Azadirachta indica Modulates Electrical Properties and Type of Cell Death in NDEA-Induced Hepatic Tumors

Tissue electrical conductivity is an important indicator of tissue structure and composition. Present study demonstrates modulatory effect of Azadirachta indica on the electrical conductivity and cell death in hepatic tumors. Hepatic tumors were generated by intraperitoneal injection of N-nitrosodiethylamine (cumulative dose: 200 μg/g body mass) to male BALB/c mice. Aqueous A. indica leaf extract (AAILE) was administered orally at a dosage of 100 μg/g body mass till the termination of experiment. At the end of experiment, electrical conductivity of hepatic tumors was measured with four-pin electrode method. Tissues and tumors were then processed for TUNEL assay and DNA fragmentation analysis. The levels of TNF-α were also determined in the normal hepatic and tumor tissue. Hepatic tumors had higher electrical conductivity compared to normal liver tissue. An increased necrotic cell percentage along with elevated TNF-α was also observed. Although, AAILE co-treatment resulted in tumors with higher electrical conductivity compared to normal animals. However, the electrical conductivity was decreased significantly compared to untreated tumors. A significant increase in apoptotic cell percentage and concomitant decrease in necrotic cell percentage along with the increased TNF-α level was observed in these tumors. The results suggest that A. indica modulated mode of cell death in tumors and type of cell death had significant contribution in determining hepatic tumor electrical conductivity.     

Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity,linkage disequilibrium,and selective sweeps in cultivated watermelon

Background

A large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise F_ST distributions among worldwide cultivated watermelons to track signals of domestication.

Results

We examined 183 Citrullus lanatus var. lanatus accessions representing domesticated watermelon and generated a set of 11,485 SNP markers using genotyping by sequencing. With a diverse panel of worldwide cultivated watermelons, we identified a set of 5,254 SNPs with a minor allele frequency of ≥ 0.05, distributed across the genome. All ancestries were traced to Africa and an admixture of various ancestries constituted secondary gene pools across various continents. A sliding window analysis using pairwise F_ST values was used to resolve selective sweeps. We identified strong selection on chromosomes 3 and 9 that might have contributed to the domestication process. Pairwise analysis of adjacent SNPs within a chromosome as well as within a haplotype allowed us to estimate genome-wide LD decay. LD was also detected within individual genes on various chromosomes. Principal component and ancestry analyses were used to account for population structure in a genome-wide association study. We further mapped important genes for soluble solid content using a mixed linear model.

Conclusions

Information concerning the SNP resources, population structure, and LD developed in this study will help in identifying agronomically important candidate genes from the genomic regions underlying selection and for mapping quantitative trait loci using a genome-wide association study in sweet watermelon.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-767) contains supplementary material, which is available to authorized users.     

OdoriFy: A conglomerate of artificial intelligence–driven prediction engines for olfactory decoding

The molecular mechanisms of olfaction, or the sense of smell, are relatively underexplored compared with other sensory systems, primarily because of its underlying molecular complexity and the limited availability of dedicated predictive computational tools. Odorant receptors (ORs) allow the detection and discrimination of a myriad of odorant molecules and therefore mediate the first step of the olfactory signaling cascade. To date, odorant (or agonist) information for the majority of these receptors is still unknown, limiting our understanding of their functional relevance in odor-induced behavioral responses. In this study, we introduce OdoriFy, a Web server featuring powerful deep neural network–based prediction engines. OdoriFy enables (1) identification of odorant molecules for wildtype or mutant human ORs (Odor Finder); (2) classification of user-provided chemicals as odorants/nonodorants (Odorant Predictor); (3) identification of responsive ORs for a query odorant (OR Finder); and (4) interaction validation using Odorant–OR Pair Analysis. In addition, OdoriFy provides the rationale behind every prediction it makes by leveraging explainable artificial intelligence. This module highlights the basis of the prediction of odorants/nonodorants at atomic resolution and for the ORs at amino acid levels. A key distinguishing feature of OdoriFy is that it is built on a comprehensive repertoire of manually curated information of human ORs with their known agonists and nonagonists, making it a highly interactive and resource-enriched Web server. Moreover, comparative analysis of OdoriFy predictions with an alternative structure-based ligand interaction method revealed comparable results. OdoriFy is available freely as a web service at https://odorify.ahujalab.iiitd.edu.in/olfy/.     

