Characterization and identification of compost bacteria based on 16S rRNA gene sequencing

The aim of this study was to isolate and characterize bacteria from the compost of fruit and vegetable waste (FVW) for plant growth-promoting (PGP) activities and investigate the pro-active influence of bacterial isolates on wheat growth. Fourteen bacterial strains (RHC-1 to RHC-14) were isolated and purified in tryptic soya agar (TSA). In addition to being biochemically characterized, these bacterial strains were also tested for their PGP traits, such as phosphate (P)-solubilization, nifH gene amplification, indole-3-acetic acid (IAA) quantification and the production of ammonia, oxidase and catalase. Based on 16S rRNA gene sequencing, these bacterial strains were identified as belonging to species of Bacillus, Lysinibacillus, Lysobacter, Staphylococcus, Enterobacter, Pseudomonas and Serratia. All bacterial strains solubilized tri-calcium phosphate and produced IAA. Two bacterial strains RHC-8 (Enterobacter sp.) and RHC-13 (Pseudomonas sp.) solubilized the maximum amount of tri-calcium phosphate, i.e. 486 and 464 μg/ml, respectively. P-solubilization was associated with a significant drop in the pH of the broth culture from an initial pH of 7 to pH 4.43. In addition to P-solubilization and IAA production, six bacterial strains also carried the nifH gene and were further evaluated for their effect on wheat (Triticum aestivum) growth under controlled conditions. All six bacterial strains enhanced wheat growth as compared to uninoculated control plants. Two of the bacterial strains, RHC-8 and RHC-13, identified as Enterobacter aerogenes and Pseudomonas brenneri, respectively, were assessed as potential PGP rhizobacteria due to exhibiting characteristics of four or more PGP traits and enhancing wheat growth though their specific mechanism of action.     

Salt-induced modulation in growth,photosynthesis and antioxidant system in two varieties of Brassica juncea

The present study was carried out to examine salt-induced modulation in growth, photosynthetic characteristics and antioxidant system in two cultivars of Brassica juncea Czern and Coss varieties (Varuna and RH-30). The surface sterilized seeds of these varieties were sown in the soil amended with different levels (2.8, 4.2 or 5.6 dsm⁻¹) of sodium chloride under a simple randomized block design. The salt treatment significantly decreased growth, net photosynthetic rate and its related attributes, chlorophyll fluorescence, SPAD value of chlorophyll, leaf carbonic anhydrase activity and leaf water potential, whereas electrolyte leakage, proline content, and activity of catalase, peroxidase and superoxide dismutase enzymes increased in both the varieties at 30 d stage of growth. The variety Varuna was found more resistant than RH-30 to the salt stress and possessed higher values for growth, photosynthetic attributes and antioxidant enzymes. Out of the graded concentrations (2.8, 4.2 or 5.6 dsm⁻¹) of sodium chloride, 2.8 sm⁻¹ was least toxic and 5.6 dsm⁻¹ was most harmful. The variation in the responses of these two varieties to salt stress is attributed to their differential photosynthetic traits, SPAD chlorophyll value and antioxidant capacity, which can be used as potential markers for screening mustard plants for salt tolerance.     

Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment

Background

Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analysis of many samples constitutes a significant cost, which could be reduced by pooling samples before capture. Another limitation to the number of cancer samples that can be analyzed is often the amount of available tumor DNA. We evaluated the performance of whole genome amplified DNA and the power to detect subclonal somatic single nucleotide variants in non-indexed pools of cancer samples using the HaloPlex technology for target enrichment and next generation sequencing.

Results

We captured a set of 1528 putative somatic single nucleotide variants and germline SNPs, which were identified by whole genome sequencing, with the HaloPlex technology and sequenced to a depth of 792–1752. We found that the allele fractions of the analyzed variants are well preserved during whole genome amplification and that capture specificity or variant calling is not affected. We detected a large majority of the known single nucleotide variants present uniquely in one sample with allele fractions as low as 0.1 in non-indexed pools of up to ten samples. We also identified and experimentally validated six novel variants in the samples included in the pools.

Conclusion

Our work demonstrates that whole genome amplified DNA can be used for target enrichment equally well as genomic DNA and that accurate variant detection is possible in non-indexed pools of cancer samples. These findings show that analysis of a large number of samples is feasible at low cost, even when only small amounts of DNA is available, and thereby significantly increases the chances of indentifying recurrent mutations in cancer samples.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-856) contains supplementary material, which is available to authorized users.     

Peristaltic motion of Phan–Thien–Tanner fluid in the presence of slip condition

This investigation considers the peristaltic flow of a Phan–Thien–Tanner fluid in the presence of slip condition and induced magnetic field. By use of the long wavelength and low Reynolds number approximations, closed form series solutions for stream function, pressure gradient, magnetic force function, axial induced magnetic field, and current density were obtained. The pressure gradient and frictional forces per wavelength were computed by numerical integration. The velocity slip condition in terms of shear stress is taken into account. Graphical results show the comparison between no-slip and viscous fluid cases. Pumping and trapping phenomena are discussed.     

