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1.  Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions 
BMC Genomics  2014;15:29.
Background
The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments.
Results
Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions.
Conclusions
The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers.
doi:10.1186/1471-2164-15-29
PMCID: PMC3897974  PMID: 24433256
Wheat; Chapatti; Processing quality; Development; Interaction; Transcriptome; Gene expression
2.  Phenotypic Heterogeneity of Asian Indian Inversion Deletions Gγ(Aγδβ)0 Breakpoint A and Breakpoint B 
Asian Indian inversion deletion Gγ (Aγδβ)0-thalassemia is a rare entities characterized by high HbF. Due to interaction with various genetic factors, patients with Gγ (Aγδβ)0-thalassemia showed clinical variability. Here we are presenting the phenotypic expression of Gγ(Aγδβ)0 thalassemia under influence of various co-inherited factors. Patient with α-globin gene deletion had mild phenotype than the patient with β-globin mutations. Patient with alpha gene deletion were presenting clinical character like thalassemia intermedia while Gγ (Aγδβ)0-thalassemia patients with co- presence of beta thalssemia mutation clinically behaved like thalassemia major.
doi:10.1007/s12291-012-0232-9
PMCID: PMC3547438  PMID: 24381431
Thalassemia; PCR; Delta beta thalassemia; Gap-PCR
3.  Biotransformation of Acetamide to Acetohydroxamic Acid at Bench Scale Using Acyl Transferase Activity of Amidase of Geobacillus pallidus BTP-5x MTCC 9225 
Indian Journal of Microbiology  2011;52(1):76-82.
The bioprocess employing acyl transferase activity of intracellular amidase of Geobacillus pallidus BTP-5x MTCC 9225 was harnessed for the synthesis of pharmaceutically important acetohydroxamic acid. G. pallidus BTP-5x exhibited highest acyl transferase activity with acetamide: hydroxylamine in ratio of 1:5 in 0.1 M NaH2PO4/Na2HPO4 buffer (pH 7.5) at 65°C. In one liter fed-batch reaction containing 1:5 ratio of two substrates total of eight feedings of 0.05 M/20 min of acetamide were made and it was found that maximum acetohydroxamic production was achieved at 3:5 ratios of substrate and cosubstrate. In 1 l bench scale batch reaction containing 0.3 M acetamide, 0.5 M hydroxylamine in 0.1 M NaH2PO4/Na2HPO4 buffer (pH 7.5, 50°C, 400 rpm) and 0.5 mg/ml (dry cell weight) of whole cells of G. pallidus BTP-5x (as biocatalyst) resulted in an yield of 0.28 M of acetohydroxamic acid after 20 min reaction time at 50°C. The acetamide bioconversion rate was 90–95% (mol mol−1) and 51 g powder containing 40% (w/w) acetohydroxamic acid was recovered after lyophilization.
doi:10.1007/s12088-011-0211-5
PMCID: PMC3298591  PMID: 23449317
Geobacillus pallidus BTP-5x MTCC 9225; Acetohydroxamic acid; Thermophilic amidase; Acyl transferase activity; Hydroxamic acid
4.  Nocardia globerula NHB-2 nitrilase catalysed biotransformation of 4-cyanopyridine to isonicotinic acid 
AMB Express  2012;2:25.
Isonicotinic acid (INA) is an important pyridine derivative used in the manufacture of isoniazid (antituberculosatic drug) and other pharmaceutically important drugs. Nitrilase catalysed processes for the synthesis of pharmaceutically important acids from their corresponding nitriles are promising alternative over the cumbersome, hazardous, and energy demanding chemical processes. Nitrilase of Nocardia globerula NHB-2 (NitNHB2) is expressed in presence of isobutyronitrile in the growth medium (1.0% glucose, 0.5% peptone, 0.3% beef extract, and 0.1 % yeast extract, pH 7.5). NitNHB2 hydrolyses 4-cyanopyridine (4-CP) to INA without accumulation of isonicotinamide, which is common in the reaction catalysed via fungal nitrilases. The NitNHB2 suffers from substrate inhibition effect and hydrolysing activity up to 250 mM 4-CP was recorded. Complete conversion of 200 mM 4-CP to INA was achieved in 40 min using resting cell concentration corresponding to 10 U mL-1 nitrilase activity in the reaction. Substrate inhibition effect in the fed batch reaction (200 mM substrate feed/40min) led to formation of only 729 mM INA. In a fed batch reaction (100 mM 4-CP/20min), substrate inhibition effect was encountered after 7th feed and a total of 958 mM INA was produced in 400 min. The fed batch reaction scaled up to 1 L and 100% hydrolysis of 700 mM of 4-CP to INA at 35°C achieved in 140 min. The rate of INA production was 21.1 g h-1 mgDCW-1. This is the fastest biotransformation process ever reported for INA production with time and space productivity of 36 g L-1 h-1 using a bacterial nitrilase.
