Effect of different Mg/Ca ratios and electrolyte concentrations in irrigation water on the nutrient content of wheat crop

Summary A study conducted in pots to evaluate the effect of different Mg/Ca ratios (2, 4, 8 and 16) and electrolyte concentrations (20 and 80 meq/l) at SAR 10 in irrigation water on the nutrient uptake and yield of wheat crop in two soils revealed that the average grain and dry matter yields of wheat decreased significantly with an increase in Mg/Ca ratio in irrigation water, but the magnitude of decrease was greater at higher electrolyte concentration than at lower electrolyte concentration. The concentration of Na in both straw and grain of wheat increased and that of K decreased with an increase in Mg/Ca ratio and electrolyte concentration of irrigation water, which led to higher Na/Ca and Na/K ratios in the plant. Further, the concentration of Ca and Mg both in straw as well as in grain increased with increasing electrolyte concentration of the irrigation water. An increasing proportion of Mg in saline irrigation water resulted in decreased concentration of Ca and increased concentration of Mg in both straw and grain of wheat crop. It was also noticed that the increasing proportion of Mg over Ca in the poor quality irrigation water increased the P content of both straw and grain of wheat crop.     

Hypofractionated radiotherapy in young versus older women with breast cancer: a retrospective study from India

BackgroundYoung women with breast cancer (BC) are not represented in the trials on hypofractionation. In this study we compared outcomes in young patients with BC to their older counterparts treated with hypofractionated radiotherapy (RT) in a regional cancer centre in India.Materials and methodsBetween January 1990 to December 2010, women with BC, treated with hypofractionated RT dose of 35–40 Gy/15#/3 weeks were divided into two groups, ≤ 35 years and > 35 years. Outcomes compared were locoregional recurrence rate (LRR), locoregional recurrence-free survival (LRRFS), disease-free survival (DFS), overall survival (OS) and toxicities. LRRFS, DFS and OS were estimated using the Kaplan-Meier method.ResultsOf total 2244 patients, 359 were ≤ 35 years of age and 1885 were > 35 years. Patient and disease characteristics were comparable between the two groups, except that comorbidities were significantly higher in the > 35 years age group, more patients aged ≤ 35 years had nodal N3 disease, received chemotherapy and RT to internal mammary nodes and more patients in the > 35 years group received hormonal therapy. Median follow up was 10 years (range 1–30 years). LRR and distant metastases were comparable between the two groups. However, synchronous LRR and distant metastases were significantly higher in the ≤ 35 years group 18 (5.1%) as compared to the > 35 years group 39 (2.1%) with p = 0.018. Estimated 10-year LRRFS, DFS and OS were 92% vs. 94% (p = 0.95), 68% vs. 73%(p = 0.058) and 78% vs. 76% (p = 0.10) in ≤ 35 years and > 35 years, respectively. OS for stage 1 was comparable between the two groups. However, for stage 2 and 3 it was 77% vs. 82% (p = 0.048) and 53% vs. 62% (p = 0.045) in the ≤ 35 years and > 35 years group, respectively. Acute and late toxicity were similar in the two groups.ConclusionYoung BC patients had higher LRR and distant metastases. LRRFS, DFS and toxicities were comparable between the two groups. However, OS was poorer in young BC patients with stage 2 and 3 disease.     

Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

The statistical validation of database search results is a complex issue in bottom-up proteomics. The correct and incorrect peptide spectrum match (PSM) scores overlap significantly, making an accurate assessment of true peptide matches challenging. Since the complete separation between the true and false hits is practically never achieved, there is need for better methods and rescoring algorithms to improve upon the primary database search results. Here we describe the calibration and False Discovery Rate (FDR) estimation of database search scores through a dynamic FDR calculation method, FlexiFDR, which increases both the sensitivity and specificity of search results. Modelling a simple linear regression on the decoy hits for different charge states, the method maximized the number of true positives and reduced the number of false negatives in several standard datasets of varying complexity (18-mix, 49-mix, 200-mix) and few complex datasets (E. coli and Yeast) obtained from a wide variety of MS platforms. The net positive gain for correct spectral and peptide identifications was up to 14.81% and 6.2% respectively. The approach is applicable to different search methodologies- separate as well as concatenated database search, high mass accuracy, and semi-tryptic and modification searches. FlexiFDR was also applied to Mascot results and showed better performance than before. We have shown that appropriate threshold learnt from decoys, can be very effective in improving the database search results. FlexiFDR adapts itself to different instruments, data types and MS platforms. It learns from the decoy hits and sets a flexible threshold that automatically aligns itself to the underlying variables of data quality and size.     

