SUMMARYMammalian genomic imprinting is essential for development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. Here, we compared chromatin structure of the two conserved imprinted domains... more
SUMMARYMammalian genomic imprinting is essential for development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. Here, we compared chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints—theIgf2-H19and theDlk1-Dio3domains—and assessed the involvement of the insulator protein CTCF. At both domains, CTCF binds the maternal allele of a differentially-methylated region (DMR), in addition to multiple instances of bi-allelic CTCF binding in their surrounding TAD (Topologically Associating Domain). On the paternal chromosome, bi-allelic CTCF binding alone is sufficient to structure a first level of sub-TAD organization. Maternal-specific CTCF binding at the DMRs adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal sub-TAD organisation. Genome-editing experiments at theDlk1-Dio3locus confirm that the maternal sub-TADs are essential during development t...
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... between Page 6. J. Agric. Res. Kafer El-Sheikh Univ., 37(1) 2011 62 cultivars, similar results were obtained by Pal et al. (1988), Mohamed and Gamie (1999), El-Damarany and Obiadalla-Ali (2005), and Gamie and yaso (2007). B ...
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Coriander (Coriandrum sativum L.) is an annual spice herb that belongs to umbel family Apiaceae with diversified uses. We investigated the extent of variability among 22 Indian varieties of coriander using phenotypic and genetic markers.... more
Coriander (Coriandrum sativum L.) is an annual spice herb that belongs to umbel family Apiaceae with diversified uses. We investigated the extent of variability among 22 Indian varieties of coriander using phenotypic and genetic markers. Multilocus genotyping by nine RAPD primers detected an average of intraspecific variations amounting to 66.18% polymorphism in banding patterns. Analysis of molecular variance indicated that a greater proportion of total genetic variation exists within population (98%) rather than among populations (2%). Higher values of Nei's gene diversity (h) and Shannon Information Index (i) and genetic distance analysis validate wider genetic diversity among Indian coriander varieties. Besides total internal transcribed spacer (ITS) length variations and single nucleotide polymorphisms, insertions/deletions (INDELS) were detected at seven sites in ITS-1 region. Multiple sequence alignment of 12 sequenced varieties revealed cent per cent identities of 5.8S g...
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Chemoresistance of cisplatin therapy is related to extensive repair of cisplatin-modified DNA in the nucleus by the nucleotide excision repair (NER). Delivering cisplatin to the mitochondria to attack mitochondrial genome lacking NER... more
Chemoresistance of cisplatin therapy is related to extensive repair of cisplatin-modified DNA in the nucleus by the nucleotide excision repair (NER). Delivering cisplatin to the mitochondria to attack mitochondrial genome lacking NER machinery can lead to a rationally designed therapy for metastatic, chemoresistant cancers and might overcome the problems associated with conventional cisplatin treatment. An engineered hydrophobic mitochondria-targeted cisplatin prodrug, Platin-M, was constructed using a strain-promoted alkyne-azide cycloaddition chemistry. Efficient delivery of Platin-M using a biocompatible polymeric nanoparticle (NP) based on biodegradable poly(lactic-co-glycolic acid)-block-polyethyleneglycol functionalized with a terminal triphenylphosphonium cation, which has remarkable activity to target mitochondria of cells, resulted in controlled release of cisplatin from Platin-M locally inside the mitochondrial matrix to attack mtDNA and exhibited otherwise-resistant advan...
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Prosopis cineraria significantly contribute to sand dune stabilization, soil fertility rejuvenation and is an integral component of agro-forestry systems in arid regions of India. Effect of different rhizobacterial seed treatments on seed... more
Prosopis cineraria significantly contribute to sand dune stabilization, soil fertility rejuvenation and is an integral component of agro-forestry systems in arid regions of India. Effect of different rhizobacterial seed treatments on seed germination and seedling traits in two genotypes of P. cineraria (HPY-1) and (FG-1) were tested. Observations on seed germination (%) and seedling traits viz., root length (cm), shoot length (cm), seedling weight (g) and seedling length of different treatments were recorded. Whereas, germination index (GI), seedling vigour index (SVI) and root/shoot length ratio were derived from the observed data. The scarification treatment with sulphuric acid for 10 minutes substantially enhanced germination from < 20% to 80-82% in control treatments. Treatments with co-inoculations of Bacillus licheniformis and Sinorhizobium kostiense or S. saheli supported the maximum seed germination and seedling growth and vigour. The maximum germination per cent (92.5%),...
