Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.
Herein, we report ag eneral iminium ion-based catalytic method for the enantioselective conjugate addition of carbon-centered radicals to aliphatic and aromatic enals.T he process uses an organic photoredox catalyst, whicha bsorbs blue light to generate radicals from stable precursors,i n combination with ac hiral amine catalyst, which secures ac onsistently high level of stereoselectivity.T he generality of this catalytic platform is demonstrated by the stereoselective interception of aw ide variety of radicals,i ncluding nonstabilized primary ones whichare generally difficult to engage in asymmetric processes.T he system also served to develop organocatalytic cascade reactions that combine an iminiumion-based radical trap with an enamine-mediated step,affording stereochemically dense chiral products in one-step.
Traditionally, the functional analysis of gene expression data has used pathway and network enrichment algorithms. These methods are usually gene rather than transcript centric and hence fall short to unravel functional roles associated to posttranscriptional regulatory mechanisms such as Alternative Splicing (AS) and Alternative PolyAdenylation (APA), jointly referred here as Alternative Transcript Processing (AltTP). Moreover, short-read RNA-seq has serious limitations to resolve full-length transcripts, further complicating the study of isoform expression. Recent advances in long-read sequencing open exciting opportunities for studying isoform biology and function. However, there are no established bioinformatics methods for the functional analysis of isoform-resolved transcriptomics data to fully leverage these technological advances. Here we present a novel framework for Functional Iso-Transcriptomics analysis (FIT). This framework uses a rich isoform-level annotation database of functional domains, motifs and sites -both coding and noncoding-and introduces novel analysis methods to interrogate different aspects of the functional relevance of isoform complexity. The Functional Diversity Analysis (FDA) evaluates the variability at the inclusion/exclusion of functional domains across annotated transcripts of the same gene. Parameters can be set to evaluate if AltTP partially or fully disrupts functional elements. FDA is a measure of the potential of a multiple isoform transcriptome to have a functional impact. By combining these functional labels with expression data, the Differential Analysis Module evaluates the relative contribution of transcriptional (i.e. gene level) and post-transcriptional (i.e. transcript/protein levels) regulation on the biology of the system. Measures of inclusion of NLS, transmembrane domains or DNA binding motifs, for example.Some of these findings were experimentally validated by others and us.In summary, we propose a novel framework for the functional analysis of transcriptomes at isoform resolution. We anticipate the tappAS tool will be an important resource for the adoption of the Functional Iso-Transcriptomics analysis by functional genomics community.
Resumen Objetivo: Determinar la eficacia y seguridad de cápsulas de extracto etanólico de hojas de Annona muricata L (guanábana) más glibenclamida para un mejor control de los niveles glicemia comparado con la administración de glibenclamida sola, en pacientes con diabetes mellitus tipo 2. Diseño: Estudio clínico, aleatorio, grupo paralelo, doble ciego. Lugar: Servicio de Medicina Interna, Hospital I EsSalud, ciudad de Tingo María, Departamento de Huánuco. Pacientes: Pacientes con diagnóstico de diabetes mellitus tipo 2, tratados con glibenclamida. Intervenciones: Entre mayo y setiembre de 2007, 60 pacientes fueron asignados a 6 grupos de manera aleatoria; 3 grupos recibieron cápsulas conteniendo 180 mg de extracto etanólico de hojas de Annona muricata L [CEAM] más 5 mg de glibenclamida y los otros 3 grupos continuaron solo con glibenclamida. Principales medidas de resultados: Evaluación de los niveles de glicemia. Resultados: El rango de edad de los pacientes estuvo entre 38 y 54 años de edad. Se encontró disminución del nivel de glicemia, siendo mayor el efecto en aquellos que recibieron guanábana más glibenclamida. Se presentó efectos adversos en 5 pacientes; dos de