doi:10.1186/2191-0855-2-25
PMCID: PMC3403844  PMID: 22537922
4-Cyanopyridine; Isonicotinic acid; Isobutyronitrile; Bacterial nitrilase; Biotransformation; Substrate inhibition; Fed batch
5.  Genotypic influence of α-deletions on the phenotype of Indian sickle cell anemia patients 
The Korean Journal of Hematology  2011;46(3):192-195.
Background
Some reports have shown that co-inheritance of α-thalassemia and sickle cell disease improves hematological parameters and results in a relatively mild clinical picture for patients; however, the exact molecular basis and clinical significance of the interaction between α-thalassemia and sickle cell disease in India has not yet been described. There is little agreement on the clinical effects of α-thalassemia on the phenotype of sickle cell disease.
Methods
Complete blood count and red cell indices were measured by an automated cell analyzer. Quantitative assessment of hemoglobin variants HbF, HbA, HbA2, and HbS was performed by high performance liquid chromatography (HPLC). DNA extraction was performed using the phenol-chloroform method, and molecular study for common α-deletions was done by gap-PCR.
Results
Out of 60 sickle cell anemia patients, the α-thalassemia genotype was found in 18 patients. Three patients had the triplicated α-genotype (Anti α-3.7 kb), and the remaining patients did not have α-deletions. This study indicates that patients with co-existing α-thalassemia and sickle cell disease had a mild phenotype, significantly improved hematological parameters, and fewer blood transfusions than the patients with sickle cell anemia without co-existing α-deletions.
Conclusion
Co-existence of α-thalassemia and sickle cell anemia has significant effects on the phenotype of Indian sickle cell patients.
doi:10.5045/kjh.2011.46.3.192
PMCID: PMC3208203  PMID: 22065975
α-thalasemia; Sickle cell anemia; Hemoglobinopathies
6.  Common Parasite With Uncommon Associations 
doi:10.4084/MJHID.2011.015
PMCID: PMC3103260  PMID: 21625318
7.  ATRA Induced Reactive Hemophagocytosis: a Case Report 
All trans-retinoic acid (ATRA) is a targeted therapy, used in Acute Promyelcytic leukemia (APL) and causes the abnormal promyelocytes to differentiate in to mature leucocytes, however their clearance in vivo is not known. ATRA has been found to be associated with hemophagocytosis, but sometimes one may find phagocytosis of differentiated cells by histiocytes without the overt manifestations of hemophagocytic syndrome. We report a case of APL showing differentiated cells being phagocytosed by marrow histiocytes while patient was getting ATRA therapy.
doi:10.4084/MJHID.2011.034
PMCID: PMC3212967  PMID: 22084649
8.  Studies on leaf spot disease of Withania somnifera and its impact on secondary metabolites 
Indian Journal of Microbiology  2009;48(4):432-437.
During an investigation of the disease profile of Withania somnifera, it was observed that leaf spot is the most prevalent disease. Repeated isolations from infected leaf tissues and pathogenicity tests showed the association of fungal pathogen identified as Alternaria alternata (Fr.) Keissler. Scanning electron microscopy showed various histological changes in the leaf tissues of infected plants. A decrease in total content of reducing sugars (20%) and chlorophyll (26.5%) was observed in diseased leaves whereas an increase was noticed in proline (25%), free amino acids (3%) and proteins (74.3%). High performance thin layer chromatography (HPTLC) analysis of secondary metabolites viz. withanolides, withaferin-A and total alkaloids of the diseased leaves vis-à-vis control revealed reduction in withaferin-A and withanolides contents by 15.4% and 76.3% respectively, in contrast to an increase in total alkaloids by 49.3%, information hitherto unreported in W. somnifera.
doi:10.1007/s12088-008-0053-y
PMCID: PMC3476785  PMID: 23100743
Alternaria alternata; Biochemical changes; HPTLC; Scanning electron microscopy; Microbial deterioration

Results 1-8 (8)