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ABSTRACT Breeding in Ziziphus mauritiana through hybridization is limited by its small sized flowers, cross incompatibility, low fruit set and poor retention. Correct identification of a hybrid is often difficult when it resembles more... more
ABSTRACT Breeding in Ziziphus mauritiana through hybridization is limited by its small sized flowers, cross incompatibility, low fruit set and poor retention. Correct identification of a hybrid is often difficult when it resembles more with one parent or when new morphological combination of characters arise from recombination of distinct genotypes. Under present study three varieties of Z. mauritiana viz., Tikadi, Seb and Katha were found cross compatible and resulted in improved hybrids viz., F1 (Seb × Tikadi), F1 × Seb and Seb × Katha. Ten RAPD primers revealed a total of 108 bands in the range of 150 bp to 3 kb. Among these, 69 bands were polymorphic and exhibited 33.33–90.9 % polymorphism in the banding patterns. The dendrogram clearly delineated variety Tikadi and Katha from Seb. All the three hybrids formed a single cluster with the variety Seb. The 5.8S gene region was found to be highly conserved (99.39 %) followed by ITS-2 (97.77 %). and ITS-1 (90.6–90.8 %). Heterozygous positions in ITS sequences clearly show their hybrid nature and could perform as highly polymorphic molecular markers. Despite SNPs, INDELS and total length polymorphism among parents and their hybrids, all were molecularly identified as Z. mauritiana and did not cause any phylogenetic error. The nucleotide polymorphism in ITS-1 region can serve as a bar code to detect and address genetic diversity within Z. mauritiana.
Several reports have elaborated on the role of efflux pumps in drug resistance in Mycobacterium tuberculosis by analysing the mRNA expression profiles. However, there is no uniformity in the subinhibitory concentrations of drugs chosen in... more
Several reports have elaborated on the role of efflux pumps in drug resistance in Mycobacterium tuberculosis by analysing the mRNA expression profiles. However, there is no uniformity in the subinhibitory concentrations of drugs chosen in these studies. Some investigators studied the expression of efflux pumps under a drug concentration of 1/2 minimum inhibitory concentration (MIC), while others used 1/3, 1/4 or 1/8MIC. The present study was planned to understand the effect of different concentrations of antituberculosis drugs on the expression of efflux pump genes. Log phase culture of the laboratory strain M. tuberculosis H37Rv was exposed to rifampicin (RIF), isoniazid (INH), streptomycin (SM) and ethambutol (EMB) at different drug concentrations (1/2MIC, 1/3MIC and 1/4MIC). The expression of 10 putative efflux pump genes was studied using quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). We observed an optimal expression of efflux pumps at higher concentrations of INH; and at lower concentrations of RIF and EMB. However, in the presence of SM, a decreased expression of efflux genes with increasing concentrations of the drug was confounded by a significant reduction in Colony Forming Units (CFU).
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A highly fluorescent Zn(2+) complex of the triazole linked salicyl-imino-thiophenyl conjugate of calix[4]arene, [ZnL] has been demonstrated to be a chemo-sensing ensemble for the recognition of His and Cys among the naturally occurring... more
A highly fluorescent Zn(2+) complex of the triazole linked salicyl-imino-thiophenyl conjugate of calix[4]arene, [ZnL] has been demonstrated to be a chemo-sensing ensemble for the recognition of His and Cys among the naturally occurring amino acids in HEPES buffer milieu. The recognition behaviour of the [ZnL] towards these amino acids has been shown on the basis of fluorescence, absorption and visual fluorescent colour changes. The species of recognition were shown by ESI MS titrations, AFM &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp; TEM microscopy and cell studies.
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Abstract Fenugreek (Trigonella foenum-graecum) is receiving global attention due to rare medicinal properties of significance to human health. Gene banks possess scanty germplasm and very little background information regard-ing its... more
Abstract Fenugreek (Trigonella foenum-graecum) is receiving global attention due to rare medicinal properties of significance to human health. Gene banks possess scanty germplasm and very little background information regard-ing its genetic variability that has hampered its ...
