RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes

BACKGROUND: RNA-dependent gene silencing is becoming a routine tool used in laboratories worldwide. One of the important remaining hurdles in the selection of the target sequence, if not the most important one, is the designing of tools that have minimal off-target effects (i.e. cleaves only the desired sequence). Increasingly, in the current dawn of the post-genomic era, there is a heavy reliance on tools that are suitable for high-throughput functional genomics, consequently more and more bioinformatic software is becoming available. However, to date none have been designed to satisfy the ever-increasing need for the accurate selection of targets for a specific silencing reagent. RESULTS: In order to overcome this hurdle we have developed RiboSubstrates . This integrated bioinformatic software permits the searching of a cDNA database for all potential substrates for a given ribozyme. This includes the mRNAs that perfectly match the specific requirements of a given ribozyme, as well those including Wobble base pairs and mismatches. The results generated allow rapid selection of sequences suitable as targets for RNA degradation. The current web-based RiboSubstrates version permits the identification of potential gene targets for both SOFA-HDV ribozymes and for hammerhead ribozymes. Moreover, a minimal template for the search of siRNAs is also available. This flexible and reliable tool is easily adaptable for use with any RNA tool (i.e. other ribozymes, deoxyribozymes and antisense), and may use the information present in any cDNA bank. CONCLUSION: RiboSubstrates should become an essential step for all, even including "non-RNA biologists", who endeavor to develop a gene-inactivation system

Louis-Bernard Guyton de Morveau e a revolução química das Luzes

O objetivo deste artigo é investigar a concepção enciclopédica de revolução científica posta em prática pelo químico francês L.-B. Guyton de Morveau (1737-1816). Deslocando a análise do conhecimento químico das Luzes do programa traçado por Lavoisier (1743-1794), sugerimos uma concepção revolucionária republicana, proclamada como resultado do esforço de uma coletividade. Daremos destaque a três abordagens revolucionárias de Guyton de Morveau no âmbito da química. A primeira foi sua atuação no ensino dessa ciência, cuja pedagogia e métodos de ensino foram fundamentais para sua imersão social. Além disso, entre 1770 e 1790, Guyton de Morveau teve desempenhos decisivos no seio da empresa enciclopédica e no seio da escola química francesa

Development and Experimental Validation of a 20K Atlantic Cod (Gadus morhua) Oligonucleotide Microarray Based on a Collection of over 150,000 ESTs

The collapse of Atlantic cod (Gadus morhua) wild populations strongly impacted the Atlantic cod fishery and led to the development of cod aquaculture. In order to improve aquaculture and broodstock quality, we need to gain knowledge of genes and pathways involved in Atlantic cod responses to pathogens and other stressors. The Atlantic Cod Genomics and Broodstock Development Project has generated over 150,000 expressed sequence tags from 42 cDNA libraries representing various tissues, developmental stages, and stimuli. We used this resource to develop an Atlantic cod oligonucleotide microarray containing 20,000 unique probes. Selection of sequences from the full range of cDNA libraries enables application of the microarray for a broad spectrum of Atlantic cod functional genomics studies. We included sequences that were highly abundant in suppression subtractive hybridization (SSH) libraries, which were enriched for transcripts responsive to pathogens or other stressors. These sequences represent genes that potentially play an important role in stress and/or immune responses, making the microarray particularly useful for studies of Atlantic cod gene expression responses to immune stimuli and other stressors. To demonstrate its value, we used the microarray to analyze the Atlantic cod spleen response to stimulation with formalin-killed, atypical Aeromonas salmonicida, resulting in a gene expression profile that indicates a strong innate immune response. These results were further validated by quantitative PCR analysis and comparison to results from previous analysis of an SSH library. This study shows that the Atlantic cod 20K oligonucleotide microarray is a valuable new tool for Atlantic cod functional genomics research

Tumor Copy Number Alteration Burden as a Predictor for Resistance to Immune Checkpoint Blockade across Different Cancer Types

Immune checkpoint blockade (ICB) benefits only a subset of advanced cancer patients, and predictive biomarkers for immunotherapy response are needed. Recently, copy number alteration (CNA) burden has been proposed to predict ICB resistance. We assessed this finding using the publicly accessible data for 1661 ICB-treated patients whose tumors were profiled by MSK-IMPACT, an approved targeted assay in clinical care. We tested the hypothesis that the continuous increase in CNA burden is associated with poor overall survival following ICB. In addition, we hypothesized that the combinatorial biomarkers of tumor mutational burden (TMB) and CNA burden would better stratify patients for immune status and ICB response. Of the 1661 cases, 79% (n = 1307) were treated with anti PD-1/PD-L1 and the remaining 21% (n = 354) with anti CTLA-4 or the combination of both. In a multivariate analysis, increase in CNA burden was associated with poor overall survival [HR = 1.52, 95% CI (1.01–2.30), p = 0.04]. The combination of biomarkers TMB and CNA burden stratified patients into four clinically distinct subsets among which “LowTMB/HighCNA” showed the worst survival (p < 0.0001). The four patient subsets had unique CNA profiles and enriched pathways, which could predict transcriptional and phenotypic effects related to immune signaling and CD8+ T-cell abundance in the tumor microenvironment. CNA burden was associated with poor overall survival in patients receiving ICB and could improve patient stratification when incorporated with TMB. These findings may guide patient selection for immunotherapy or alternative strategies

