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1.  Determination of 17 Organophosphate Pesticide Residues in Mango by Modified QuEChERS Extraction Method Using GC-NPD/GC-MS and Hazard Index Estimation in Lucknow, India 
PLoS ONE  2014;9(5):e96493.
A total of 162 samples of different varieties of mango: Deshehari, Langra, Safeda in three growing stages (Pre-mature, Unripe and Ripe) were collected from Lucknow, India, and analyzed for the presence of seventeen organophosphate pesticide residues. The QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) method of extraction coupled with gas chromatography was validated for pesticides and qualitatively confirmed by gas chromatography- mass spectrometry. The method was validated with different concentrations of mixture of seventeen organophosphate pesticides (0.05, 0.10, 0.50 mg kg−1) in mango. The average recovery varied from 70.20% to 95.25% with less than 10% relative standard deviation. The limit of quantification of different pesticides ranged from 0.007 to 0.033 mg kg−1. Out of seventeen organophosphate pesticides only malathion and chlorpyriphos were detected. Approximately 20% of the mango samples have shown the presence of these two pesticides. The malathion residues ranged from ND-1.407 mg kg−1 and chlorpyriphos ND-0.313 mg kg−1 which is well below the maximum residues limit (PFA-1954). In three varieties of mango at different stages from unpeeled to peeled sample reduction of malathion and chlorpyriphos ranged from 35.48%–100% and 46.66%–100% respectively. The estimated daily intake of malathion ranged from 0.032 to 0.121 µg kg−1 and chlorpyriphos ranged from zero to 0.022 µg kg−1 body weight from three different stages of mango. The hazard indices ranged from 0.0015 to 0.0060 for malathion and zero to 0.0022 for chlorpyriphos. It is therefore indicated that seasonal consumption of these three varieties of mango may not pose any health hazards for the population of Lucknow, city, India because the hazard indices for malathion and chlorpyriphos residues were below to one.
doi:10.1371/journal.pone.0096493
PMCID: PMC4014508  PMID: 24809911
2.  Structural Changes in the Insular Cortex in Alcohol Dependence: A cross sectional study 
Iranian Journal of Psychiatry  2011;6(4):133-137.
Objective
This study was conducted to determine the changes in the insular cortex in alcohol dependent subjects, and to compare the same with controls, the associated clinical findings.
Methods
The study group consisted of 30 subjects with alcohol dependence syndrome (ADS) selected randomly from the out patient services of the department of psychiatry of a tertiary care hospital. The control group consisted of 30 matched subjects selected randomly from the out patient department and from patients screened for uncomplicated headache. Both groups were examined by a computerized scan (CT), and Mini Mental Status Examination (MMSE).
Results
Chi square, and ‘t’ test were done after calculating the Evan's ratio. The two groups were compared to assess the cortical atrophy and ventricular enlargement. Cognitive functions were tested by MMSE, and the scores were compared. Atrophy was significantly higher in the experimental group; however, it was not significant. Cognitive functioning was found to be significantly impaired in the experimental group.
Discussion
The study showed that alcohol dependence leads to cortical atrophy which is age independent. The statistically significant disturbance in the MMSE scores along with the frontal and parietal cortical atrophy is also indicative of the insular cortex involvement in the experimental group.
Conclusion
Alcohol dependence leads to cerebral atrophy along with the involvement of the insular cortex.
PMCID: PMC3395958  PMID: 22952538
Alcohol related disorders; Cerebral cortex; Cognition; Computed tomography
3.  Effect of Genetic Variant (rs11887534) in ABCG8 Gene in Coronary Artery Disease and Response to Atorvastatin Therapy 
Disease markers  2010;28(5):307-313.
Background: ATP-binding cassette transporter ABCG8 plays an important role in excretion of cholesterol from liver. Common genetic polymorphisms in ABCG8 gene may genetically predispose an individual to coronary artery disease (CAD) along with response to atorvastatin therapy. Thus, we aimed to examine the role of ABCG8 D19H polymorphism (rs11887534) in susceptibility to CAD and its influence on atorvastatin response.
Methodology: The study included 213 CAD patients and 220 controls. Genotyping of ABCG8 D19H polymorphism was done by PCR-RFLP.
Results: Our results showed that ABCG8 ‘H’ allele was conferring significant risk for CAD in a dominant model (OR = 2.54; p = 0.014). This increased risk for CAD was more pronounced in males (OR = 2.69; p = 0.030). No correlation of ABCG8 genotypes with the risk factors (diabetes, hypertension and smoking) of CAD was observed. On atorvastatin treatment there was a significant decrease in the LDL-C levels (p = 0.021). However, stepwise multiple regression analysis showed that this decease was not associated with ABCG8 genetic variant (p = 0.845). Observed determinants of variation in interindividual response to atorvastatin therapy were pre-treatment LDL-C (p = 0.024) and TC (p = 0.017).
