop opposite to the ligation junction. The observed ligation was magnesium(II) dependent and appears to form a 2'-5' phosphodiester linkage. The fact that such a small RNA motif can function as a catalyst supports a scenario in which RNA or other primordial nucleic acids played a central role in chemical evolution of life.

| S-EPMC10219994 | biostudies-literature

Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.

| S-EPMC10946891 | biostudies-literature