Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Performance comparison of four exome capture systems for deep sequencing

Background

Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen’s SeqCap EZ v3.0, Agilent’s SureSelect v4.0, Illumina’s TruSeq Exome, and Illumina’s Nextera Exome, all applied to the same human tumor DNA sample.

Results

Each capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content.

Conclusions

We show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-449) contains supplementary material, which is available to authorized users.     

The Vibrio cholerae Extracellular Chitinase ChiA2 Is Important for Survival and Pathogenesis in the Host Intestine

In aquatic environments, Vibrio cholerae colonizes mainly on the chitinous surface of copepods and utilizes chitin as the sole carbon and nitrogen source. Of the two extracellular chitinases essential for chitin utilization, the expression of chiA2 is maximally up-regulated in host intestine. Recent studies indicate that several bacterial chitinases may be involved in host pathogenesis. However, the role of V. cholerae chitinases in host infection is not yet known. In this study, we provide evidence to show that ChiA2 is important for V. cholerae survival in intestine as well as in pathogenesis. We demonstrate that ChiA2 de-glycosylates mucin and releases reducing sugars like GlcNAc and its oligomers. Deglycosylation of mucin corroborated with reduced uptake of alcian blue stain by ChiA2 treated mucin. Next, we show that V. cholerae could utilize mucin as a nutrient source. In comparison to the wild type strain, ΔchiA2 mutant was 60-fold less efficient in growth in mucin supplemented minimal media and was also ∼6-fold less competent to survive when grown in the presence of mucin-secreting human intestinal HT29 epithelial cells. Similar results were also obtained when the strains were infected in mice intestine. Infection with the ΔchiA2 mutant caused ∼50-fold less fluid accumulation in infant mice as well as in rabbit ileal loop compared to the wild type strain. To see if the difference in survival of the ΔchiA2 mutant and wild type V. cholerae was due to reduced adhesion of the mutant, we monitored binding of the strains on HT29 cells. The initial binding of the wild type and mutant strain was similar. Collectively these data suggest that ChiA2 secreted by V. cholerae in the intestine hydrolyzed intestinal mucin to release GlcNAc, and the released sugar is successfully utilized by V. cholerae for growth and survival in the host intestine.     

Studies on the production and application of cellulase from Trichoderma reesei QM-9414

High yielding mutant strain, Trichoderma reesei QM-9414, was employed for the cellulase enzyme production. Enzyme production conditions (pH, inoculum age and concentration, and organic supplements) were optimized. The ability of partially purified enzyme to hydrolyze various regionally abundant lignocellulosic raw materials was studied. Enzymatic hydrolysis conditions (temperature, pH, enzyme and substrate concentrations) were optimized. Temperature 50v°C, pH 4.5, enzyme concentration 40 FPU/g substrate and substrate concentration 2.5% were found to be optimum for the maximum yields of sugars. #-glucosidase supplementation was found to increase both the sugar yield and hydrolysis rate, and shorten the reaction time significantly.     

Proteins containing non-native disulfide bonds generated by oxidative stress can act as signals for the induction of the heat shock response

While oxidative stress can induce a heat shock response, the primary signals that initiate activation have not been identified. To identify such signals, HepG2 and V 79 cells were exposed to menadione, a compound that redox-cycles to generate superoxide. The oxidative stress generated by menadione resulted in oxidation of protein thiols in a dose-dependent manner. This was followed by protein destabilization and denaturation, as determined by differential scanning calorimetry of whole cells. To directly evaluate the effect of non-native disulfides on protein conformation, Ca²⁺-ATPase, isolated from rabbit sarcoplasmic reticulum, was chemically modified to contain non-native intermolecular or glutathione (GHS)-mixed disulfides. Differential scanning calorimetry profiles and 1-anilinonaphthalene-8-sulfonic acid fluorescence indicated that formation of non-native disulfides produced protein destabilization, denaturation, and exposure of hydrophobic domains. Cellular proteins shown to contain oxidized thiols formed detergent-insoluble aggregates. Cells treated with menadione exhibited activation of HSF-1, accumulated Hsp 70 mRNA, and increased synthesis of Hsp 70. This work demonstrates that formation of physiologically relevant, non-native intermolecular and GSH-mixed disulfides causes proteins to destabilize, unfold such that hydrophobic domains are exposed, and initiate a signal for induction of the heat shock response. J. Cell. Physiol. 171:143–151, 1997. © 1997 Wiley-Liss, Inc.     