Conclusion: Although the genetic variant 19H of ABCG8 confers risk for CAD in North Indian population, it is not associated with interindividual response to atorvastatin therapy.
doi:10.3233/DMA-2010-0710
PMCID: PMC3833422  PMID: 20592455
Coronary artery disease; polymorphism; ABCG8; Atorvastatin therapy; PCR-RFLP
4.  SELDI-TOF MS Whole Serum Proteomic Profiling with IMAC Surface Does Not Reliably Detect Prostate Cancer 
Clinical chemistry  2007;54(1):53-60.
BACKGROUND
The analysis of bodily fluids using SELDI-TOF MS has been reported to identify signatures of spectral peaks that can be used to differentiate patients with a specific disease from normal or control patients. This report is the 2nd of 2 companion articles describing a validation study of a SELDI-TOF MS approach with IMAC surface sample processing to identify prostatic adenocarcinoma.
METHODS
We sought to derive a decision algorithm for classification of prostate cancer from SELDI-TOF MS spectral data from a new retrospective sample cohort of 400 specimens. This new cohort was selected to minimize possible confounders identified in the previous study described in the companion paper.
RESULTS
The resulting new classifier failed to separate patients with prostate cancer from biopsy-negative controls; nor did it separate patients with prostate cancer with Gleason scores <7 from those with Gleason scores ≥7.
CONCLUSIONS
In this, the 2nd stage of our planned validation process, the SELDI-TOF MS– based protein expression profiling approach did not perform well enough to advance to the 3rd (prospective study) stage. We conclude that the results from our previous studies—in which differentiation between prostate cancer and noncancer was demonstrated—are not generalizable. Earlier study samples likely had biases in sample selection that upon removal, as in the present study, resulted in inability of the technique to discriminate cancer from non-cancer cases.
doi:10.1373/clinchem.2007.091496
PMCID: PMC4332515  PMID: 18024530
5.  Oxidative Stress and Major Depression 
Background: Major causative factor for major depression is inflammation, autoimmune tissue damage and prolonged psychological stress, which leads to oxidative stress. The aim of this study was to know the association of free radicals and antioxidant status in subjects suffering from major depression.
Materials and Methods: Sixty patients diagnosed as a case of unipolar depression as per DSM IV, fulfilling the inclusion and exclusion criteria were compared with 40 healthy age and sex matched controls. The sera of both the groups were collected taking aseptic precautions and were evaluated for the markers of oxidative stress and for the antioxidants. The age group of the sample and the controls was between 18-60 y, both males and females were equally represented in the groups.
Results: A significantly high level of malondialdehyde (MDA) was found in the patients with major depression (1.95 ± 1.04 mmol/L) as compared to healthy controls (0.366 ± 0.175 mmol/L) (p < 0.0001). The serum level of nitrite was found to be lower in cases (23.18 ± 12.08 μmol/L) in comparison to controls (26.18 ± 8.68 μmol/L) (p = 0.1789). Similarly the serum level of ascorbic acid and superoxide dismutase (SOD) were significantly below as compared to healthy controls (all p < 0.0001). Ceruloplasmin levels were also depressed in cases (p = 0.3943).
Conclusion: The study concluded that in the absence of known oxidative injury causative agents, the lowered levels of antioxidants and higher levels of MDA implicate the high degree of oxidative stress in unipolar depression.
doi:10.7860/JCDR/2014/10258.5292
PMCID: PMC4316245  PMID: 25653939
Malondialdehyde; Major depression; Nitric oxide; Reactive oxygen Species; Super oxide dismutase
6.  Functionalized Graphene Sheets As Immobilization Matrix for Fenugreek β-Amylase: Enzyme Kinetics and Stability Studies 
PLoS ONE  2014;9(11):e113408.
β-Amylase finds application in food and pharmaceutical industries. Functionalized graphene sheets were customised as a matrix for covalent immobilization of Fenugreek β-amylase using glutaraldehyde as a cross-linker. The factors affecting the process were optimized using Response Surface Methodology based Box-Behnken design of experiment which resulted in 84% immobilization efficiency. Scanning and Transmission Electron Microscopy (SEM, TEM) and Fourier Tansform Infrared (FTIR) spectroscopy were employed for the purpose of characterization of attachment of enzyme on the graphene. The enzyme kinetic studies were carried out for obtaining best catalytic performance and enhanced reusability. Optimum temperature remained unchanged, whereas optimum pH showed shift towards acidic range for immobilized enzyme. Increase in thermal stability of immobilized enzyme and non-toxic nature of functionalized graphene can be exploited for production of maltose in food and pharmaceutical industries.
doi:10.1371/journal.pone.0113408
PMCID: PMC4239066  PMID: 25412079
7.  Coryphoid Palm Leaf Fossils from the Maastrichtian–Danian of Central India with Remarks on Phytogeography of the Coryphoideae (Arecaceae) 
PLoS ONE  2014;9(11):e111738.
