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author:("Singh, render")
1.  IL-4 Haplotype -590T, -34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral Indian Tribal Populations 
PLoS ONE  2012;7(10):e48136.
Background
Interleukin 4 (IL-4) is an anti-inflammatory cytokine, which regulates balance between TH1 and TH2 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 (χ23 = 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.
doi:10.1371/journal.pone.0048136
PMCID: PMC3480467  PMID: 23110190
2.  A case of oligoasthenoteratozoospermia with AZFc deletion and persistent oxidative stress 
Indian Journal of Human Genetics  2012;18(3):359-362.
Y-chromosomal microdeletions are associated with severe oligozoospermia or azoospermia. AZFc microdeletions have been always associated with severe oligozoospermia or azoospermia with a rare occurrence in individuals with other infertility phenotypes. We report here a rare case of an infertile man carrying AZFc deletion, whose semen picture is oligoasthenoteratozoospermia complexed with seminal oxidative stress. Anti-oxidant therapy could make no change in either oxidative stress biomarker levels of semen, seminal parameters or serum hormone levels. Therefore, oligoasthenoteratozoospermia in the present case correlates with AZFc deletion, and high content of abnormal sperm eventually might be responsible for persistently elevated reactive oxygen species levels. Understanding the function of genes in AZFc region could help decipher the exact cause of the phenotype in such cases.
doi:10.4103/0971-6866.108037
PMCID: PMC3656530  PMID: 23716949
AZFc deletion; male infertility; oligoasthenoteratozoospermia; oxidative stress
3.  Evaluation of Volvariella volvacea Strains for Yield and Diseases/Insect-Pests Resistance Using Composted Substrate of Paddy Straw and Cotton Mill Wastes 
Indian Journal of Microbiology  2011;51(2):200-205.
Out of the 3 parent strains and 4 single spore isolates of Volvariella volvacea evaluated, strain, OE-274 gave earliest yield in 11.25–11.50 days post-spawning in all 4 trials. The yield varied in different strains in different trials and it was highest in strain, OE-272 in trial 1, SSI, OE-55-08 in trial 2, and strain, OE-274 in trial 3 and 4. In overall average, highest yield was in strain, OE-272, closely followed by strain, OE-274. The number of fruiting bodies per q substrate also varied in different strains in different trials. Highest numbers were in strain, OE-272, SSIs, OE-55-08 and OE-12-22, and strain, OE-210 in trial 1, 2, 3 and 4, respectively. Highest fruiting body wt was in strain, OE-274 in all 4 trials. The yield during different weeks of cropping varied in different strains but invariably it was highest in first week, which accounted for 60–70% of the total yield. The fruiting bodies of strain, OE-274 were of bigger size, brownish, toughest and with least tendency of veil opening, while that of strain, OE-272 and SSI, OE-55-08 were whitish to grayish-white, oblong, medium size, delicate and lesser tendency of veil opening. The strain, OE-274 and SSI, OE-55-08 exhibited higher resistance against the growth of competitor moulds and infestations of insect-pests, while strain, OE-272 exhibited highest susceptibility to insect-pests infestation.
doi:10.1007/s12088-011-0126-1
PMCID: PMC3209894  PMID: 22654165
Volvariella volvacea; Strain; Single spore isolate; Yield; Quality; Disease/insect-pest
4.  Dosimetric evaluation of 3Dconformal acceleratedpartial-breast irradiation vs. whole-breast irradiation: A comparative study 
Background:
Conventional early breast cancer treatment consists of lumpectomy followed by whole-breast irradiation (WBI) therapy. Accelerated partial-breast irradiation (APBI) is also an approach to post-lumpectomy radiation for early breast cancer.
Aim:
The purpose of this study is to compare two different external-beam APBI techniques using three-dimensional (3D) conformal radiation therapy (3DCRT), with conventional whole-breast irradiation based on the radiation conformity index, dose homogeneity index, and dose to organs at risk.
Materials and Methods:
WBI treatment plans were compared with two different 3DCRT APBI plans for each of 15 patients (8 with right sided lesions, 7 with left sided lesions). The first APBI plan (APBI 1) used two small coplanar fields conformed to the planning target volume (PTV) using multileaf collimators (MLCs) and wedges, while the other APBI plan (APBI 2) used three non-coplanar fields conformed to the PTV using MLCs and wedges.
Results:
Both the APBI techniques improved the conformity index significantly over whole-breast tangents while maintaining dose homogeneity and not causing significant increase in dose to organs at risk.
