Cadmium stress-induced oxidative stress and role of nitric oxide in rice (Oryza sativa L.)

Cadmium (Cd) is a potential environmental phytotoxicant. The generation of reactive oxygen species (ROS) due to Cd stress is responsible for the induction of oxidative stress in plants. On the other hand, SNP, a NO donor is known to have effect on Cd-induced oxidative stress in plants. We evaluated the effect of NO on the regulation of Cd stress in the rice (Oryza sativa L.) variety MSE-9. Cd treatment was given in the form of 50, 100 and 200 ??M, whereas for interaction study, 100 ??M of Cd and 100 ??M of SNP were used. The result showed that Cd-induced oxidative stress in MSE-9 by generating ROS. However, when SNP was given with Cd stress, it was seen that SNP treatment regulated the stress metabolism in rice seedlings under Cd toxicity by generating NO. It can be said that the SNP in combination with Cd treatment might possess the way to protect rice seedlings under Cd stress.     

Isolation of enriched carp spermatogonial stem cells from Labeo rohita testis for in vitro propagation

The in vitro culture system for spermatogonial stem cells (SSCs) is a powerful tool for exploring molecular mechanisms of male gametogenesis and gene manipulation. Very little information is available for fish SSC biology. Our aim was to isolate highly pure SSCs from the testis of commercially important farmed carp, Labeo rohita. The minced testis of L. rohita was dissociated with collagenase. Dissociated cells purified by two-step Ficoll gradient centrifugation followed by magnetic activated cell sorting (MACS) using Thy1.2 (CD90.2) antibody dramatically heightened recovery rate for spermatogonial cells. The purified cells were cultured in vitro conditions for more than two months in L-15 media containing 10% fetal bovine serum (FBS), 1% carp serum, and other nutrients. The proliferative cells were dividing as validated by 5-bromo-2′-deoxyuridine (BrdU) incorporation assay and formed colonies/clumps with the typical characteristics of SSCs A majority of enriched cell population represented a Vasa⁺, Pou5f1/pou5f1⁺, Ssea-1⁺, Tra-1-81⁺, plzf⁺, Gfrα1/gfrα1⁻, and c-Kit/c-kit⁻ as detected by immunocytochemical and/or quantitative real-time polymerase chain reaction (RT-PCR) analyses. Thus, Thy1⁺ SSCs were enriched with greater efficiency from the mixed population of testicular cells of L. rohita. A population of enriched spermatogonial cells could be cultured in an undifferentiated state. The isolated SSCs could provide avenue for undertaking research on basic and applied reproductive biology.     

Glucose-stimulated translation regulation of insulin by the 5' UTR-binding proteins

Insulin is the key regulator of glucose homeostasis in mammals, and glucose-stimulated insulin biosynthesis is essential for maintaining glucose levels in a narrow range in mammals. Glucose specifically promotes the translation of insulin in pancreatic β-islet, and the untranslated regions of insulin mRNA play a role in such regulation. Specific factors in the β-islets bind to the insulin 5' UTR and regulate its translation. In the present study we identify protein-disulfide isomerase (PDI) as a key regulator of glucose-stimulated insulin biosynthesis. We show that both in vitro and in vivo PDI can specifically associate with the 5' UTR of insulin mRNA. Immunodepletion of PDI from the islet extract results in loss of glucose-stimulated translation indicating a critical role for PDI in insulin biosynthesis. Similarly, transient overexpression of PDI resulted in specific translation activation by glucose. We show that the RNA binding activity of PDI is mediated through PABP. PDI catalyzes the reduction of the PABP disulfide bond resulting in specific binding of PABP to the insulin 5' UTR. We also show that glucose stimulation of the islets results in activation of a specific kinase that can phosphorylate PDI. These findings identify PDI and PABP as important players in glucose homeostasis.     

