ConDeTri--a content dependent read trimmer for Illumina data

During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in sequencing costs. Particularly, Illumina/Solexa sequencing has had an increasing impact on gathering data from model and non-model organisms. However, accurate and easy to use tools for quality filtering have not yet been established. We present ConDeTri, a method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads so that sequencing reads can be standardized. Another aspect of the method is to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequence data of arbitrary length and it is independent from sequencing coverage and user interaction. ConDeTri is able to trim and remove reads with low quality scores to save computational time and memory usage during de novo assemblies. Low coverage or large genome sequencing projects will especially gain from trimming reads. The method can easily be incorporated into preprocessing and analysis pipelines for Illumina data. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://code.google.com/p/condetri.     

Propensity Scoring after Multiple Imputation in a Retrospective Study on Adjuvant Radiation Therapy in Lymph-Node Positive Vulvar Cancer

Propensity scoring (PS) is an established tool to account for measured confounding in non-randomized studies. These methods are sensitive to missing values, which are a common problem in observational data. The combination of multiple imputation of missing values and different propensity scoring techniques is addressed in this work. For a sample of lymph node-positive vulvar cancer patients, we re-analyze associations between the application of radiotherapy and disease-related and non-related survival. Inverse-probability-of-treatment-weighting (IPTW) and PS stratification are applied after multiple imputation by chained equation (MICE). Methodological issues are described in detail. Interpretation of the results and methodological limitations are discussed.     

SEASONAL CHANGES IN STRUCTURE OF A SUBMERGED BLUEGREEN ALGAL/BACTERIAL COMMUNITY FROM A GEOTHERMAL HOTSPRING1

The species (cytospecies) structure and seasonal dynamics of a thermophilic bluegreen algal/bacterial community from Mimbres, New Mexico are described. Using stereological techniques, several common quantitative ecological parameters (biomass, density, distribution measurements, Species Diversity Indices, importance values) were described for the community growing ca. 1 m beneath the water surface on the inner walls of a concrete cistern. Temperature and pH were relatively constant while water flow rates, duration and intensity of light showed seasonal variation. The total volume of the mat occupied by living organisms did not exceed 2% during the entire year. The remaining volume was occupied by gas and water bubble chambers, gelatinous matrix, empty tubes, mineral deposits, and water. The total biomass remained constant except during a period of severe, seasonal light reduction (November). Species Diversity Indices, density and importance values for the bluegreen algal and bacterial populations showed seasonal changes. The three dominant bluegreen algal cytospecies which represented the greatest amount of biomass alternated in their abundance on a seasonal basis while the three dominant bacterial cytospecies remained the same throughout the period of study. Although considerable season change occurred in the species structure of this community, the total living volume remained relatively constant with the major changes in the bluegreen algal populations. Many of the seasonal changes observed appear to correlate with seasonal changes in light intensity and duration.     

The Reproductive Behavior of Acanthurus nigrofuscus (Forskal) and other Surgeonfishes (Fam. Acanthuridae) off Eilat,Israel (Gulf of Aqaba,Red Sea)

The reproductive behavior of Acanthurus nigrofuscus, a common surgeonfish of the Red Sea, is described for two overlapping populations inhabiting the coral reefs off Eilat, Israel (Gulf of Aqaba). The spectacular daily spawning activities, often involving aggregations of thousands of individuals, as well as the often long distance migrations to and from the spawning grounds by groups in highly organized formations are characterized in detail. Evidence is provided that the precise timing of these various phenomena is controlled by ambient light levels during the late afternoon. Less detailed information is also provided on comparable activities of two other surgeonfishes from the same reefs: Ctenochaetus striatus and Zebrasoma xanthurum. Finally, comparisons are made of reproduction and its associated environmental controls among populations of the same and related species of surgeonfishes at widely distributed locations in the Indo-Pacific.     

Preferential binding and structural distortion by Fe2+ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences

Certain DNA sequences are known to be unusually sensitive to nicking via the Fe2+-mediated Fenton reaction. Most notable are a purine nucleotide followed by three or more G residues, RGGG, and purine nucleotides flanking a TG combination, RTGR. Our laboratory previously demonstrated that nicking in the RGGG sequences occurs preferentially 5' to a G residue with the nicking probability decreasing from the 5' to 3'end of these sequences. Using 1H NMR to characterize Fe2+ binding within the duplex CGAGTTAGGGTAGC/GCTACCCTAACTCG and 7-deazaguanine-containing (Z) variants of it, we show that Fe2+ binds preferentially at the GGG sequence, most strongly towards its 5' end. Substitutions of individual guanines with Z indicate that the high affinity Fe2+ binding at AGGG involves two adjacent guanine N7 moieties. Binding is accompanied by large changes in specific imino, aromatic and methyl proton chemical shifts, indicating that a locally distorted structure forms at the binding site that affects the conformation of the two base pairs 3' to the GGG sequence. The binding of Fe2+ to RGGG contrasts with that previously observed for the RTGR sequence, which binds Fe2+ with negligible structural rearrangements.     

T-cell receptor BV gene usage in colorectal carcinoma patients immunised with recombinant Ep-CAM protein or anti-idiotypic antibody

The tumour-associated antigen, Ep-CAM, is over-expressed in colorectal carcinoma (CRC). In the present study, a recombinant Ep-CAM protein or a human anti-idiotypic antibody (anti-Id) mimicking Ep-CAM, either alone or in combination, was used for vaccination of CRC patients (n=9). GM-CSF was given as an adjuvant cytokine. A cellular immune response was assessed by measuring anti-Ep-CAM lymphoproliferation, IFN- production (ELISPOT) and by analysing the TCR BV gene usage within the CD4+ and CD8+ T-cell subsets followed by CDR3 fragment analysis. A proliferative and/or IFN- T-cell response was induced against the Ep-CAM protein in eight out of nine patients, and against Ep-CAM-derived peptides in nine out of nine patients. Analysis of the TCR BV gene usage showed a significantly higher usage of BV12 family in CD4+ T cells of patients both before and after immunisation than in those of healthy control donors (p<0.05). In the CD8+ T-cell subset, a significant (p<0.05) increase in the BV19 usage was noted in patients after immunisation. In individual patients, a number of TCR BV gene families in both CD4+ and CD8+ T cells were over-expressed mainly in post-immunisation samples. Analysis of the CDR3 length polymorphism revealed a higher degree of clonality in post-immunisation samples than in pre-immunisation samples. In vitro stimulation with Ep-CAM protein confirmed the expansion of anti-Ep-CAM T-cell clones. The results indicate that immunisation with the Ep-CAM protein and/or anti-Id entails the induction of an anti-Ep-CAM T-cell response in CRC patients, and suggest that BV19+ CD8+ T cells might be involved in a vaccine-induced immune response.