Premise of research
A large number of fossil coryphoid palm wood and fruits have been reported from the Deccan Intertrappean beds of India. We document the oldest well-preserved and very rare costapalmate palm leaves and inflorescence like structures from the same horizon.
Methodology
A number of specimens were collected from Maastrichtian–Danian sediments of the Deccan Intertrappean beds, Ghughua, near Umaria, Dindori District, Madhya Pradesh, India. The specimens are compared with modern and fossil taxa of the family Arecaceae.
Pivotal results
Sabalites dindoriensis sp. nov. is described based on fossil leaf specimens including basal to apical parts. These are the oldest coryphoid fossil palm leaves from India as well as, at the time of deposition, from the Gondwana- derived continents.
Conclusions
The fossil record of coryphoid palm leaves presented here and reported from the Eurasian localities suggests that this is the oldest record of coryphoid palm leaves from India and also from the Gondwana- derived continents suggesting that the coryphoid palms were well established and wide spread on both northern and southern hemispheres by the Maastrichtian–Danian. The coryphoid palms probably dispersed into India from Europe via Africa during the latest Cretaceous long before the Indian Plate collided with the Eurasian Plate.
doi:10.1371/journal.pone.0111738
PMCID: PMC4230940  PMID: 25394208
8.  In Vitro, In Silico and In Vivo Studies of Ursolic Acid as an Anti-Filarial Agent 
PLoS ONE  2014;9(11):e111244.
As part of our drug discovery program for anti-filarial agents from Indian medicinal plants, leaves of Eucalyptus tereticornis were chemically investigated, which resulted in the isolation and characterization of an anti-filarial agent, ursolic acid (UA) as a major constituent. Antifilarial activity of UA against the human lymphatic filarial parasite Brugia malayi using in vitro and in vivo assays, and in silico docking search on glutathione-s-transferase (GST) parasitic enzyme were carried out. The UA was lethal to microfilariae (mf; LC100: 50; IC50: 8.84 µM) and female adult worms (LC100: 100; IC50: 35.36 µM) as observed by motility assay; it exerted 86% inhibition in MTT reduction potential of the adult parasites. The selectivity index (SI) of UA for the parasites was found safe. This was supported by the molecular docking studies, which showed adequate docking (LibDock) scores for UA (−8.6) with respect to the standard antifilarial drugs, ivermectin (IVM −8.4) and diethylcarbamazine (DEC-C −4.6) on glutathione-s-transferase enzyme. Further, in silico pharmacokinetic and drug-likeness studies showed that UA possesses drug-like properties. Furthermore, UA was evaluated in vivo in B. malayi-M. coucha model (natural infection), which showed 54% macrofilaricidal activity, 56% female worm sterility and almost unchanged microfilaraemia maintained throughout observation period with no adverse effect on the host. Thus, in conclusion in vitro, in silico and in vivo results indicate that UA is a promising, inexpensive, widely available natural lead, which can be designed and developed into a macrofilaricidal drug. To the best of our knowledge this is the first ever report on the anti-filarial potential of UA from E. tereticornis, which is in full agreement with the Thomson Reuter's ‘Metadrug’ tool screening predictions.
doi:10.1371/journal.pone.0111244
PMCID: PMC4222910  PMID: 25375886
9.  Serum Prolidase Activity and Oxidative Stress in Diabetic Nephropathy and End Stage Renal Disease: A Correlative Study with Glucose and Creatinine 
Association of oxidative stress and serum prolidase activity (SPA) has been reported in many chronic diseases. The study was aimed at evaluating the correlation of glucose and creatinine to SPA and oxidative stress in patients with diabetic nephropathy (DN) and end stage renal disease (ESRD) concerned with T2DM. 50 healthy volunteers, 50 patients with T2DM, 86 patients with DN, and 43 patients with ESRD were considered as control-1, control-2, case-1, and case-2, respectively. Blood glucose, creatinine, SPA, total oxidant status (TOS), total antioxidant status (TAS), and oxidative stress index (OSI) were measured by colorimetric tests. SPA, TOS, and OSI were significantly increased in case-1 and case-2 than control-1 and control-2, while TAS was significantly decreased (P < 0.001). Blood glucose was linearly correlated to SPA, TOS, TAS, and OSI in control-2, case-1 and case-2 (P < 0.001). Serum creatinine was linearly correlated with SPA, TOS, TAS and OSI in control-2 and case-1 (P < 0.001). In case-2, serum creatinine was significantly correlated with SPA only (P < 0.001). Thus, the study concluded that SPA and oxidative stress significantly correlated with blood glucose and creatinine. SPA, TOS, TAS, and OSI can be used as biomarkers for diagnosis of kidney damage.
doi:10.1155/2014/291458
PMCID: PMC4172940  PMID: 25276429
10.  Predominance of ERG-negative high-grade prostate cancers in African American men 
Molecular and Clinical Oncology  2014;2(6):982-986.