Solid-Phase Synthesis of N-Substituted Glycine Oligomers (α-Peptoids) and Derivatives

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Multi-gene biomarker panel for reference free prostate cancer diagnosis : determination and independent validation

Identification of biomarkers that can accurately and reliably diagnose prostate cancer is clinically highly desirable. A novel classification method, K-closest resemblance was applied to several high-quality transcriptomic datasets of prostate cancer leading to the discovery of a panel of eight gene biomarkers that can detect prostate cancer with over 96% specificity and sensitivity in leave-one-out cross-validation. Independent validation on clinical samples confirmed the discriminatory power of this gene panel, yielding over 95% accuracy of diagnosis based on receiver-operating characteristic curve analyses. Different levels of validation of the proposed biomarker panel have shown that it allows extremely accurate diagnosis of prostate cancer. Application of this panel can possibly add a fast and objective tool to the pathologist\u2019s arsenal following further clinical testing.L\u2019identification de biomarqueurs qui permettent de diagnostiquer de mani\ue8re fiable et pr\ue9cise le cancer de la prostate est tr\ue8s recherch\ue9e sur le plan clinique. Une nouvelle m\ue9thode de classification, la K-closest resemblance, a \ue9t\ue9 appliqu\ue9e \ue0 plusieurs ensembles de donn\ue9es transcriptomiques de grande qualit\ue9 du cancer de la prostate, ce qui a men\ue9 \ue0 la d\ue9couverte d\u2019un groupe de marqueurs form\ue9 de huit g\ue8nes qui peuvent d\ue9pister le cancer de la prostate avec une sp\ue9cificit\ue9 et une sensibilit\ue9 sup\ue9rieures \ue0 96 % dans une validation crois\ue9e de type \uab leave-one-out \ubb (avec retrait d\u2019un \ue9l\ue9ment). Une validation ind\ue9pendante, men\ue9e sur des \ue9chantillons cliniques, confirme le pouvoir discriminant de ce groupe de g\ue8nes, fournissant un diagnostic pr\ue9cis dans plus de 95 % des cas \ue0 partir d\u2019analyses de courbe de la fonction d\u2019efficacit\ue9 du r\ue9cepteur. Diff\ue9rents niveaux de validation du groupe de biomarqueurs propos\ue9 montrent qu\u2019il permet de diagnostiquer avec une grande exactitude le cancer de la prostate. Apr\ue8s avoir fait l\u2019objet d\u2019essais cliniques plus pouss\ue9s, la mise en application de ce groupe de biomarqueurs pourrait s\u2019ajouter \ue0 l\u2019arsenal du pathologiste comme outil diagnostique rapide et objectif.Peer reviewed: YesNRC publication: Ye

Fuzzy J-Means and VNS Methods for Clustering Genes from Microarray Data

Motivation: In the interpretation of gene expression data from a group of microarray experiments that include samples from either different patients or conditions, special consideration must be given to the pleiotropic and epistatic roles of genes, as observed in the variation of gene co-expression patterns. Crisp clustering methods assign each gene to one cluster, thereby omitting information about the multiple roles of genes.Results: Here we present the application of a local search heuristic, Fuzzy J-Means, embedded into the Variable Neighborhood Search metaheuristic for the clustering of microarray gene expression data. We show that for all data sets studied this algorithm outperforms the standard Fuzzy C-Means heuristic. Different methods for the utilization of cluster membership information in determining gene co-regulation are presented. The clustering and data analyses were performed on simulated data sets as well as experimental cDNA microarray data for breast cancer and human blood from the Stanford Microarray Database.Motivation : Dans l'interpr\ue9tation des donn\ue9es d'expression g\ue9nique tir\ue9es d'un groupe d'exp\ue9riences sur des micror\ue9seaux comportant des \ue9chantillons correspondant \ue0 des conditions ou des patients diff\ue9rents, on doit porter une attention toute sp\ue9ciale aux r\uf4les pl\ue9iotropique et \ue9pistatique des g\ue8nes, observ\ue9s dans la variation des motifs de co expression de ces derniers. Les m\ue9thodes de groupage exact assignent un g\ue8ne \ue0 chaque famille ou groupe, ce qui ne permet pas de tenir compte des renseignements sur les r\uf4les multiples des g\ue8nes.R\ue9sultats : Nous pr\ue9sentons ici une application d'un algorithme de recherche heuristique locale, la moyenne J floue, int\ue9gr\ue9 \ue0 la m\ue9thode m\ue9taheuristique de recherche dans un voisinage variable, pour le groupage des donn\ue9es d'expression g\ue9n\ue9tique d'un micror\ue9seau. Nous d\ue9montrons que, pour tous les ensembles de donn\ue9es \ue9tudi\ue9s, cet algorithme est sup\ue9rieur \ue0 l'algorithme heuristique de la moyenne C floue. Nous pr\ue9sentons \ue9galement diff\ue9rentes m\ue9thodes d'utilisation des informations sur l'appartenance \ue0 une famille pour d\ue9terminer la co r\ue9gulation g\ue9n\ue9tique. Les analyses de donn\ue9es et le groupage ont \ue9t\ue9 effectu\ue9s sur des ensembles de donn\ue9es de simulation, ainsi que sur des donn\ue9es exp\ue9rimentales sur des micror\ue9seaux ADNc concernant le cancer du sein et le sang humain, tir\ue9es de la base de donn\ue9es de Stanford sur les micror\ue9seaux.NRC publication: Ye