Discovering Putative Peptides Encoded from Noncoding RNAs in Ribosome Profiling Data of <i>Arabidopsis thaliana</i>

Most noncoding RNAs are considered by their expression at low levels and as having a limited phylogenetic distribution in the cytoplasm, indicating that they may be only involved in specific biological processes. However, recent studies showed the protein-coding potential of ncRNAs, indicating that they might be a source of some special proteins. Although there are increasing noncoding RNAs identified to be able to code proteins, it is challenging to distinguish coding RNAs from previously annotated ncRNAs, and to detect the proteins from their translation. In this article, we designed a pipeline to identify these noncoding RNAs in <i>Arabidopsis thaliana</i> from three NCBI GEO data sets with coding potential and predict their translation products. 31 311 noncoding RNAs were predicted to be translated into peptides, and they showed lower conservation rate than common proteins. In addition, we built an interaction network between these peptides and annotated <i>Arabidopsis</i> proteins using BIPS, which included 69 peptides from noncoding RNAs. Peptides in the interaction network showed different characteristics from other noncoding RNA-derived peptides, and they participated in several crucial biological processes, such as photorespiration and stress-responses. All the information of putative ncPEPs and their interaction with proteins predicted above are finally integrated in a database, PncPEPDB (http://bis.zju.edu.cn/PncPEPDB). These results showed that peptides derived from noncoding RNAs may play important roles in noncoding RNA regulation, which provided another hypothesis that noncoding RNA may regulate the metabolism <i>via</i> their translation products

Strategies used for searching PubMed for eligible publications.

Strategies used for searching PubMed for eligible publications.</p

Meta-analysis results of different interventions after 48 h.

Meta-analysis results of different interventions after 48 h.</p

SUCRA probability ranking after 24 h of treatment.

SUCRA, surface under the cumulative ranking curve.</p

Meta-analysis results of different interventions after 24 h.

Meta-analysis results of different interventions after 24 h.</p

Effect of vibration on pain control at 48 h after orthodontic treatment.

Effect of vibration on pain control at 48 h after orthodontic treatment.</p

Funnel plots for publication bias.

(A) Outcomes at 24 h after treatment; (B) Outcomes at 48 h after treatment.</p

Flow chart of study selection.

ObjectivePain is a frequent adverse reaction during orthodontic treatment, which can significantly reduce treatment compliance and compromise the expected treatment effect. Physical interventions have been used to alleviate pain after orthodontic treatment, but their effectiveness is controversial. This study used a network meta-analysis to assess the efficacy of various physical interventions typically used in managing pain after orthodontic treatment, with a view to provide evidence-based recommendations for representative interventions for orthodontic pain relief during peak pain intensity.MethodsA systematic search of six electronic databases, from their respective inception dates, was conducted to identify relevant literature on the efficacy of various typical physical interventions for managing pain after orthodontic treatment. Literature screening was performed according to the Cochrane System Evaluator’s Manual. Stata 16.0 was used to assess heterogeneity, inconsistency, publication bias, and sensitivity to generate an evidence network diagram and conduct a network meta-analysis.ResultsIn total, 771 articles were reviewed to collect literature on interventions, including low-level laser therapy (LLLT), vibration, acupuncture, and chewing. Of these, 28 studies using a visual analog scale (VAS) as an outcome indicator were included. The results showed that LLLT, vibration, acupuncture, and chewing effectively relieved the pain symptoms in patients after orthodontic treatment. At 24 h post-treatment, LLLT (surface under the cumulative ranking curve [SUCRA] = 80.8) and vibration (SUCRA = 71.1) were the most effective interventions. After 48 h of treatment, acupuncture (SUCRA = 89.6) showed a definite advantage as the best intervention.ConclusionLLLT, vibration, acupuncture, and chewing can alleviate pain associated with orthodontic treatment. Among these interventions, acupuncture was found to be the most effective at 48 h after orthodontic treatment. In addition, acupuncture demonstrated long-lasting and stable pain-relieving effects. However, further studies are needed to determine the most suitable equipment-specific parameters for acupuncture in relieving pain associated with orthodontic treatment.</div

Implementation details of the studies.