Erythroblast transformation-specific-related gene (ERG) fusions, the most common and validated prostate cancer (CaP) genome alteration, result in alterations in the expression of the ERG oncoprotein. Significantly lower frequencies of ERG have been reported in tumors of African American (AA) in comparison to Caucasian American (CA) men. Building on our preliminary observations, this study has focused on the increased association of the ERG-negative status with higher-grade prostate tumors in AA men. Representative whole-mount prostate sections from a matched cohort of 63 AA and 63 CA men with Gleason scores of 4+3 and those with Gleason scores of 8–10 were analyzed for ERG oncoprotein by immunohistochemistry. The striking finding of this study was that ERG expression was 3 times more likely to be present in the higher-grade index tumors of CA men compared to AA men (31 of 63 vs. 10 of 63 patients, respectively; P<0.0001). Although the mechanisms underlying these differences have not been elucidated, the present study along with our previous observations underscores that ERG typing may enhance the understanding of ethnic differences and future targeted therapy of CaP.
doi:10.3892/mco.2014.378
PMCID: PMC4179793  PMID: 25279185
prostate cancer; erythroblast transformation-specific-related gene; transmembrane protease serine 2 gene fusion; race; ethnicity
11.  Impact of CCL2 and Its Receptor CCR2 Gene Polymorphism in North Indian Population: A Comparative Study in Different Ethnic Groups Worldwide 
Chemokine are small, inducible pro-inflammatory cytokines involved in many biological processes, such as migration of leukocytes, atherosclerosis, angiogenesis, tumor growth, and metastasis. Chemokine are also known to influence tumor cell’s activity. Specifically, tumor cells express chemokine receptors in a non random manner suggesting a role of chemokine in metastatic destination of tumor cells. The present study was conducted to determine distribution of (Chemokine receptor 2) CCR2 V64I, Chemokine ligand 2 CCL2 I/D, and CCL2 2518 A>G gene polymorphisms in North Indian population and compare with different populations globally. Polymerase chain reaction (PCR)-based analysis was conducted in 200 normal healthy individuals of similar ethnicity. Allelic frequencies in wild type (GG) of CCR2 V64I G>A were 63 % G; CCL2 I/D 42 % II; CCL2 2518 A>G 40.5 % A. The minor variant allele frequency in our population was as follows: 19.5 % for CCR2 V64I, 35.5 % for CCL2 I/D, 35.3 % for CCL2 2518 A>G. We further compared frequency distribution for these genes with various published studies in different ethnicity. Our results suggested that frequency in chemokine genes exhibit distinctive pattern in India that could be attributed to ethnicity variation. This could assist in high-risk screening of human exposed to environmental carcinogens and cancer predisposition in different ethnic groups. Thus, they signify an impact of ethnicity and provide a basis for future epidemiological and clinical studies.
doi:10.1007/s12291-012-0265-0
PMCID: PMC3689333  PMID: 24426221
Chemokine gene; SNPs; Bladder cancer; PCR–RFLP; North India
12.  The significance of TNFAIP8 in prostate cancer response to radiation and docetaxel and disease recurrence 
TNFAIP8 is a NF-κB-inducible, oncogenic molecule. Previous “promoter array” studies have identified differential methylation and regulation of TNFAIP8 in prostate epithelial and cancer cell lines. Here we demonstrate that TNFAIP8 expression is induced by androgen in hormone-responsive LNCaP prostate cancer cells. In athymic mice bearing hormone-refractory PC-3 prostate tumor xenografts, intravenous treatment with a liposomal formulation of TNFAIP8 antisense oligonucleotide (LE-AS5) caused reduced expression of TNFAIP8 in tumor tissues, and a combination of LE-AS5 and radiation or docetaxel treatment resulted in significant inhibition of PC-3 tumor growth as compared to single agents. The immunohistochemical evaluation of TNFAIP8 expression revealed correlation of both cytoplasmic and nuclear TNFAIP8 overexpression with high grade prostatic adenocarcinomas, while nuclear overexpression was found to be an independent predictor of disease recurrence controlling for tumor grade. Increased nuclear TNFAIP8 expression was statistically significantly associated with a 2.44 fold (95 % confidence interval: 1.01–5.91) higher risk of prostate cancer recurrence. Mechanistically, TNFAIP8 seems to function as a scaffold (or adaptor) protein. In the antibody microarray analysis of proteins associated with the TNFAIP8 immune-complex, we have identified Karyopherin alpha2 as a novel binding partner of nuclear TNFAIP8 in PC-3 cells. The Ingenuity Pathway Analysis of the TNFAIP8 interacting proteins suggested that TNFAIP8 influences cancer progression pathways and networks involving integrins and matrix metalloproteinases. Taken together, present studies demonstrate that TNFAIP8 is a novel therapeutic target in prostate cancer, and indicate a potential relationship of the nuclear trafficking of TNFAIP8 with adverse outcomes in a subset of prostate cancer patients.