Flow‐injection determination of vitamin A in pharmaceutical formulations using Tris(2,2′‐bipyridyl)Ru(II)–Ce(IV) chemiluminescence detection

A flow injection method with chemiluminescence detection is reported for the determination of vitamin A. The method is based on the enhancement effect of vitamin A on chemiluminescence of tris(2,2′‐bipyridyl)Ru(II)–Ce(IV) in acidic medium. The proposed procedure is used to quantitate vitamin A in the range 1.0–100 × 10^?6 mol/L with a correlation coefficient of 0.9991 (n = 9) and relative standard deviation in the range 1.2–2.3% (n = 4). The limit of detection (3 × blank) was 8.0 × 10^?8 mol/L with a sample throughput of 100/h. The effect of common excipients used in pharmaceutical formulations and some clinically important compounds was also studied. The method was applied to determine vitamin A in pharmaceutical formulations and the results obtained were in reasonable agreement with the amount quoted. The results were compared using spectrophotometric method and no significant difference was found between the results of the two methods at 95% confidence limit. Copyright © 2009 John Wiley & Sons, Ltd.     

The polyembryo gene (OsPE) in rice

T-DNA insertional mutagenesis is one of the most important approaches for gene discovery and cloning. A fertile polyembryo mutant generated by T-DNA/Ds insertion in Oryza sativa, cv. Basmati 370 showed twin or triple seedlings at a frequency of 15–20%. T-DNA insertion was confirmed by 950 bp hpt gene amplification in the promoter region of the candidate gene. The annotated protein corresponding to the OsPE candidate gene has been reported as a hypothetical protein in O. sativa. OsPE gene lacked functional homologs in other species. No OsPE paralog was found in rice. No conserved domains were found in the protein coded by OsPE. RT-PCR showed the expression of OsPE gene in Basmati 370 shoots. Full-length OsPE gene was cloned in Basmati 370. The combined use of Southern blot, genome walking, TAIL-PCR, RT-PCR techniques, and bioinformatics led to the identification of a candidate gene controlling the multiple embryos in rice. There is gain of function, i.e., multiple embryos in the seeds in the knockout mutant OsPE whereas its wild-type allele strictly controls single embryo per seed. The seeds with multiple embryos are distributed at random in the rice mutant panicle. The origin of multiple embryos, whether apomictic, zygotic or both is under investigation.     

Heat Shock Protein 90 as a Drug Target against Protozoan Infections: BIOCHEMICAL CHARACTERIZATION OF HSP90 FROM PLASMODIUM FALCIPARUM AND TRYPANOSOMA EVANSI AND EVALUATION OF ITS INHIBITOR AS A CANDIDATE DRUG*

Using a pharmacological inhibitor of Hsp90 in cultured malarial parasite, we have previously implicated Plasmodium falciparum Hsp90 (PfHsp90) as a drug target against malaria. In this study, we have biochemically characterized PfHsp90 in terms of its ATPase activity and interaction with its inhibitor geldanamycin (GA) and evaluated its potential as a drug target in a preclinical mouse model of malaria. In addition, we have explored the potential of Hsp90 inhibitors as drugs for the treatment of Trypanosoma infection in animals. Our studies with full-length PfHsp90 showed it to have the highest ATPase activity of all known Hsp90s; its ATPase activity was 6 times higher than that of human Hsp90. Also, GA brought about more robust inhibition of PfHsp90 ATPase activity as compared with human Hsp90. Mass spectrometric analysis of PfHsp90 expressed in P. falciparum identified a site of acetylation that overlapped with Aha1 and p23 binding domain, suggesting its role in modulating Hsp90 multichaperone complex assembly. Indeed, treatment of P. falciparum cultures with a histone deacetylase inhibitor resulted in a partial dissociation of PfHsp90 complex. Furthermore, we found a well known, semisynthetic Hsp90 inhibitor, namely 17-(allylamino)-17-demethoxygeldanamycin, to be effective in attenuating parasite growth and prolonging survival in a mouse model of malaria. We also characterized GA binding to Hsp90 from another protozoan parasite, namely Trypanosoma evansi. We found 17-(allylamino)-17-demethoxygeldanamycin to potently inhibit T. evansi growth in a mouse model of trypanosomiasis. In all, our biochemical characterization, drug interaction, and animal studies supported Hsp90 as a drug target and its inhibitor as a potential drug against protozoan diseases.     