BBProF: An Asynchronous Application Server for Rapid Identification of Proteins Associated with Bacterial Bioleaching

Recovery of metal value, especially from low-grade ores and overburden minerals using acidophilic bacteria through the process of bioleaching is an environmentally benign and commercially scalable biotechnology. In recent years, while the “OMICS” landscape has been witnessing extensive application of computational tools to understand and interpret global biological sequence data, a dedicated bioinformatic server for analysis of bacterial information in the context of its bioleaching ability is not available. We have developed an on-line Bacterial Bioleaching Protein Finder (BBProF) System, which rapidly identifies novel proteins involved in a bacterial bioleaching process and also performs phylogenetic analysis of 16S rRNA genes. BBProF uses the features of Asynchronous Java Script and XML (AJAX) to provide an efficient and fast user experience with minimal requirement of network bandwidth. In the input module the server accepts any bacterial or archaeal complete genome sequence in RAW format and provides a list of proteins involved in the microbial leaching process. BBProF web server is integrated with the European Bioinformatics Institute (EBI) web services such as BLAST for homology search and InterProScan for functional characterization of output protein sequences. Studying evolutionary relationship of bacterial strains of interest using Muscle and ClustalW2 phylogeny web services from EBI is another key feature of our server, where 16S rRNA gene sequences are considered as input through a JQUERY interface along with the sequences present in the BBProF database library. Complete genome sequences of 24 bioleaching microorganism characterized by genomic and physiological study in the laboratory and their respective 16S rRNA gene sequences were stored in the database of the BBProF library. To our knowledge BBProF is the first integrated bioinformatic web server that demonstrates its utility in identifying potential bioleaching bacteria. We hope that the server facilitate ongoing comparative genomic studies on of bioleaching microorganisms and also assist in identification and design of novel microbial consortia that are optimally efficient bioleaching agents.     

Insect Barcode Information System

Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client– server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.

Availability

http://www.nabg-nbaii.res.in/barcode     

Improved production of laccase by Daedalea flavida: consideration of evolutionary process optimization and batch-fed culture

The genetic algorithm was used effectively to find the optimal values of eight process variables for the maximum laccase production by Daedalea flavida in a stationary culture. The algorithm was modified suitably to improve laccase production with 18 parallel experiments in 4 generations. A high enzyme titer of 65 % was achieved after the optimization and compared to the titer obtained before optimization. To study the effect of the surface immobilized growth on the enzyme production, the fungus was grown on three solid carriers. When cultured on polymer composite fibers, polyurethane foam, or steel wool, at least 2.5 times more biomass was produced, compared to the biomass produced in support-free growth. On the contrary, the mycelia grown on solid support produced much less laccase than non-adhering mycelia. Four parallel runs of batch-fed cultures were done, using the cell mass of D. flavida to evaluate the influence of four different volumes of medium exchanged on laccase production. For sustainable production of the enzyme, complete exchange of medium was favorable, where the laccase activity increased continuously in six consecutive cycles, though, 50 % exchange of medium produced the maximum laccase in terms of mean enzyme activity obtained in six cycles.     

Extraction and characterization of biocompatible hydroxyapatite from fresh water fish scales for tissue engineering scaffold

In bone tissue engineering, porous hydroxyapatite (HAp) is used as filling material for bone defects, augmentation, artificial bone graft and scaffold material. The present paper compares the preparation and characterization of HAp from fish scale (FS) and synthetic body fluid (SBF) solution. Thermo gravimetric analysis, differential thermal analysis, Fourier transform infrared spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM) and particle size analysis of the samples have been performed. The analysis indicates that synthesized HAp consists of sub-micron HAp particle with Ca/P ratio corresponding to FS and SBF 1.62 and 1.71, respectively. MTT assay and quantitative DNA analysis show growth and proliferation of cells over the HA scaffold with the increase in time. The shape and size (morphology) of mesenchymal stem cells after 3 days show a transition from rounded shape to elongated and flattened shape expressing its spreading behavior. These results confirm that HAp bio-materials from fish scale are physico-chemically and biologically equivalent to the chemically synthesized HAp from SBF. Biological HAp, thus, possesses a great potential for conversion of industrial by-product into highly valuable compounds using simple effective and novel processes.     

Inhibition of pathogenic bacterial biofilm by biosurfactant produced by Lysinibacillus fusiformis S9

A biosurfactant producing microbe isolated from a river bank was identified as Lysinibacillus fusiformis S9. It was identified with help of biochemical tests and 16S rRNA gene phylogenetic analysis. The biosurfactant S9BS produced was purified and characterized as glycolipid. The biosurfactant showed remarkable inhibition of biofilm formation by pathogenic bacteria like Escherichia coli and Streptococcus mutans. It was interesting to note that at concentration of 40 μg ml^?1 the biosurfactant did not show any bactericidal activity but restricted the biofilm formation completely. L. fusiformis is reported for the first time to produce a glycolipid type of biosurfactant capable of inhibiting biofilm formation by pathogenic bacteria. The biosurfactant inhibited bacterial attachment and biofilm formation equally well on hydrophilic as well as hydrophobic surfaces like glass and catheter tubing. This property is significant in many biomedical applications where the molecule should help in preventing biofouling of surfaces without being toxic to biotic system.     