doi:10.1002/ijc.27996
PMCID: PMC3620960  PMID: 23280553
prostate cancer; therapy response; prognosis; TNFAIP8; KPNA2
13.  A combined approach for the enhancement and segmentation of mammograms using modified fuzzy C-means method in wavelet domain 
In this paper, a combined approach for enhancement and segmentation of mammograms is proposed. In preprocessing stage, a contrast limited adaptive histogram equalization (CLAHE) method is applied to obtain the better contrast mammograms. After this, the proposed combined methods are applied. In the first step of the proposed approach, a two dimensional (2D) discrete wavelet transform (DWT) is applied to all the input images. In the second step, a proposed nonlinear complex diffusion based unsharp masking and crispening method is applied on the approximation coefficients of the wavelet transformed images to further highlight the abnormalities such as micro-calcifications, tumours, etc., to reduce the false positives (FPs). Thirdly, a modified fuzzy c-means (FCM) segmentation method is applied on the output of the second step. In the modified FCM method, the mutual information is proposed as a similarity measure in place of conventional Euclidian distance based dissimilarity measure for FCM segmentation. Finally, the inverse 2D-DWT is applied. The efficacy of the proposed unsharp masking and crispening method for image enhancement is evaluated in terms of signal-to-noise ratio (SNR) and that of the proposed segmentation method is evaluated in terms of random index (RI), global consistency error (GCE), and variation of information (VoI). The performance of the proposed segmentation approach is compared with the other commonly used segmentation approaches such as Otsu's thresholding, texture based, k-means, and FCM clustering as well as thresholding. From the obtained results, it is observed that the proposed segmentation approach performs better and takes lesser processing time in comparison to the standard FCM and other segmentation methods in consideration.
doi:10.4103/0971-6203.139007
PMCID: PMC4154185  PMID: 25190996
Mammogram segmentation; mammogram enhancement; modified fuzzy c-means segmentation; mutual information; performance evaluation; wavelet based segmentation
14.  Functional antagonism of TMPRSS2-ERG splice variants in prostate cancer 
Genes & Cancer  2014;5(7-8):273-284.
The fusion between ERG coding sequences and the TMPRSS2 promoter is the most prevalent in prostate cancer (CaP). The presence of two main types of TMPRSS2-ERG fusion transcripts in CaP specimens, Type I and Type II, prompted us to hypothesize that the cumulative actions of different ERG variants may impact CaP development/progression. Using TMPRSS2-ERG3 (Type I) and TMPRSS2-ERG8 (Type II) expression vectors, we determined that the TMPRSS2- ERG8 encoded protein is deficient in transcriptional regulation compared to TMPRSS2-ERG3. Co-transfection of vectors resulted in decreased transcriptional regulation compared to TMPRSS2-ERG3 alone, suggesting transdominance of ERG8. Expression of exogenous ERG8 protein resulted in a decrease in endogenous ERG3 protein levels in TMPRSS2-ERG positive VCaP cells, with a concomitant decrease in C-MYC. Further, we showed a physical association between ERG3 and ERG8 in live cells by the bimolecular fluorescence complementation assay, providing a basis for the observed effects. Inhibitory effects of TMPRSS2-ERG8 on TMPRSS2- ERG3 were also corroborated by gene expression data from human prostate cancers, which showed a positive correlation between C-MYC expression and TMPRSS2-ERG3/TMPRSS2- ERG8 ratio. We propose that an elevated TMPRSS2-ERG3/TMPRSS2-ERG8 ratio results in elevated C-MYC in CaP, providing a strong rationale for the biomarker and therapeutic utility of ERG splice variants, along with C-MYC.
PMCID: PMC4162137  PMID: 25221645
ERG; Splice variants; Prostate cancer; Dominant negative; C-MYC
15.  Basal Expression of Pluripotency-Associated Genes Can Contribute to Stemness Property and Differentiation Potential 
Stem Cells and Development  2013;22(12):1802-1817.
Pluripotency and stemness is believed to be associated with high Oct-3/4, Nanog, and Sox-2 (ONS) expression. Similar to embryonic stem cells (ESCs), high ONS expression eventually became the measure of pluripotency in any cell. The threshold expression of ONS genes that underscores pluripotency, stemness, and differentiation potential is still unclear. Therefore, we raised a question as to whether pluripotency and stemness is a function of basal ONS gene expression. To prove this, we carried out a comparative study between basal ONS expressing NIH3T3 cells with pluripotent mouse bone marrow mesenchymal stem cells (mBMSC) and mouse ESC. Our studies on cellular, molecular, and immunological biomarkers between NIH3T3 and mBMSC demonstrated stemness property of undifferentiated NIH3T3 cells that was similar to mBMSC and somewhat close to ESC as well. In vivo teratoma formation with all three germ layer derivatives strengthen the fact that these cells in spite of basal ONS gene expression can differentiate into cells of multiple lineages without any genetic modification. Conclusively, our novel findings suggested that the phenomenon of pluripotency which imparts ability for multilineage cell differentiation is not necessarily a function of high ONS gene expression.
doi:10.1089/scd.2012.0261
PMCID: PMC3668502  PMID: 23343006
16.  Overexpression, purification, crystallization and preliminary X-ray analysis of putative molybdenum cofactor biosynthesis protein C (MoaC2) from Mycobacterium tuberculosis H37Rv 
Rv0864, an enzyme of the Moco biosynthesis pathway from M. tuberculosis, has been overexpressed, purified and crystallized. Diffraction data to 2.5 Å were collected and the structure solved by molecular replacement.