Integrative computational immunogenomic profiling of cortisol-secreting adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare but highly aggressive malignancy. Nearly half of ACC tumours overproduce and secrete adrenal steroids. Excess cortisol secretion, in particular, has been associated with poor prognosis among ACC patients. Furthermore, recent immunotherapy clinical trials have demonstrated significant immunoresistance among cortisol-secreting ACC (CS-ACC) patients when compared to their non-cortisol-secreting (nonCS-ACC) counterparts. The immunosuppressive role of excess glucocorticoid therapies and hypersecretion is known; however, the impact of the cortisol hypersecretion on ACC tumour microenvironment (TME), immune expression profiles and immune cell responses remain largely undefined. In this study, we characterized the TME of ACC patients and compared the immunogenomic profiles of nonCS-ACC and CS-ACC tumours to assess the impact of differentially expressed genes (DEGs) by utilizing The Cancer Genome Atlas (TCGA) database. Immunogenomic comparison (CS- vs. nonCS-ACC tumour TMEs) demonstrated an immunosuppressive expression profile with a direct impact on patient survival. We identified several primary prognostic indicators and potential targets within ACC tumour immune landscape. Differentially expressed immune genes with prognostic significance provide additional insight into the understanding of potential contributory mechanisms underlying failure of initial immunotherapeutic trials and poor prognosis of patients with CS-ACC.     

Comparison of different carbon ink based screen-printed electrodes towards amperometric immunosensing

The aim of the present work was to make amperometric immunosensors based on the principle of enzyme-linked immunosorbent assay (ELISA). For this purpose, screen-printed electrodes (SPEs) were fabricated using various carbon inks (commercially available inks Gwent, Acheson, Eltecks and two homemade inks PSG & PVCG) to determine the best ink in realizing immunosensors. Amperometric immunosensors made by different carbon inks were compared with standard ELISA in terms of total assay time, amount of biological materials used and sensitivity of detection. A model system containing rabbit anti-mouse immunoglobulin G (RαMIgG) as the capturing antibody, mouse IgG (MIgG) as antigen and alkaline phosphatase conjugated RαMIgG as revealing antibody was used. In these studies, 1-naphthyl phosphate was used as substrate. The experiments done include electrochemical characterization of electrodes, optimization of dilutions of antibodies, immobilization of antibody on the electrode were carried out. The minimum detection limit for the best results of MIgG determination were obtained on screen-printed electrode made by Gwent carbon ink and PSG carbon ink, with a detection limit of 1.0 and 2.0 ng/ml respectively. The time required for detection of mouse IgG was 40 min for SPEs. By using the conventional spectrophotometric method (ELISA method), the minimum detection limit for the MIgG (antigen) detection was 50 ng/ml and the time required for analysis was found to be 140 min.     

QUANTITATIVE ULTRASTRUCTURE AND PROTEIN COMPOSITION OF DATE PALM (PHOENIX DACTYLIFERA) SEEDS: A COMPARATIVE STUDY OF ENDOSPERM VS. EMBRYO

Comparative studies on the ultrastructure and protein composition of the embryo and endosperm of date palm (Phoenix dactylifera L.) were conducted. Cells of the embryo cotyledon and endosperm function in reserve storage and contained cell walls, nuclei, and cytoplasm rich in lipid and protein bodies. Morphometric analysis from light and electron micrographs showed that the cell walls of the endosperm occupied 65% of the total cell volume, but only 6% in the embryo. The protein bodies of the endosperm accounted for 11%, whereas those of the embryo occupied more than half of the total cell volume. The volume of organelles and organelle-free cytoplasm in the endosperm was negligible, suggesting that most of the extractable endosperm proteins are localized in the protein bodies. Extractable proteins in the embryo may come from cytoplasm, protein bodies, and other organelles. The endosperm contains relatively lower amounts of proteins than does the embryo. Proteins extracted from both tissues were compared using SDS-polyacrylamide gel electrophoresis, tube gel isoelectric focusing, and two-dimensional electrophoresis. Proteins of both the tissues were heterogeneous in molecular mass and charge. The majority of the proteins were similar in molecular mass and charge in the two tissues, suggesting that most of the storage proteins are probably the same. However, there were also several embryo- and endosperm-specific proteins apparent in both the first- and second-dimension gels. The endosperm-specific proteins may play an important role in germination and seedling development.     

Substrate Temperature Effect on Microstructure,Optical, and Glucose Sensing Characteristics of Pulsed Laser Deposited Silver Nanoparticles

This work reports the substrate temperature-influenced change in the structural, morphological, optical, and glucose sensing properties of silver (Ag) nanoparticles (NPs) deposited on p-type Si (100) wafers. AgNP films grown at temperatures ranging from RT to 600 °C clearly show a dependence of orientation texture and surface morphology on substrate temperature (T _s). As T _s increases from RT towards 600 °C, the preferred orientation of AgNP film changes from (111) to (200). The AgNPs size, that is T _s-dependent, reaches the maximum value at T _s = 300 °C. This result is attributed to restructuring of AgNPs texture. Moreover, the AgNP shape also changes from ellipsoid to sphere as T _s increases from RT to 600 °C. Surface plasmon enhancement in photoluminescence intensity is observed with increase in T _s. It is found also that the AgNP film deposited at 300 °C has considerable reflectance reduction relative to the silicon substrate, in wavelength range of 300–800 nm and a progressive red shift of localized surface plasmon resonances caused by the adding of increasing quantities of glucose has been observed. As a proof of concept, we also demonstrate the capability of grown AgNP substrates for glucose detection based on surface enhanced Raman spectroscopy in physiological concentration range with short integration time 10 s, varying with T _s.