IL-4 Haplotype -590T, -34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral Indian Tribal Populations

Background

Interleukin 4 (IL-4) is an anti-inflammatory cytokine, which regulates balance between T_H1 and T_H2 immune response, immunoglobulin class switching and humoral immunity. Polymorphisms in this gene have been reported to affect the risk of infectious and autoimmune diseases.

Methods

We have analyzed three regulatory IL-4 polymorphisms; -590C>T, -34C>T and 70 bp intron-3 VNTR, in 4216 individuals; including: (1) 430 ethnically matched case-control groups (173 severe malaria, 101 mild malaria and 156 asymptomatic); (2) 3452 individuals from 76 linguistically and geographically distinct endogamous populations of India, and (3) 334 individuals with different ancestry from outside India (84 Brazilian, 104 Syrian, and 146 Vietnamese).

Results

The -590T, -34T and intron-3 VNTR R2 alleles were found to be associated with reduced malaria risk (P<0.001 for -590C>T and -34C>T, and P = 0.003 for VNTR). These three alleles were in strong LD (r²>0.75) and the TTR2 (-590T, -34T and intron-3 VNTR R2) haplotype appeared to be a susceptibility factor for malaria (P = 0.009, OR = 0.552, 95% CI = 0.356 –0.854). Allele and genotype frequencies differ significantly between caste, nomadic, tribe and ancestral tribal populations (ATP). The distribution of protective haplotype TTR2 was found to be significant (χ² ₃ = 182.95, p-value <0.001), which is highest in ATP (40.5%); intermediate in tribes (33%); and lowest in caste (17.8%) and nomadic (21.6%).

Conclusions

Our study suggests that the IL-4 polymorphisms regulate host susceptibility to malaria and disease progression. TTR2 haplotype, which gives protection against malaria, is high among ATPs. Since they inhabited in isolation and mainly practice hunter-gatherer lifestyles and exposed to various parasites, IL-4 TTR2 haplotype might be under positive selection.     

Purification and partial characterization of an extracellular alginate lyase from <Emphasis Type="Italic">Aspergillus oryzae</Emphasis> isolated from brown seaweed

The extracellular enzyme alginate lyase produced from marine fungus Aspergillus oryzae isolated from brown alga Dictyota dichotoma was purified, partially characterized, and evaluated for its sodium alginate depolymerization abilities. The enzyme characterization studies have revealed that alginate lyase consisted of two polypeptides with about 45 and 50 kDa each on 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis and showed 140-fold higher activity than crude enzyme under optimized pH (6.5) and temperature (35°C) conditions. Zn²⁺, Mn²⁺, Cu²⁺, Mg²⁺, Co²⁺ and NaCl were found to enhance the enzyme activity while (Ca²⁺, Cd²⁺, Fe²⁺, Hg²⁺, Sr²⁺, Ni²⁺), glutathione, and metal chelators (ethylenediaminetetraacetic acid and ethylene glycol tetraacetic acid) suppressed the activity. Fourier transform infrared and thin-layer chromatography analysis of depolymerized sodium alginate indicated the enzyme specificity for cleaving at the β-1,4 glycosidic bond between polyM and polyG blocks of sodium alginate and therefore resulted in estimation of relatively higher polyM content than polyG. Comparison of chemical shifts in ¹³C nuclear magnetic resonance spectra of both polyM and polyG from that of sodium alginate also showed further evidence for enzymatic depolymerization of sodium alginate.     

Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin

Background

Although genomic DNA isolation using the Chelex 100 resin is rapid and inexpensive, the DNA obtained by this method has a low concentration in solution and contains suspended impurities. The presence of debris in the DNA solution may result in degradation of DNA on long term storage and inhibition of the polymerase chain reaction. In order to remove impurities and concentrate the DNA in solution, we have introduced modifications in the existing DNA isolation protocol using Chelex-100. We used ammonium acetate to precipitate proteins and a sodium acetate- isopropanol mixture to pellet out DNA which was washed with ethanol.