Rv0864 (MoaC2) from Mycobacterium tuberculosis is one of the enzymes in the molybdenum cofactor (Moco) biosynthesis pathway. Together with MoaA, MoaC is involved in the conversion of guanosine triphosphate (GTP) to precursor Z, the first step in Moco synthesis. Full-length MoaC2 (17.5 kDa, 167 residues) was cloned in Escherichia coli and purified to homogeneity. Crystals of recombinant M. tuberculosis MoaC2 were grown by vapour diffusion using a hanging-drop setup. Diffracting crystals grew in a condition in which 3 µl protein solution at 10.5 mg ml−1 was mixed with 1.5 µl reservoir solution (0.025 M potassium sodium tartrate tetrahydrate pH 8.0) and equilibrated against 1000 µl reservoir solution. Diffraction data extending to 2.5 Å resolution were collected at 100 K. The crystal belonged to the cubic space group P213, with unit-cell parameter 94.5 Å. Matthews coefficient (V M) calculations suggested the presence of two molecules in the asymmetric unit, corresponding to a solvent content of about 39%. Molecular-replacement calculations using the E. coli homologue as the search model gave an unambiguous solution.
doi:10.1107/S174430911201665X
PMCID: PMC3370911  PMID: 22684071
MoaC2; Mycobacterium tuberculosis H37Rv; molybdenum cofactor biosynthesis
17.  Pharmacognostical study and establishment of quality parameters of aerial parts of Costus speciosus-a well known tropical folklore medicine 
Objective
To evaluate the diagnostic pharmacognostical characters of Costus speciosus (aerial parts) along with their physico-chemical parameters and fluorosence analysis.
Method
The pharmacognostical characters were determined in terms of macroscopy, microscopy, powder microscopy, leaf constant, fluorescence analysis and preliminary phytochemical investigation.
Results
The findings of macroscopy revealed that leaves elliptic to oblong or oblong-lancoelate, thick, spirally arranged, with stem clasping sheaths up to 4 cm, flowers large, white, cone-like terminal spikes, with bright red bracts. Transverse section of leaflet showed the presence of cuticularised epidermis with polygonal cells on adaxial surface and bluntly angled cells on abaxial surface of lamina, mesophyll cells differentiated in to single layered palisade cells on each surface and 2-3 layered spongy parenchyma, unicellular and uniseriate multicellular covering trichomes, paracytic stomata and vascular bundles surrounded by sclerenchymatous multicellular sheath. Preliminary phytochemical screening exhibited the presence of various phytochemical groups like alkaloids, glycosides, steroids, phenolic constituents. Further, the leaf constants, powder microscopy and fluorescence characteristics indicated outstanding results from this investigation
Conclusions
Various pharmacognostical and physico-chemical parameters have pivotal roles in identification, authentication and establishment of quality parameters of the species.
doi:10.12980/APJTB.4.2014C1103
PMCID: PMC3994359  PMID: 25182951
Costus speciosus; Quality control; Physico-chemical parameters; Microscopy; Fluorescence analysis
18.  Evaluation of MC4R [rs17782313, rs17700633], AGRP [rs3412352] and POMC [rs1042571] Polymorphisms with Obesity in Northern India 
Oman Medical Journal  2014;29(2):114-118.
Objective
Genetic variants of the melanocortin-4 receptor gene (MC4R), agouti related protein (AGRP) and proopiomelanocortin (POMC) are reported to be associated with obesity. Therefore, the aim of this study is to examine MC4R rs17782313, MC4R rs17700633, AGRP rs3412352 and POMCrs1042571 for any association with obesity in North Indian subjects.
Methods
The variants were investigated for association in 300 individuals with BMI ≥30 kg/m2 and 300 healthy non-obese individuals BMI <30 kg/m2. The genotyping were analyzed by Taqman probes. The statistical analysis was performed by the SPSS software, ver.19 and p≤0.05 was considered statistically significant.
Results
The genotypes of MC4R rs17782313 and POMC rs1042571 were significantly associated with obesity (C), (p=0.02; OR=1.7 and p=0.01; OR=1.6, respectively); however, MC4Rrs17700633 (p=0.001; OR=0.55) was associated with low risk. In addition, AGRPrs3412352 (p=0.93; OR=0.96) showed no association with obesity (BMI ≥30 kg/m2) in North Indian subjects.