ellos refirieron dolor urente en epigastrio asociado en uno a náuseas, y en otros 3 solo náuseas. No se observó alteración de los exámenes de laboratorio. Conclusiones: El uso de las cápsulas conteniendo extracto etanólico de Annona muricata L más glibenclamida durante 30 días produjo una mayor disminución de los niveles de glicemia en diabéticos tipo 2. Palabras clave: Annona; extractos vegetales; diabetes mellitus tipo 2; glibenclamida; glucemia. AbstractObjective: To determine efficacy and security of of Annona muricata L (guanábana) leaves ethanolic extract plus glibenclamide capsules in controlling glucose levels in type 2 diabetes mellitus patients compared to patients receiving with glibenclamide alone. Design: Randomized, double-blind, parallel-group controlled clinical trial. Setting: Internal Medicine service, Tingo María-EsSalud Hospital I, Huanuco city. Participants: Type 2 diabetes mellitus patients. Interventions: Between May 2007 and September 2007 sixty 38 to 60 year-old patients were randomly assigned to 6 groups, 3 receiving capsules containing 180 mg of Annona muricata L leaves ethanolic extract plus glibenclamide 5 mg and 3 receiving glibenclamide 5 mg tablets only. Main outcome measurements: Reduction of glycemia. Results: There was reduction of glycemic levels, higher in those receiving guanabana plus glibenclamida. Auxiliary exams did not reveal adverse effects. Two cases presente epigastric pain, one of them associated with nausea, and three cases presented only nausea. Conclusions: Treatment with capsules containing Annona muricata L leaves ethanolic extract 180 mg plus glibenclamide during thirty days produced better glycemic control in type 2 diabetic patients.Key words: Annona; plant extracts; diabetes mellitus, type 2; glyburide; blood glucose. INTRODUCCIÓNLa diabetes mellitus tipo 2 (DM2) es un desorden metabólico com...
We currently lack effective treatments for the devastating loss of neural function associated with spinal cord injury (SCI). In this study, we evaluated a combination therapy comprising human neural stem cells derived from induced pluripotent stem cells (iPSC-NSC), human mesenchymal stem cells (MSC), and a pH-responsive polyacetal–curcumin nanoconjugate (PA-C) that allows the sustained release of curcumin. In vitro analysis demonstrated that PA-C treatment protected iPSC-NSC from oxidative damage in vitro, while MSC co-culture prevented lipopolysaccharide-induced activation of nuclear factor-κB (NF-κB) in iPSC-NSC. Then, we evaluated the combination of PA-C delivery into the intrathecal space in a rat model of contusive SCI with stem cell transplantation. While we failed to observe significant improvements in locomotor function (BBB scale) in treated animals, histological analysis revealed that PA-C-treated or PA-C and iPSC-NSC + MSC-treated animals displayed significantly smaller scars, while PA-C and iPSC-NSC + MSC treatment induced the preservation of β-III Tubulin-positive axons. iPSC-NSC + MSC transplantation fostered the preservation of motoneurons and myelinated tracts, while PA-C treatment polarized microglia into an anti-inflammatory phenotype. Overall, the combination of stem cell transplantation and PA-C treatment confers higher neuroprotective effects compared to individual treatments.
The evaluation and application of glassy carbon electrodes modified with bimetallic nanoparticle deposits.
Radical cascade processes are invaluable for their ability to rapidly construct complex chiral molecules from simple substrates. However, implementing catalytic asymmetric variants is difficult. Reported herein is a visible‐light‐mediated organocatalytic strategy that exploits the excited‐state reactivity of chiral iminium ions to trigger radical cascade reactions with high enantioselectivity. By combining two sequential radical‐based bond‐forming events, the method converts unactivated olefins and α,β‐unsaturated aldehydes into chiral adducts in a single step. The implementation of an asymmetric three‐component radical cascade further demonstrates the complexity‐generating power of this photochemical strategy.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
334 Leonard St
Brooklyn, NY 11211
Copyright © 2023 scite Inc. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.