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Research Interests: Thermodynamics, Inorganic Chemistry, Organic Chemistry, Biomimetics, Quantum Theory, and 12 moreOxidative Stress, Magnetic Resonance Spectroscopy, Macromolecular X-Ray Crystallography, Humans, Zinc, Metallothionein, Electrons, Hydrogen Peroxide, Liquid Chromatography / Electrospray Ionization Mass Spectrometry, Buffers, Triazoles, and Calixarenes
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Pyridyl-based triazole-linked calix[4]arene conjugates, viz. L(1) and L(2), were synthesized and characterized. These two conjugates were shown to be selective and sensitive for Zn(2+) among the 12 metal ions studied in HEPES buffer... more
Pyridyl-based triazole-linked calix[4]arene conjugates, viz. L(1) and L(2), were synthesized and characterized. These two conjugates were shown to be selective and sensitive for Zn(2+) among the 12 metal ions studied in HEPES buffer medium by fluorescence, absorption, and visual color change with the detection limit of ~31 and ~112 ppb, respectively, by L(1) and L(2). Moreover, the utility of the conjugates L(1) and L(2) in showing the zinc recognition in live cells has also been demonstrated using HeLa cells as monitored by fluorescence imaging. The zinc complexes of L(1) and L(2) were isolated, and the structure of [ZnL(1)] has been established by single-crystal XRD and that of [ZnL(2)] by DFT calculations. TDDFT calculations were performed in order to demonstrate the electronic properties of receptors and their zinc complexes. The isolated zinc complexes, viz. [ZnL(1)] and [ZnL(2)], have been used as molecular tools for the recognition of anions on the basis of their binding affinities toward Zn(2+). [ZnL(2)] was found to be sensitive and selective toward phosphate-bearing ions and molecules and in particular to pyrophosphate (PPi) and ATP among the other 18 anions studied; however, [ZnL(1)] was not sensitive toward any of the anions studied. The selectivity has been shown on the basis of the changes observed in the emission and absorption spectral studies through the removal of Zn(2+) from [ZnL(2)] by PPi. Thus, [ZnL(2)] has been shown to detect PPi up to 278 ± 10 ppb at pH 7.4 in aqueous methanolic (1/2 v/v) HEPES buffer.
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Genetic Algorithms are search techniques for global optimization in a complex search space. One of the interesting features of a Genetic Algorithm is that they lend themselves very well for parallel and distributed processing. This... more
Genetic Algorithms are search techniques for global optimization in a complex search space. One of the interesting features of a Genetic Algorithm is that they lend themselves very well for parallel and distributed processing. This feature of Genetic Algorithm is useful in improving its computation efficiency for complex optimization problems. In this paper, we have implemented Genetic Algorithm in a
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A benzimidazole appended triazole linked 1,3-diconjugate of calix[4]arene (L) has been synthesized and characterized. The conjugate L has been found to recognize Cu(2+) among the thirteen different metal ions studied by exhibiting... more
A benzimidazole appended triazole linked 1,3-diconjugate of calix[4]arene (L) has been synthesized and characterized. The conjugate L has been found to recognize Cu(2+) among the thirteen different metal ions studied by exhibiting ratiometric fluorescence changes through newly generated excimer band at ∼380 nm. Fluorescence off-on-off behavior has been clearly demonstrated on the basis of the binding variability of Cu(2+) to L. The binding has been elicited through the changes observed in the fluorescence, ESI MS and (1)H NMR titrations. All the other metal ions studied do not show any new band and further do not interfere with the recognition of Cu(2+) by L, even when these are present in the same medium. The structural features of both the mono- and di-nuclear complexes were established by DFT computational calculations and found to display highly distorted geometry about the copper centers that deviate from both the tetrahedral and the square planar.
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The ability to rationally design and construct a platform technology to develop new platinum(IV) [Pt(IV)] prodrugs with functionalities for installation of targeting moieties, delivery systems, fluorescent reporters from a single... more
The ability to rationally design and construct a platform technology to develop new platinum(IV) [Pt(IV)] prodrugs with functionalities for installation of targeting moieties, delivery systems, fluorescent reporters from a single precursor with the ability to release biologically active cisplatin by using well-defined chemistry is critical for discovering new platinum-based therapeutics. With limited numbers of possibilities considering the sensitivity of Pt(IV) centers, we used a strain-promoted azide-alkyne cycloaddition approach to provide a platform, in which new functionalities can easily be installed on cisplatin prodrugs from a single Pt(IV) precursor. The ability of this platform to be incorporated in nanodelivery vehicle and conjugation to fluorescent reporters were also investigated.
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A fluorescence turn-on receptor based on triazole linked calix[4]arene (L) for selective recognition of Zn(2+) in aqueous-methanolic HEPES buffer has been developed and showed its utility for sensing Zn(2+) in blood serum milieu.