Results

A pure DNA pellet that can be dissolved in water or Tris-EDTA buffer and stored for a long time at ??80 °C was obtained. We also observed a 20-fold change in the DNA concentration following precipitation and re-dissolution.

Conclusion

Our method is different from other extraction methods since it uses non-toxic, easily available and inexpensive reagents as well as minimal amounts of blood or tissue samples for the DNA extraction process. Besides its use in sex determination and genotyping in lab animals as described in this paper, it may also have applications in forensic science and diagnostics such as the easy detection of pathogenic DNA in blood.

     

Differential responses of antioxidant enzymes to aluminum toxicity in two rice (Oryza sativa L.) cultivars with marked presence and elevated activity of Fe SOD and enhanced activities of Mn SOD and catalase in aluminum tolerant cultivar

Seedlings of two Indica rice (Oryza sativa L.) cvs. HUR-105 and Vandana, differing in Al-tolerance were used to identify the key mechanisms involved in their differential behaviour towards Al toxicity. Cv. HUR-105 appeared to be Al sensitive by showing significant reduction (p ≤ 0.01) in root/shoot length, fresh weight, dry weight and water content in presence of 421 μM Al³⁺ in growth medium whereas cv. Vandana appeared to be fairly Al³⁺ tolerant. A conspicuous and significant reduction in dry weight of root and shoot was observed in Al sensitive cv. HUR-105 with 178 μM Al³⁺ treatment for 3 days. Al was readily taken up by the roots and transported to shoots in both the rice cultivars. Localization of absorbed Al was always greater in roots than in shoots. Our results of the production of reactive oxygen species (ROS) H₂O₂ and O₂ ^.? and activities of major antioxidant enzymes such as total superoxide dismutase (SOD), Cu/Zn SOD, Mn SOD, Fe SOD, catalase (CAT) and guaiacol peroxidase revealed Al induced higher oxidative stress, greater production of ROS and lesser capacity to scavenge ROS in cv. HUR-105 than Vandana. With Al treatment, higher oxidative stress was noted in shoots than in roots. Greatly enhanced activities of SOD (especially Fe and Mn SOD) and CAT in Al treated seedlings of cv. Vandana suggest the role of these enzymes in Al tolerance. Furthermore, a marked presence of Fe SOD in roots and shoots of the seedlings of Al tolerant cv. Vandana and its significant (p ≤ 0.01) increase in activity due to Al-treatment, appears to be the unique feature of this cultivar and indicates a vital role of Fe SOD in Al-tolerance in rice.     

Directionlet transform based sharpening and enhancement of mammographic X-ray images

Due to difficulty in detecting the low contrast and noisy nature of X-ray mammography images, they have to be enhanced to obtain a clear and good view. Though Sharpening Technique (ST) is used to enhance the contrast, it introduces noise in the enhancement process, and they do not include anisotropic features. This paper proposes a ST, which uses multiscale linear and anisotropic geometrical features obtained from directionlet transform (DT). The newly formulated method that combines multidirectional geometrical information has various tunable parameters and improved noise control by means of multiscale features. The DT that uses skewed and elongated directional basis functions not only captures the point singularities, but also links them into linear structure. The performance of the proposed DT ST is compared with non-linear unsharp masking (NLUSM). While the DT and LoG based sharpened images are given to the input of standard AHE, their performance is improved. Enhancement Measure and structural similarity measure are used to analyze the performance of the proposed method. Though the images are enhanced, the quality of the image is not degraded. As a specific application, the enhanced images are used to detect the microcalcification and spiculated masses in mammograms.     

