Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis.

RNA-seq is currently considered the most powerful, robust and adaptable technique for measuring gene expression and transcription activation at genome-wide level. As the analysis of RNA-seq data is complex, it has prompted a large amount of research on algorithms and methods. This has resulted in a substantial increase in the number of options available at each step of the analysis. Consequently, there is no clear consensus about the most appropriate algorithms and pipelines that should be used to analyse RNA-seq data. In the present study, 192 pipelines using alternative methods were applied to 18 samples from two human cell lines and the performance of the results was evaluated. Raw gene expression signal was quantified by non-parametric statistics to measure precision and accuracy. Differential gene expression performance was estimated by testing 17 differential expression methods. The procedures were validated by qRT-PCR in the same samples. This study weighs up the advantages and disadvantages of the tested algorithms and pipelines providing a comprehensive guide to the different methods and procedures applied to the analysis of RNA-seq data, both for the quantification of the raw expression signal and for the differential gene expression.

Systematic review and meta-analysis of artemisinin based therapies for the treatment and prevention of schistosomiasis.

BACKGROUND: Chemotherapy based on repeated doses of praziquantel is still the most effective control strategy against Schistosomiasis, however artemisinin derivatives emerged as a family of compounds with schistomicide activity. The aim of the present work is to compare the efficacy of artemisinin-based therapies in the treatment and prophylaxis of human schistosomiasis. The design of this work involved a quantitative systematic review and meta-analysis. METHODOLOGY/PRINCIPAL FINDINGS: Retrieval of published studies was carried out through an electronic search of the PubMed (MEDLINE), EMBASE, Cochrane Library and CINAHL databases. This included reports comparing the therapeutic efficacy of artesunate alone, artesunate plus sulfadoxine-pyrimethamine and a combination of artemisinin derivatives plus praziquantel against praziquantel alone on different types of schistosomiasis. Moreover, studies on artesunate and artemether used as preventive drugs were also analyzed against placebo. The primary outcome measure for schistosomiasis treatment was "parasitological cure", whereas for the prophylaxis the outcome evaluated was "infection rate". Our results show that patients treated with artesunate alone have significantly lower cure rates than those treated with praziquantel (OR = 0.27 (95% C.I. 0.13-0.53; p<0.001)) and that the combined therapy of artesunate plus sulfadoxine-pyrimethamine is also significantly less effective than praziquantel treatment (OR = 0.14 (95% C.I. 0.02-0.92; p = 0.04)). However, the combination of an artemisinin derivatives plus praziquantel showed a higher cure rate than praziquantel monotherapy with OR = 2.07 (95% C.I. 1.27-3.36; p = 0.003). Finally, chemoprophylaxis with either artesunate (RR = 0.11 (95% C.I. 0.06-0.22; p<0.001)) or artemether (RR = 0.25 (95% C.I. 0.16-0.40; p<0.001)) was significantly better than a placebo in both cases. CONCLUSIONS/SIGNIFICANCE: This meta-analysis confirms that artemisinin derivatives used in combination with praziquantel have the potential to increase the cure rates in schistosomiasis treatment, but not artesunate alone. It is also confirmed that repeated doses of artemisinin derivatives play a prophylactic role, significantly reducing the incidence of Schistosoma japonicum infections compared with placebo.

Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia.

With the proliferation of related microarray studies by independent groups, a natural approach to analysis would be to combine the results across studies. In this article, we address a meta-analysis of the gene expression data on imatinib resistance in chronic myelogenous leukemia. First, an analysis of the overlapping among 6 published studies revealed that only 3 genes were coincident between 2 studies. A later reprocessing using different methods on 4 publicly available datasets revealed that 2 extra genes were overlapped between two sets. Both poor overlappings may be due to large differences in the sample source, the microarray platforms used, and a small difference in gene expression between the imatinib non-responder and responder patients. A search of common genes inside 4 public datasets afforded 404 well defined genes. Nevertheless, this necessary condition for meta-analysis caused the loss of many genes of possible interest. The expression signals of the common genes in the four datasets were reanalyzed using three summary statistical methods for combining quantitative information: Fisher, Stouffer and effect-size. Taking the three methods together and using an FDR<0.10 threshold, a gene-list with 33 differentially expressed genes was found. Considering all the reanalysis approaches used in this work, a final gene-list with 38 differentially expressed genes is reported. Despite the important limitations to this microarray meta-analysis, the presented procedures and integrated gene-list may have some potential value as regards imatinib resistance in CML patients since it is the first attempt to integrate evidence about gene-lists in this area.

Modelling the simultaneous processes occurring during the BOD(5) test using synthetic waters as a pattern.

Synthetic waters imitating BOD(5) test conditions have been studied to model the progress curves of cell growth, organic matter consumption and oxygen demand. Glucose and glutamic acid were used as organic matter and Bacillus subtilis, Escherichia coli and Pseudomonas putida as microorganisms. The concentrations of all the products were measured simultaneously over time and were fitted to the Logistic and Monod models. Following this, the goodness of fit was analysed. Discrimination between models allowed us to conclude that the Logistic model has acceptable accuracy to describe the kinetic behaviour inside a BOD(5) bottle, while the extra parameter in the Monod model would not be statistically justified. Thus, the logistic parameters were determined under different conditions by non-linear regression and their biological meaning was interpreted.

A comparative study of the adsorption of humic acid, fulvic acid and phenol onto Bacillus subtilis and activated sludge.

The adsorption of humic acid and fulvic acid onto Bacillus subtilis cells and activated sludge biomass was studied as a function of pH and incubation time. The adsorption of humic and fulvic acids was strongly pH-dependent and followed the same trend on both surfaces, increasing in a sigmoidal way with decreasing pH over the 2-10 pH range. This behaviour is explained in terms of hydrophobic interactions between the uncharged biomass and the uncharged humic and fulvic acids. In contrast, the adsorption of phenol onto B. subtilis cells and activated sludge biomass showed in both cases an optimum pH at around 7.0. This optimum value may be interpreted in terms of a combination of hydrophobic interactions and hydrogen bonds between undissociated phenol and polar groups on the cell walls. Kinetic studies on the adsorption of humic acid, fulvic acid and phenol onto B. subtilis cells and sludge biomass pointed to a rapid uptake of the substances, with an equilibrium time of about 30 min. In all cases, the kinetic curves were acceptably fitted by non-linear regression to an exponential function, suggesting a first-order kinetic phenomenon. The specific adsorption values collected at optimum pH revealed that with the materials used in this work both B. subtilis and activated sludge follow the same adsorption trend: humic>fulvic>phenol. The lower adsorption of fulvic acid as compared with humic acid may be explained in terms of its lower hydrophobicity rather than its lower molecular size. On comparing the specific adsorption values of activated sludge versus B. subtilis, similar but lower figures were found for the three organic compounds studied. This similar behaviour suggests that both types of biomass base their adsorption capacity on the general characteristics of the bacterial cell wall, and the lower adsorption by the sludge would be due to a lower specific area due to clustering of the cells. This is remarkable, since sludge is a heterogeneous and cheap material in comparison with cultured bacterial cells.