Comparison of Phenacoccus solenopsis specimens from different regions of Pakistan using COI molecular barcoding (Hemiptera: Pseudococcidae)

Because correct identification of insects is crucial for pest management involving chemical or biological control agents, we have used a molecular approach to identify and characterize specimens of the cotton pest Phenacoccus solenopsis Tinsley (Sternorrhyncha: Pseudococcidae) present in different regions of Pakistan. The specimens were analyzed through DNA sequence analysis of their mitochondrial COI (mtCOI) gene using an improved procedure that could distinguish between the pest and its associated parasitoid. Our analysis showed no variation among the mealybug specimens from different geographical locations of Pakistan and confirmed that this is the same species and haplotype that is infesting cotton plants in other parts of Asia. This information will assist in the development of biological control programs against P. solenopsis in Pakistan and other Asian countries.     

TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues

Transmembrane beta barrel (TMB) proteins are found in the outer membranes of bacteria, mitochondria and chloroplasts. TMBs are involved in a variety of functions such as mediating flux of metabolites and active transport of siderophores, enzymes and structural proteins, and in the translocation across or insertion into membranes. We present here TMBHMM, a computational method based on a hidden Markov model for predicting the structural topology of putative TMBs from sequence. In addition to predicting transmembrane strands, TMBHMM also predicts the exposure status (i.e., exposed to the membrane or hidden in the protein structure) of the residues in the transmembrane region, which is a novel feature of the TMBHMM method. Furthermore, TMBHMM can also predict the membrane residues that are not part of beta barrel forming strands. The training of the TMBHMM was performed on a non-redundant data set of 19 TMBs. The self-consistency test yielded Q(2) accuracy of 0.87, Q(3) accuracy of 0.83, Matthews correlation coefficient of 0.74 and SOV for beta strand of 0.95. In this self-consistency test the method predicted 83% of transmembrane residues with correct exposure status. On an unseen, non-redundant test data set of 10 proteins, the 2-state and 3-state TMBHMM prediction accuracies are around 73% and 72%, respectively, and are comparable to other methods from the literature. The TMBHMM web server takes an amino acid sequence or a multiple sequence alignment as an input and predicts the exposure status and the structural topology as output. The TMBHMM web server is available under the tmbhmm tab at: http://service.bioinformatik.uni-saarland.de/tmx-site/.     

Lipid contribution to the affinity of antigen association with specific antibodies conjugated to liposomes

Immunoliposomes, directed to clinically relevant cell-surface molecules with antibodies, antibody fragments or peptides, are used for site-specific diagnostic evaluation or delivery of therapeutic agents. We have developed intrinsically echogenic liposomes (ELIP) covalently linked to fibrin(ogen)-specific antibodies and Fab fragments for ultrasonic imaging of atherosclerotic plaques. In order to determine the effect of liposomal conjugation on the molecular dynamics of fibrinogen binding, we studied the thermodynamic characteristics of unconjugated and ELIP-conjugated antibody molecules. Utilizing radioimmunoassay and enzyme-linked immunosorbent assay protocols, binding affinities were derived from data obtained at three temperatures. The thermodynamic functions ΔH°, ΔG° and ΔS° were determined from van't Hoff plots and equations of state. The resultant functions indicated that both specific and nonspecific associations of antibody molecules with fibrinogen occurred through a variety of molecular interactions, including hydrophophic, ionic and hydrogen bonding mechanisms. ELIP conjugation of antibodies and Fab fragments introduced a characteristic change in both ΔH° and ΔS° of association, which corresponded to a variable contribution to binding by phospholipid gel-liquid crystal phase transitions. These observations suggest that a reciprocal energy transduction, affecting the strength of antibody-antigen binding, may be a singular characteristic of immunoliposomes, having utility for optimization and further development of the technology.     

Peristaltic flow of a couple stress fluid in an asymmetric channel

This paper presents an analysis of the peristaltic flow of a couple stress fluid in an asymmetric channel. The asymmetric nature of the flow is introduced through the peristaltic waves of different amplitudes and phases on the channel walls. Mathematical modelling corresponding to a two-dimensional flow has been carried out. The flow analysis is presented under long wavelength and low Reynolds number approximations. Closed form solutions for the axial velocity, stream function and the axial pressure gradient are given. Numerical computations have been carried out for the pressure rise per wavelength, friction forces and trapping. It is noted that there is a decrease in the pressure when the couple stress fluid parameter increases. The variation of the couple stress fluid parameter with the size of the trapped bolus is also similar to that of pressure. Furthermore, the friction force on the lower channel wall is greater than that on the upper channel wall.