Conclusion
This study provides the report about the significant association of MC4R (rs17782313) and POMC (rs1042571) with morbid obesity (BMI ≥30 kg/m2), but MC4R (rs17700633) and AGRP (rs34123523) did not show any association with obesity in the studied North Indian population.
doi:10.5001/omj.2014.28
PMCID: PMC3976726  PMID: 24715938
Obesity; Genetic variants; Genotype; Phenotype; MC4R; AGRP; POMC
20.  A report on biocompounds from palm fossil of India 
Bioinformation  2014;10(5):316-319.
The occurrence of a large number of fossil woods having resemblance in anatomical features with the modern palm genus, Phoenix L in Deccan Intertrappean fossil flora of Maastrichtian-Danian age (i. e. Late Cretaceous and Earliest Tertiary (65-67 my)) indicates the most primitive record of date palm. Present discovery of biocompounds from fossil wood of Phoenix collected from Deccan Intertrappean having affinity with the biocompounds known from modern plant further exemplify the earliest documentation of Phoenix in Indian peninsula.
doi:10.6026/97320630010316
PMCID: PMC4070043  PMID: 24966541
Fossil wood; Indian date palm; Phoenix; Biocompounds; First record
21.  Doxycycline Poly E-Caprolactone Nanofibers in Patients with Chronic Periodontitis – A Clinical Evaluation 
Aim: To develop a low-dose controlled-release delivery system for the treatment of periodontal infections. A new sustained release drug system of Poly e-caprolactone (PCL) nanofibers containing doxycycline (DOX) was successfully electrospun and evaluated clinically for periodontal diseases. The retentive doxycycline nanofibres were shown to provide a controlled delivery of the drug.
Material and Methods: Nanofibers were prepared with DOX in PCL by electrospinning technique. The drug-coated nanofibres provided sustained effect up to a period of 11 days (264 h) and followed first order release. Forty sites in 7 patients (4 females and 3 males) with chronic periodontitis (5-8mm probing depth) were allocated in 2 experimental treatment groups, Group A-SRP (Scaling and Root Planing)
+ DOX nanofibers and Group B –SRP (Scaling and Root Planing) alone (control group). All these patients were evaluated clinically for probing depth (PD), plaque index (PI) and gingival index (GI).
Results: Both the treatment groups were found to be efficacious in the treatment of periodontal disease as demonstrated by improvement in PD, PI and GI.
Conclusion: Combination of SRP (Scaling and Root Planing) + DOX nanofibers (Group A) resulted in added benefits compared to the control group.
doi:10.7860/JCDR/2013/5858.3519
PMCID: PMC3843393  PMID: 24298524
Chronic periodontitis; Doxycycline; Nanofibers; Poly e-caprolactone
22.  Serum Proteome Changes in Dengue Virus-Infected Patients from a Dengue-Endemic Area of India: Towards New Molecular Targets? 
Abstract
The global burden of dengue continues to worsen, specifically in tropical and subtropical countries, and has evolved as a major public health problem. We investigated the changes in serum proteome in dengue fever (DF) patients from a dengue-endemic area of India to obtain mechanistic insights about the disease pathogenesis, the host immune response, and identification of potential serum protein biomarkers of this infectious disease. In this study, serum samples from DF patients, healthy subjects, and patients with falciparum malaria (an infectious disease control) were investigated by 2D-DIGE in combination with MALDI-TOF/TOF MS. The findings were validated with Western blotting. Functional clustering of the identified proteins was performed using PANTHER and DAVID tools. Compared to the healthy controls, we found significant changes in the expression levels of 48 protein spots corresponding to 18 unique proteins (7 downregulated and 11 upregulated) in DF patients (p<0.05). Among these differentially-expressed proteins, 11 candidates exhibited different trends in dengue fever compared to falciparum malaria. Importantly, our results suggest that dengue virus infection leads to alterations in expression levels of multiple serum proteins involved in diverse and vital physiological pathways, including acute phase response signaling, complement cascades, hemostasis, and blood coagulation. For the first time we report here that the serum levels of hemopexin, haptoglobin, serum amyloid P, and kininogen precursor, are altered in DF. This study informs the pathogenesis and host immune response to dengue virus infection, as well as the current search for new diagnostic and molecular drug targets.
doi:10.1089/omi.2012.0037
PMCID: PMC3459427  PMID: 22917478
23.  Chooramani technique: A novel method of omental transposition in traumatic spinal cord injury 
Asian Journal of Neurosurgery  2013;8(4):179-182.
Background:
Spinal cord injury often results in significant catastrophic disability. Placement of the intact omentum upon a recently traumatized spinal cord was found to be effective. It represents a very suitable organ for revascularization of the ischemic nervous tissue, due to its abundance in blood and lymph vessels and its capability to adhere to the surface of the lesion, with capillary overgrowing in 4-6 h. The traditional method of omentum transposition is a hectic and time-consuming two-stage procedure in which position is changed twice. The major disadvantage of this two-staged procedure is that it takes longer operative time, and there is high risk of infection due to change of position with an open wound. So there is a need for modifications so that the procedure can be made easier and complications can be avoided.
