A teleost polymeric Ig receptor exhibiting two Ig-like domains transports tetrameric IgM into the skin

The skin mucus IgM is an important molecule in the mucosal immune system of teleost skin. However, the transport mechanism associated with this molecule has yet to be clarified. In this study, we isolated a gene encoding a polymeric Ig receptor (pIgR) from a species of teleost fish, Takifugu rubripes (fugu). This gene is known to be an Ig transporter in the intestine of mammals. Our studies further demonstrated that fugu pIgR was expressed in the skin and that a fragment of pIgR bound to tetrameric IgM in the skin mucus. These results indicate that the skin pIgR transports tetrameric IgM into the skin mucus. The fugu pIgR exhibits a unique structure containing only two Ig-like domains corresponding to domain 1 and domain 4/5 of mammalian pIgR. This structure was sufficient for successful binding to tetrameric IgM. Teleost skin thus adopts the same Ig transport system as mammalian intestine via a unique pIgR.     

Physiological traits associated with heat tolerance in bread wheat (Triticum aestivum L.)

Field experiments for evaluating heat tolerance-related physiological traits were conducted for two consecutive years using a mapping population of recombinant inbred lines (RILs) from the cross RAJ4014/WH730. Chlorophyll content (Chl) and chlorophyll fluorescence (CFL) were recorded under timely sown (TS) and late sown (LS) conditions. Late sowing exposes the terminal stage of plants to high temperature stress. Pooled analysis showed that CFL and Chl differed significantly under TS and LS conditions. The mean value of CFL (Fv/Fm) and Chl under both timely and late sown conditions were used as physiological traits for association with markers. Regression analysis revealed significant association of microsatellite markers viz., Xpsp3094 and Xgwm131 with coefficients of determination (R²) values for CFL (Fv/Fm) and Chl as 12 and 8 %, respectively. The correlation between thousand grain weight (TGW) with Chl and CFL were 14 and 7 % and correlation between grain wt./spike with Chl and CFL were 15 and 8 %, respectively. The genotypes showing tolerance to terminal heat stress as manifested by low heat susceptibility index (HSI = 0.43) for thousand grain weight, were also found having very low Chl, HSI (−0.52). These results suggest that these physiological traits may be used as a secondary character for screening heat-tolerant genotypes.     

Identification of indels in next-generation sequencing data

Background

The discovery and mapping of genomic variants is an essential step in most analysis done using sequencing reads. There are a number of mature software packages and associated pipelines that can identify single nucleotide polymorphisms (SNPs) with a high degree of concordance. However, the same cannot be said for tools that are used to identify the other types of variants. Indels represent the second most frequent class of variants in the human genome, after single nucleotide polymorphisms. The reliable detection of indels is still a challenging problem, especially for variants that are longer than a few bases.

Results

We have developed a set of algorithms and heuristics collectively called indelMINER to identify indels from whole genome resequencing datasets using paired-end reads. indelMINER uses a split-read approach to identify the precise breakpoints for indels of size less than a user specified threshold, and supplements that with a paired-end approach to identify larger variants that are frequently missed with the split-read approach. We use simulated and real datasets to show that an implementation of the algorithm performs favorably when compared to several existing tools.

Conclusions

indelMINER can be used effectively to identify indels in whole-genome resequencing projects. The output is provided in the VCF format along with additional information about the variant, including information about its presence or absence in another sample. The source code and documentation for indelMINER can be freely downloaded from www.bx.psu.edu/miller_lab/indelMINER.tar.gz.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0483-6) contains supplementary material, which is available to authorized users.     

Receiver operating characteristic curve analysis of BMI in assessing obesity among adult Bengalee males in India

The present study attempted to understand the appropriateness of different body mass index (BMI) cut-off points in assessing obesity. Four hundred thirty adult Bengalee males with mean age 36.48 +/- 12.23 years (mean +/- SD) from West Bengal, India were studied. Height, weight and percent body fat were measured and BMI was derived following standard equation. Receiver operating characteristic (ROC) curve analysis demonstrated low sensitivity and high specificity of international (> or = 30 kg/m2) and proposed (> or = 25 kg/m2) BMI cut-off points in identifying individuals with obesity. Furthermore, these international and proposed BMI cut-off points also found to be in substantial misclassification to assess obesity as much as 32.09% and 17.44% respectively. However, based on ROC curve analysis, a BMI cut-off point of > or = 24 kg/m2 revealed optimal sensitivity (83.66%) and specificity (90.61%) and as well as less misclassification (11.86%) in assessing obesity among the adult Bengalee males. The present study accentuated that the international and proposed BMI cut-off points so far might not be appropriate in assessing obesity and on the other hand, lower BMI cut-off point (> or = 24 kg/m2) has relatively high sensitivity and specificity in assessing obesity as well. Therefore, the present study envisages the requirement of further lowering down of BMI cut-off point in assessing excess body fat in adult Bengalee males.     

Controlled Synthesis of Saponin-Capped Silver Nanotriangles and Their Optical Properties

Here, in this report, saponin-capped triangular silver nanocrystals have been synthesized in aqueous system by using only Trigonella foenum-graecum seed extract as a reducing agent. X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), and atomic force microscope (AFM) have been used for the study of their morphological and structural characterization, which indicate that the synthesized nanoparticles are crystalline in nature with triangular morphology having the edge length of the triangle as 80 nm approximately. UV/Vis study of the nanoparticle solution shows three absorption peaks at wavelength of 360 nm, 432 nm, and 702 nm, and these are respectively related to the transverse and longitudinal oscillations of electron, which remain almost in the same position for more than 6 months, indicating the formation of silver nanocrystals with a higher stability. Further, Fourier transform infrared spectroscopy (FTIR) spectra clearly indicate the capping of nanoparticles by saponin, one of the components of Trigonella foenum-graecum extract.

     

Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex

Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the coexistence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative quantitative trait loci (QTL) underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.     

New 1,3,5-trioxygenated xanthones in Canscora decussata

Aerial parts of Canscora decussata have been shown to contain 1-methoxy-3,5-dihydroxyxanthone and its 3-O-rutinosyl derivative. The identity of these compounds was established by chemical transformation and spectral (UV, IR, PMR, MS) evidence of the compounds and their derivatives. This is the first demonstration of the occurrence of the two compounds in nature.