Conclusion:
Both the 3DCRT APBI techniques are technically feasible and dosimetrically appealing,with better target coverage and relative sparing of normal critical organs
doi:10.4103/2229-516X.96810
PMCID: PMC3657992  PMID: 23776810
Accelerated partial-breast irradiation; planning target volume; whole-breast irradiation; 3D conformal radiation therapy
5.  Analysis of simple sequence repeats (SSRs)dynamics in fungus Fusarium graminearum 
Bioinformation  2011;5(10):402-404.
The abundance and inherent potential for variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in eukaryotes. We describe the organization and abundance of SSRs in fungus Fusarium graminearum (causative agent for Fusarium head blight or head scab of wheat). We identified 1705 SSRs of various nucleotide repeat motifs in the sequence database of F. graminearum. It is observed that mononucleotide repeats (62%) were most abundant followed by di- (20%) and trinucleotide repeats (14%). It is noted that tetra-, penta- and hexanucleotide repeats accounted for only 4% of SSRs. The estimated frequency of Class I SSRs (perfect repeats ≥20 nucleotides) was one SSR per 124.5 kb, whereas the frequency of Class II (perfect repeats >10 nucleotides and ≫20 nucleotides) was one SSR per 25.6 kb. The dynamics of SSRs will be a powerful tool for taxonomic, phylogenetic, genome mapping and population genetic studies as SSR based markers show high levels of allelic variation, codominant inheritance and ease of analysis.
PMCID: PMC3055161  PMID: 21423884
SSR; microsatellites; Fusarium graminearum; EST
6.  Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.) 
Bioinformation  2011;6(4):144-148.
Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis depicts the involvement of six amino acids in hydrogen bonding (AGP-SThr422-AGP-LMet138, AGP- SArg420-AGP-LGly47, AGP-SSer259-AGP-LSer306, AGP-SGlu241-AGP-LIle311, AGPSGln113- AGP-LGlu286 and AGP-SGln70-AGP-LLys291). Fifteen amino acids of small subunit were able to make hydrophobic contacts with seventeen amino acids of large subunit. Furthermore, decrease in the solvent accessible surface area in the amino acids involved in interaction were also reported. All the distances were formed in between 2.27 to 3.78Å. The present study focussed on heterodimeric structure of (AGPase). This predicted complex not only enhance our understanding of the interaction mechanism between these subunits (AGP-L and AGP-S) but also enable to further study to obtain better variants of this enzyme for the improvement of the plant yield.
PMCID: PMC3092947  PMID: 21572880
AGPase; ADP-glucose pyrophosphorylase; AGP-S; AGP-L; modelling; molecular docking; hydrogen bonding; hydrophobic contacts; accessible surface area
7.  Modeling and phylogeny analysis of bread wheat MnSOD 
Bioinformation  2011;6(6):209-211.
Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn(III) at the active site. Therefore, it is of interest to study MnSOD from bread wheat (a grain crop). However, a structure model is not yet solved for bread wheat MnSOD. Hence, we describe the structure model of bread wheat MnSOD developed using homology model. The model provides molecular insight to metal binding molecular function towards the understanding of oxidative stress resistance in plants. The distinction of bread wheat (a monocot) MnSOD from dicots is also shown using phylogenetic analysis.
PMCID: PMC3124787  PMID: 21738317
MnSOD; monocots; dicots; structure model; stress
8.  Mining and survey of simple sequence repeats in wheat rust Puccinia sp 
Bioinformation  2011;7(6):291-295.
The abundance and inherent potential for extensive allelic variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in eukaryotes. In this study, we analyzed and compared the abundance and organisation of SSR in the genome of two important fungal pathogens of wheat, brown or leaf rust (Puccinia triticina) and black or stem rust (Puccinia graminis f. sp. tritici). P. triticina genome with two fold genome size as compared to P. graminis tritici has lower relative abundance and SSR density. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of dinucleotide followed by trinucleotide repeats. More than two-hundred different types of repeat motifs were observed in the genomes. The longest SSR motifs varied in both genomes and some of the repeat motifs are found in higher frequency. The information about survey of relative abundance, relative density, length and frequency of different repeat motifs in Puccinia sp. will be useful for developing SSR markers that could find several applications in analysis of fungal genome such as genetic diversity, population genetics, race identification and acquisition of new virulence.
PMCID: PMC3280497  PMID: 22355223
9.  Courveilhier Baumgarten Syndrome: A Rare Syndrome Revisited 
A 25 year old male had presented with history of abdominal distension of 20 days duration and on examination he had prominent abdominal vein and a venous hum with Ascites. He had no history of altered sensorium, melena. The clinical scenario was suggestive of Cruveilhier Baumgarten syndrome.
PMCID: PMC3068787  PMID: 21475517

Results 1-9 (9)