X‐Ray Microscopy of Halide Perovskites: Techniques,Applications, and Prospects

X‐ray microscopy can provide unique chemical, electronic, and structural insights into perovskite materials and devices leveraging bright, tunable synchrotron X‐ray sources. Over the last decade, fundamental understanding of halide perovskites and their impressive performance in optoelectronic devices has been furthered by rigorous research regarding their structural and chemical properties. Herein, studies of perovskites are reviewed that have used X‐ray imaging, spectroscopy, and scattering microscopies that have proven valuable tools toward understanding the role of defects, impurities, and processing on perovskite material properties and device performance. Together these microscopic investigations have augmented the understanding of the internal workings of perovskites and have helped to steer the perovskite community toward promising directions. In many ways, X‐ray microscopy of perovskites is still in its infancy, which leaves many exciting paths unexplored including new ptychographic, multimodal, in situ, and operando experiments. To explore possibilities, pioneering X‐ray microscopy along these lines is briefly highlighted from other semiconductor systems including silicon, CdTe, GaAs, CuIn_xGa_1?xSe₂, and organic photovoltaics. An overview is provided on the progress made in utilizing X‐ray microscopy for perovskites and present opportunities and challenges for future work.     

Value Addition in the Efficacy of Conventional Antibiotics by Nisin against Salmonella

Frequent and indiscriminate use of existing battery of antibiotics has led to the development of multi drug resistant (MDR) strains of pathogens. As decreasing the concentration of the antibiotic required to treat Salmonellosis might help in combating the development of resistant strains, the present study was designed to assess the synergistic effects, if any, of nisin, in combination with conventional anti-Salmonella antibiotics against Salmonella enterica serovar Typhimurium. Minimum inhibitory concentrations (MICs) of the selected antimicrobial agents were determined by micro and macro broth dilution assays. In-vitro synergy between the agents was evaluated by radial diffusion assay, fractional inhibitory concentration (FIC) index (checkerboard test) and time-kill assay. Scanning electron microscopy (SEM) was also performed to substantiate the effect of the combinations. In-vivo synergistic efficacy of the combinations selected on the basis of in-vitro results was also evaluated in the murine model, in terms of reduction in the number of Salmonellae in liver, spleen and intestine. Nisin-ampicillin and nisin-EDTA combinations were observed to have additive effects, whereas the combinations of nisin-ceftriaxone and nisin-cefotaxime were found to be highly synergistic against serovar Typhimurium as evident by checkerboard test and time-kill assay. SEM results revealed marked changes on the outer membrane of the bacterial cells treated with various combinations. In-vivo synergy was evident from the larger log unit decreases in all the target organs of mice treated with the combinations than in those treated with drugs alone. This study thus highlights that nisin has the potential to act in conjunction with conventional antibiotics at much lower MICs. These observations seem to be significant, as reducing the therapeutic concentrations of antibiotics may be a valuable strategy for avoiding/reducing the development of emerging antibiotic resistance. Value added potential of nisin in the efficacy of conventional antibiotics may thus be exploited not only against Salmonella but against other Gram-negative infections as well.     

Silymarin- and melatonin-mediated changes in the expression of selected genes in pesticides-induced Parkinsonism

Expression of angiotensin II (Ang II) and its receptors (AT₁/AT₂) is undetected in the mature microglia in normal brain. We report here that the immunoexpression of Ang II and AT₁/AT₂ was altered in activated microglia notably at 1 week in rats subjected to middle cerebral artery occlusion (MCAO). Immunolabeled activated microglia were widely distributed in the infarcted cerebral tissue after MCAO. By enzyme immunoassay, Ang II protein expression levels of the ischemic tissues were decreased drastically at 12 h after ischemia, then rose rapidly at 3 days and 1 week after MCAO when compared with the control. On the other hand, AT₁ and AT₂ receptor mRNA and protein levels were up-regulated after MCAO, peaking at 12 h, but declined thereafter. Expression of tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) mRNA and protein levels was concomitantly increased. Edaravone significantly suppressed Ang II and AT₁/AT₂ receptor expression as well as that of TNF-α and IL-1β suggesting that microglia-derived Ang II can act through an autocrine manner via its receptor that may be linked partly to the production of proinflammatory cytokines. We conclude that neuroinflammation in MCAO may be attenuated by Edaravone which acts through suppression of expression of Ang II and its receptors and proinflammatory cytokines in activated microglia.