Incidence of mycoflora and mycotoxins in some edible fruits and seeds of forest origin

Twelve fungi namelyAlternaria alternata, Aspergillus flavus, A niger, A ochraceus, Actinomucor repens, Capnodoium spp., Curvularia lunata, Fusarium pallidoroseum, F solani, F verticillioides, Penicillium citrinum and Rhizopus stolonifer were recorded from samples ofAegle marmelos, Aesculus indica, Buchanania lanzan andPinus gerardiana. In case ofPrunus amygdalus only Rstolonifer was recorded. A significant variation in pattern of mycoflora incidence was observed in terms of source and season. Fungal infestation in most of the substrates was found to be highest during monsoon. Aflatoxins were the most common mycotoxins elaborated by different isolates ofA flavus obtained fromA marmelos, B lanzan andP gerardiana. The amount of aflatoxins produced by the toxigenic isolates ofA flavus was in the range of traces to 0.9–26.0 μg/ml inA marmelos, 0.8–17.5 μg/ml inP gerardiana and 0.65–13.2 μg/ml inB lanzan. The percentage toxigenicity was comparatively lower in the isolates of other mycotoxigenic fungi. Aflatoxins were detected almost in all the samples analyzed for mycotoxin contamination. However, traces of zearalenone were detected inA marmelos. The concentration of aflatoxin B₁ was in the range of 0.13–0.75 μg/g inA marmelos, 0.09–0.60 μg/g inP gerardiana and 0.01–0.20 ug/g inB lanzan. Mycotoxins were not detected inAesculus indica andPrunus amygdalus.     

Detection of nonlinear interactions of EEG alpha waves in the brain by a new coherence measure and its application to epilepsy and anti-epileptic drug therapy

EEG and field potential rhythms established in the cortex and thalamus may accommodate the propagation of seizures. This article describes the interaction between thalamus and cortex during pentylenetetrazol (PTZ) seizures in rats with and without prior treatment with ethosuximide (ESM), a well-known antiepileptic drug (AED) that raises the threshold for seizures, was given before PTZ. The AED was given before PTZ convulsant administration. We track this thalamo-cortical association with a novel measure we have called the cross-bicoherence gain, or BISCOH. This quantity allows us to measure the spectral coherence in a purely higher order spectralmethodology. BISCOH is able to track the formation of nonlinearities at specific frequencies in the recorded EEG. BISCOH showed a strong increase in low alpha wave harmonic generationat 10 and 12.5 Hz after ESM treatment (p < 0.02 and p < 0.007, respectively). Conventional coherence failed to show distinctive and significant changes in thalamo-cortical coupling after ESM treatment at those frequencies and instead showed changes at 5 Hz. This rise in cortical rhythms is evidence of harmonic generation or new frequency formation in the thalamo-cortical system withAED therapy. BISCOH could become a powerful tool in unraveling changes in coherence due to neuroelectric modulation resulting from drug treatment or electrical stimulation.     

Role of Organic Amendments to Mitigate Cd Toxicity and Its Assimilation in <i>Triticum aestivum</i> L.

In soil biota, higher and enduring concentration of heavy metals like cadmium (Cd) is hazardous and associated with great loss in growth, yield, and quality parameters of most of the crop plants. Recently, in-situ applications of eco-friendly stabilizing agents in the form of organic modifications have been utilized to mitigate the adverse effects of Cd-toxicity. This controlled experiment was laid down to appraise the imprints of various applied organic amendments namely poultry manure (PM), farmyard manure (FYM), and sugarcane press mud (PS) to immobilize Cd in polluted soil. Moreover, phytoavailability of Cd in wheat was also accessed under an alkaline environment. Results revealed that the addition of FYM (5–10 ton ha^-1 ) in Cd-contaminated soil significantly increased germination rate, leaf chlorophyll content, plant height, spike length, biological and grain yield amongst all applied organic amendments. Moreover, the addition of FYM (5–10 ton ha^-1 ) also reduced the phytoavailability of Cd by 73–85% in the roots, 57–83% in the shoots, and 81–90% in grains of wheat crop. Thus, it is affirmed that incorporation of FYM (5–10 ton ha^-1 ) performed better to enhance wheat growth and yield by remediating Cd. Thus, the application of FYM (5–10 ton ha^-1 ) reduced the toxicity induced by Cd to plants by declining its uptake and translocation as compared to all other applied organic amendments to immobilize Cd under sandy alkaline polluted soil.