ObjectivePain is a frequent adverse reaction during orthodontic treatment, which can significantly reduce treatment compliance and compromise the expected treatment effect. Physical interventions have been used to alleviate pain after orthodontic treatment, but their effectiveness is controversial. This study used a network meta-analysis to assess the efficacy of various physical interventions typically used in managing pain after orthodontic treatment, with a view to provide evidence-based recommendations for representative interventions for orthodontic pain relief during peak pain intensity.MethodsA systematic search of six electronic databases, from their respective inception dates, was conducted to identify relevant literature on the efficacy of various typical physical interventions for managing pain after orthodontic treatment. Literature screening was performed according to the Cochrane System Evaluator’s Manual. Stata 16.0 was used to assess heterogeneity, inconsistency, publication bias, and sensitivity to generate an evidence network diagram and conduct a network meta-analysis.ResultsIn total, 771 articles were reviewed to collect literature on interventions, including low-level laser therapy (LLLT), vibration, acupuncture, and chewing. Of these, 28 studies using a visual analog scale (VAS) as an outcome indicator were included. The results showed that LLLT, vibration, acupuncture, and chewing effectively relieved the pain symptoms in patients after orthodontic treatment. At 24 h post-treatment, LLLT (surface under the cumulative ranking curve [SUCRA] = 80.8) and vibration (SUCRA = 71.1) were the most effective interventions. After 48 h of treatment, acupuncture (SUCRA = 89.6) showed a definite advantage as the best intervention.ConclusionLLLT, vibration, acupuncture, and chewing can alleviate pain associated with orthodontic treatment. Among these interventions, acupuncture was found to be the most effective at 48 h after orthodontic treatment. In addition, acupuncture demonstrated long-lasting and stable pain-relieving effects. However, further studies are needed to determine the most suitable equipment-specific parameters for acupuncture in relieving pain associated with orthodontic treatment.</div

Characteristics of included studies.

ObjectivePain is a frequent adverse reaction during orthodontic treatment, which can significantly reduce treatment compliance and compromise the expected treatment effect. Physical interventions have been used to alleviate pain after orthodontic treatment, but their effectiveness is controversial. This study used a network meta-analysis to assess the efficacy of various physical interventions typically used in managing pain after orthodontic treatment, with a view to provide evidence-based recommendations for representative interventions for orthodontic pain relief during peak pain intensity.MethodsA systematic search of six electronic databases, from their respective inception dates, was conducted to identify relevant literature on the efficacy of various typical physical interventions for managing pain after orthodontic treatment. Literature screening was performed according to the Cochrane System Evaluator’s Manual. Stata 16.0 was used to assess heterogeneity, inconsistency, publication bias, and sensitivity to generate an evidence network diagram and conduct a network meta-analysis.ResultsIn total, 771 articles were reviewed to collect literature on interventions, including low-level laser therapy (LLLT), vibration, acupuncture, and chewing. Of these, 28 studies using a visual analog scale (VAS) as an outcome indicator were included. The results showed that LLLT, vibration, acupuncture, and chewing effectively relieved the pain symptoms in patients after orthodontic treatment. At 24 h post-treatment, LLLT (surface under the cumulative ranking curve [SUCRA] = 80.8) and vibration (SUCRA = 71.1) were the most effective interventions. After 48 h of treatment, acupuncture (SUCRA = 89.6) showed a definite advantage as the best intervention.ConclusionLLLT, vibration, acupuncture, and chewing can alleviate pain associated with orthodontic treatment. Among these interventions, acupuncture was found to be the most effective at 48 h after orthodontic treatment. In addition, acupuncture demonstrated long-lasting and stable pain-relieving effects. However, further studies are needed to determine the most suitable equipment-specific parameters for acupuncture in relieving pain associated with orthodontic treatment.</div