Improving yield performance of Pleurotus pulmonarius through hyphal anastomosis fusion of dikaryons

High production and good quality are always the principal goals for agriculturally important crops, without the exception of mushrooms. P. pulmonarius is one of the commercially important edible mushrooms throughout the world. The yield performance improvement was carried out by cross bred P. pulmonarius with P. sapidus and P. ostreatus. The highest rate of 0.587 mm/days for spawn ramification and 53.33 % for percentage spawn productivity were obtained in hybrids LN LL910. The least day (11 and 12th) of the primodia mushroom sporophore were recorded in LL910 and LN 97 respectively, while longest day of 19th was recorded in wild type (NE 07). The highest biological efficiency (109.30 %) and production rate (3.77 %) obtained by LL910, while the least of 33.0 and 0.79 % were obtained by NE 07 for biological efficiency and production rate respectively. The morphological and molecular characterization of the hybrid strains established their true variation from their wild type. LL 910 (JF68088) is located at seventh subclusters from the root with boostrap value of 32 %, while only one parent (LAU 09: JF736658) out of the two has the close boostrap value of 43 % at the first subcluster to the root, with the other parent LAU 10 (JF736659) shows distance relationship after Blast. LN 97 (JF680992) is located at outgroup, while the parent strains NE 07 (boostrap value: 11 %) and LAU 09 (boostrap value: 44 %) located at tenth and second subclusters respectively. The results obtained from this study have shown the improved performance of the hybrids strain over wild type strains.     

Interaction between Human Prion Protein and Amyloid-β (Aβ) Oligomers: ROLE OF N-TERMINAL RESIDUES*

Soluble oligomers of Aβ42 peptide are believed to play a major role in the pathogenesis of Alzheimer disease (AD). It was recently found that at least some of the neurotoxic effects of these oligomers may be mediated by specific binding to the prion protein, PrP^C, on the cell surface (Laurén, J., Gimbel, D. A., Nygaard, H. B., Gilbert, J. W., and Strittmatter, S. M. (2009) Nature 457, 1128–1132). Here we characterized the interaction between synthetic Aβ42 oligomers and the recombinant human prion protein (PrP) using two biophysical techniques: site-directed spin labeling and surface plasmon resonance. Our data indicate that this binding is highly specific for a particular conformation adopted by the peptide in soluble oligomeric species. The binding appears to be essentially identical for the Met¹²⁹ and Val¹²⁹ polymorphic forms of human PrP, suggesting that the role of PrP codon 129 polymorphism as a risk factor in AD is due to factors unrelated to the interaction with Aβ oligomers. It was also found that in addition to the previously identified ∼95–110 segment, the second region of critical importance for the interaction with Aβ42 oligomers is a cluster of basic residues at the extreme N terminus of PrP (residues 23–27). The deletion of any of these segments results in a major loss of the binding function, indicating that these two regions likely act in concert to provide a high affinity binding site for Aβ42 oligomers. This insight may help explain the interplay between the postulated protective and pathogenic roles of PrP in AD and may contribute to the development of novel therapeutic strategies as well.     

Sequence and structural characterization of Trx-Grx type of monothiol glutaredoxins from Ashbya gossypii

Glutaredoxins are enzymatic antioxidants which are small, ubiquitous, glutathione dependent and essentially classified under thioredoxin-fold superfamily. Glutaredoxins are classified into two types: dithiol and monothiol. Monothiol glutaredoxins which carry the signature “CGFS“ as a redox active motif is known for its role in oxidative stress, inside the cell. In the present analysis, the 138 amino acid long monothiol glutaredoxin, AgGRX1 from Ashbya gossypii was identified and has been used for the analysis. The multiple sequence alignment of the AgGRX1 protein sequence revealed the characteristic motif of typical monothiol glutaredoxin as observed in various other organisms. The proposed structure of the AgGRX1 protein was used to analyze signature folds related to the thioredoxin superfamily. Further, the study highlighted the structural features pertaining to the complex mechanism of glutathione docking and interacting residues.     

Protein modeling,molecular network and molecular dynamics study of newly sequenced interleukin-18 (IL-18) gene in Mus musculus

Interleukin-18 (IL-18) belongs to the superfamily of IL-1 protein and exerts a pleiotropic pro-inflammatory effect on the body. Generally, this protein is significantly involved in immune defense during infection in cells, but sometimes its anomalous activities produce some inflammatory diseases like rheumatoid arthritis and Crohn’s disease. In the present study, the IL-18 gene was isolated from mice and was subsequently cloned and sequenced. Further, the network analysis was carried out to explore the functional role of IL-18 protein in animals. The 3D protein structure of the IL-18 protein was generated and docked with appropriate 3-([3-cholamidopropyl]dimethylammonio)-1-propanesulfonate (CPS) ligand. Later the complex structure of the protein was subjected to molecular dynamics simulation (MDS) for 50 ns to determine the effect of ligand on protein. The network analysis explored the correlation of IL-18 protein with others proteins and their involvement in the different significant pathway to defend the cell from various diseases. As confirmed by MDS, the CPS:IL-18 complex was found to be highly stable. Our results further indicated that CPS ligand has the potential to act as a drug molecule, in future, for counteracting IL-18 activity. To date, no structural details were available for animal IL-18. Hence, the finding of this study will be useful in broadening the horizon towards a better understanding of the functional and structural aspects of IL-18 in animals.