Objective:
To avoid the complications and to make the procedure easier, a single-staged procedure called ‘chooramani technique’ for omental transposition in spinal cord injury is proposed.
Materials and Methods:
The study was conducted on 16 patients of post-traumatic thoraco-lumbar spinal cord injury with paraplegia.
Results:
Complications like wound infection, incisional hernia, and CSF leak were avoided. Operative time reduced to approximately half.
Conclusion:
This modification of technique is relatively easy and can be adopted for patients undergoing omental transposition for spinal cord injury.
doi:10.4103/1793-5482.125661
PMCID: PMC3912768  PMID: 24551001
Omental transposition; spinal cord injury; paraplegia
24.  Antimicrobial Property of Extracts of Indian Lichen against Human Pathogenic Bacteria 
Context. Usnea ghattensis G. Awasthi (Usneaceae) endemic fruticose lichen found growing luxuriantly in Northern Western Ghats of India, it also contains Usnic acid as a major chemical and tested against some human pathogenic bacteria. Objective. To explore antimicrobial properties of Usnea ghattensis against some human pathogenic bacteria. Materials and Methods. The lichen was extracted in acetone, methanol, and ethanol. In vitro antimicrobial activity was tested initially by Kirby-Bauer technique of disc diffusion method and was confirmed by minimum inhibitory concentration using Broth microdilution method according to the NCCLS guidelines. Results. Ethanol extract was most effective against Bacillus cereus and Pseudomonas aeruginosa with a zone of inhibition 29.8 ± 0.6 mm and 12.3 ± 0.5 mm diameters at a concentration of 0.2 mg/mL. Acetone and methanol extract demonstrated almost similar activity against Staphylococcus aureus and the zone of inhibition was 24.6 ± 0.5 and 24.7 ± 0.4 mm. Only methanol extract was showing activity against Streptococcus faecalis with a 13.5 ± 0.8 mm zone. MIC value noted against Staphylococcus aureus and Streptococcus faecalis was 6.25 μg/mL and 25 μg/mL, whereas against Bacillus cereus and Pseudomonas aeruginosa, MIC calculated was 3.125 μg/mL and 200 μg/mL, respectively. Conclusion. The present study demonstrates the relatively higher activity of this lichen against not only gram (+) but significantly also against gram (−) bacteria. This indicates that this lichen might be a rich source of effective antimicrobial agents.
doi:10.1155/2013/709348
PMCID: PMC3767054  PMID: 24062769
25.  A clinical and molecular study of artesunate + sulphadoxine-pyrimethamine in three districts of central and eastern India 
Malaria Journal  2013;12:247.
Background
Artesunate + sulphadoxine-pyrimethamine (AS + SP) is recommended throughout India as the first-line treatment for uncomplicated falciparum malaria. Due to the presence of several eco-epidemiological zones of malaria and variable drug pressure, it is necessary to evaluate the efficacy of this combination in different regions of India. The objective of this study was to use clinical and molecular methods to monitor the efficacy of AS + SP in three diverse sites.
Methods
The study was undertaken in three high endemic sites of central and eastern India. Patients with uncomplicated falciparum malaria were enrolled and followed for 28 days. Molecular genotyping was conducted for merozoite surface protein (msp1 and msp2) to differentiate between re-infection and recrudescence and for the dhfr and dhps genes to monitor antifolate drug resistance.
Results
In all, 149 patients were enrolled at the three sites. The crude cure rates were 95.9%, 100%, and 100% in Ranchi, Keonjhar, and West Garo Hills respectively. PCR-corrected cure rates were 100% at all sites. In dhfr, 27% of isolates had triple mutations, while 46% isolates were double-mutants. The most prevalent mutation was S108N followed by C59R. 164 L mutation was observed in 43/126 (34%) isolates. In dhps, most (76%) of the isolates were wild-type. Only 2.5% (2/80) isolates showed double mutation. dhfr-dhps two locus mutation were observed in 16% (13/80) isolates. Parasite clearance time was not related with antifolate mutations.
Conclusions
AS + SP combination therapy remained effective against falciparum malaria despite common mutations promoting resistance to antifolate drugs. Although the prevalence of double and triple mutations in dhfr was high, the prevalence of dhfr-dhps two locus mutations were low. Even isolates with dhfr triple and dhfr-dhps two locus mutations achieved adequate clinical and parasitological response.
doi:10.1186/1475-2875-12-247
PMCID: PMC3726327  PMID: 23866298
Artesunate + sulphadoxine-pyrimethamine; Plasmodium falciparum; Dihydrofolate reductase; Dihydropteroate synthetase; Falciparum malaria

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