RNA

Considerando la importancia de la producción de piña en la economía costarricense, se propone un modelo de medición cualitativa y cuantitativa de la calidad en la operación agroindustrial de la piña, para la certificación del proceso del cultivo, recolecta, clasificación de la fruta y embalaje. Dicho modelo, además de que permite cuantificar el rendimiento de las diferentes fases de esta agroindustria, puede servir a los productores y empacadoras como instrumento para presentar ante la Unión Europea, cuando esta viene a certificar los procesos de siembra y recolección en las fincas, así como los procesos de las empacadoras de piña. Asimismo, permite tener controles que ayuden a maximizar su eficiencia y eficacia.

A large variation in prognosis is observed despite the use of clinical prognostic factors in patients with advanced non-small cell lung cancer (NSCLC). It is likely that this variation is due to the different biological properties of the tumour cells. In this work we aimed to identify gene signature that could predict survival in advanced NSCLC. Total RNA was extracted from five 5 μm-thick sections of the FFPE using the High Pure RNA Paraffin Kit (Roche). RNA amplification was performed using WT-Ovation™ FFPE RNA Amplification System V2 (NuGen). The amplified cDNA was then labelled and hybridised onto Illumina HumanRef-8 v3.0 Expression BeadChips. Microarray data analysis was subsequently performed using Genespring GX version 9.0. Out of 75 FFPE samples, only 32 had sufficient RNA quality and quantity for microarray gene expression analysis. Patients were grouped into long and short survival groups based on the time to cancer-related death. After normalization and filtration, 19,002 genes were selected for differential gene expression analysis. A total of 440 genes differed significantly between the long and short survival groups (ANOVA, p <; 0.05, with Benjamini and Hochberg False Discovery Rate multiple testing correction). Unsupervised Hierarchial Clustering with Pearson correlation and average linkage identified two broad clusters of patients corresponding to the long and short survival. Thirteen genes were selected based on the TTest, 2-fold expression changes, principal components analysis and univariate Cox regression analysis and risk scores were calculated for each patient. These gene signatures were independent predictors of survival. The model was validated with a published microarray data from 130 patients with NSCLC. Using Gene Set Analysis (GSA), we found certain biological processes including metastasis and chemotherapy resistance were up-regulated in the short survival group while TID pathway and MAPKKK cascade were enriched in th- - e long survival group. As the conclusion, there is several distinct gene expression profiles associated with survival of patients with advanced stage NSCLC. Survival outcomes in advanced NSCLC could be predicted based on a 13-gene signature.

The 70S ribosome is a major target for antibacterial drugs. Two of the classical antibiotics, chloramphenicol (CHL) and erythromycin (ERY), competitively bind to adjacent but separate sites on the bacterial ribosome: the catalytic peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), respectively. The previously reported competitive binding of CHL and ERY might be due either to a direct collision of the two drugs on the ribosome or due to a drug-induced allosteric effect. Because of the resolution limitations, the available structures of these antibiotics in complex with bacterial ribosomes do not allow us to discriminate between these two possible mechanisms. In this work, we have obtained two crystal structures of CHL and ERY in complex with the Thermus thermophilus 70S ribosome at a higher resolution (2.65 and 2.89 Å, respectively) allowing unambiguous placement of the drugs in the electron density maps. Our structures provide evidence of the direct co...

Differential gene expression between various tissues and developmental stages or between cells in vitro under different growth conditions can be rapidly and efficiently compared using the RNA arbitrarily primed polymerase chain reaction (RAP) fingerprinting method (Welsh et al., 1992b; Liang and Pardee, 1992). In RAP, a primer of arbitrary sequence primes both first and second strand cDNA synthesis. The mixture of products is then PCR amplified and resolved electrophoretically, yielding highly reproducible fingerprints that are tissue-specific or growth condition-specific. Differences between fingerprints arise from differentially expressed genes, as verified by Northern blot analysis. RAP can be performed on the RNA samples using various DNA primers. Each two day experiment yields a sample of approximately twenty cDNA products per lane making the identification of differentially or developmentally regulated genes no longer rate limiting. Those PCR products representing genes that a...

A rapid method was developed to differentiate the genus Propionibacterium from other genera by using a modified multiplex-PCR (MPCR) approach. Three 16S rRNA-targeted oligonucleotide primers were designed to amplify simultaneously two DNA-fragments in the MPCR assay. The universal primer pair bak11w and bak4 (corresponding to the E. coli 16S rRNA positions 8-25 and 1522-1540, respectively) was used in combination with the primer pair bak4 and gd1 (5&#39;-TGCTTTCGATACGGGTTGAC-3&#39;). The later sequence corresponding to a 16S rRNA motif that is unique for the genus Propionibacterium. Propionibacteria were identified by the amplification of a Propionibacterium-genus specific 900-bp fragment whereas MPCR with DNA from other bacteria generated only a DNA fragment of 1500 bp in amplifications with the two universal primers. The whole procedure including cell lysis, MPCR amplification and analysis can be performed within 1 day, detection limits are at approximately 10(3) cfu propionibacte...