Structural and Functional Insights into the Catalytic Inactivity of the Major Fraction of Buffalo Milk Xanthine Oxidoreductase

Background

Xanthine oxidoreductase (XOR) existing in two interconvertible forms, xanthine dehydrogenase (XDH) and xanthine oxidase (XO), catabolises xanthine to uric acid that is further broken down to antioxidative agent allantoin. XOR also produces free radicals serving as second messenger and microbicidal agent. Large variation in the XO activity has been observed among various species. Both hypo and hyper activity of XOR leads to pathophysiological conditions. Given the important nutritional role of buffalo milk in human health especially in south Asia, it is crucial to understand the functional properties of buffalo XOR and the underlying structural basis of variations in comparison to other species.

Methods and Findings

Buffalo XO activity of 0.75 U/mg was almost half of cattle XO activity. Enzymatic efficiency (k _cat/K _m) of 0.11 sec⁻¹ µM⁻¹ of buffalo XO was 8–10 times smaller than that of cattle XO. Buffalo XOR also showed lower antibacterial activity than cattle XOR. A CD value (Δε_{430 nm}) of 46,000 M⁻¹ cm⁻¹ suggested occupancy of 77.4% at Fe/S I centre. Buffalo XOR contained 0.31 molybdenum atom/subunit of which 48% existed in active sulfo form. The active form of XO in buffalo was only 16% in comparison to ∼30% in cattle. Sequencing revealed 97.4% similarity between buffalo and cattle XOR. FAD domain was least conserved, while metal binding domains (Fe/S and Molybdenum) were highly conserved. Homology modelling of buffalo XOR showed several variations occurring in clusters, especially close to FAD binding pocket which could affect NAD⁺ entry in the FAD centre. The difference in XO activity seems to be originating from cofactor deficiency, especially molybdenum.

Conclusion

A major fraction of buffalo milk XOR exists in a catalytically inactive form due to high content of demolybdo and desulfo forms. Lower Fe/S content and structural factors might be contributing to lower enzymatic efficiency of buffalo XOR in a minor way.     

No Correlation between TIMP2 -418 G>C Polymorphism and Increased Risk of Cancer: Evidence from a Meta-Analysis

Aim

Tissue inhibitor of metalloproteinase (TIMP2) is involved in the regulation of matrix metalloproteinase 2 (MMP2) and shown to implicate in cancer development and progression. The results from the published studies based on the association between TIMP2 -418 G>C polymorphism and cancer risk are inconsistent. In this meta-analysis, we aimed to evaluate the potential association between TIMP2 -418 G>C polymorphism and cancer risk.

Methodology

We searched PubMed (Medline) and EMBASE web databases to cover all studies based on relationship of TIMP2 -418 G>C polymorphism and risk of cancer until October 2013. The meta-analysis was performed for selected case-control studies and pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for all genetic models.

Results

A total of 2225 cancer cases and 2532 controls were included from ten eligible case-control studies. Results from overall pooled analysis suggested no evidence of significant risk between TIMP2 -418 G>C polymorphism and cancer risk in any of the genetic models, such as, allele (C vs. G: OR = 1.293, 95% CI = 0.882 to 1.894, p = 0.188), homozygous (CC vs. GG: OR = 0.940, 95% CI = 0.434 to 2.039, p = 0.876), heterozygous (GC vs. GG: OR = 1.397, 95% CI = 0.888 to 2.198, p = 0.148), dominant (CC+GC vs. GG: OR = 1.387, 95% CI = 0.880 to 2.187, p = 0.159) and recessive (CC vs. GG+GC: OR = 0.901, 95% CI = 0.442 to 1.838, p = 0.774) models. No evidence of publication bias was detected during the analysis.

Conclusions

The present meta-analysis suggests that the TIMP2 -418 G>C polymorphism may not be involved in predisposing risk factor for cancer in overall population. However, future larger studies with group of populations are needed to analyze the possible correlation.