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Cancer-associated inflammation induces tumor progression to the metastatic stage, thus indicating that a chemo-anti-inflammatory strategy is of interest for the management of aggressive cancers. The platinum(IV) prodrug Platin-A was... more
Cancer-associated inflammation induces tumor progression to the metastatic stage, thus indicating that a chemo-anti-inflammatory strategy is of interest for the management of aggressive cancers. The platinum(IV) prodrug Platin-A was designed to release cisplatin and aspirin to ameliorate the nephrotoxicity and ototoxicity caused by cisplatin. Platin-A exhibited anticancer and anti-inflammatory properties which are better than a combination of cisplatin and aspirin. These findings highlight the advantages of combining anti-inflammatory treatment with chemotherapy when both the drugs are delivered in the form of a single prodrug.
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An in situ prepared Zn(2+) complex of triazole linked imino-thiophenyl conjugate of calix[4]arene, [ZnL], was demonstrated to be highly fluorescent in HEPES buffer solution. [ZnL] has been used as a chemo-sensing ensemble for the... more
An in situ prepared Zn(2+) complex of triazole linked imino-thiophenyl conjugate of calix[4]arene, [ZnL], was demonstrated to be highly fluorescent in HEPES buffer solution. [ZnL] has been used as a chemo-sensing ensemble for the recognition of phosphates in general and pyrophosphates in particular among the eighteen different anions studied. The chemo-sensing behavior of the [ZnL] has been demonstrated through fluorescence, absorption, visual fluorescent color changes, ESI MS, and (1)H NMR titrations. Variations in the microstructural features of L, its zinc complex and the complex upon addition of PPi have been demonstrated through atomic force microscopy and transmission electron microscopy. Such studies have been extended to see the permeability of the conjugate into the HeLa cells by fluorescence microscopy. In accession, a reversible &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;write-read-erase-read&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; logic gate property of L has been demonstrated through a feedback loop in the presence of Zn(2+) and PPi.
Research Interests: Chemical Engineering, Analytical Chemistry, Microscopy, Fluorescence Microscopy, Transmission Electron Microscopy, and 11 moreFluorescent Dyes and Reagents, Magnetic Resonance Spectroscopy, Atomic Force Microscopy, Humans, Zinc, Liquid Chromatography / Electrospray Ionization Mass Spectrometry, Buffers, HeLa cells, Triazoles, Diphosphates, and Calixarenes
The triazole linked o-imino phenol appended calix[4]arene conjugate (L) has been synthesized and characterized. The structure of L has been established based on single crystal XRD. The binding and recognition behavior of conjugate, L... more
The triazole linked o-imino phenol appended calix[4]arene conjugate (L) has been synthesized and characterized. The structure of L has been established based on single crystal XRD. The binding and recognition behavior of conjugate, L toward the transition metal ions, such as Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+), has been demonstrated using fluorescence, absorption and ESI-MS techniques. The in situ prepared complexes of these metal ions, namely, [Mn(2)L], [Fe(2)L], [Co(2)L], [Ni(2)L], [Cu(2)L], and [Zn(2)L] have shown recognition toward Glu, Asp, His and Cys. Hence L provides a multiple sensing molecular tool where the response for the recognition of biologically active amino acids of metalloproteins is elicited by the presence of specific metal ion.
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An N,N-Dimethylamine ethylimino-appended triazole-linked calix[4]arene conjugate, L, has been synthesized and characterized, and its Cd(2+) complex has been isolated and characterized. The structure of [CdL] was established by... more
An N,N-Dimethylamine ethylimino-appended triazole-linked calix[4]arene conjugate, L, has been synthesized and characterized, and its Cd(2+) complex has been isolated and characterized. The structure of [CdL] was established by computational calculation using B3LYP/LANL2DZ. Time-dependent density functional theory calculations were performed to demonstrate the electronic properties of [CdL]. This highly fluorescing [CdL] has been used to recognize Cys selectively among the 20 naturally occurring amino acids. [CdL] exhibits a minimum detection limit of 58 ppb for Cys, with reusability and reversibility being imparted to the system during sensing. Thus, the sensing of Cys was well demonstrated using various techniques, viz., fluorescence, absorption, visual color change, electrospray ionization MS, (1)H NMR, and live cell imaging experiments.
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We attempted to apply the PCR-restriction fragment length polymorphism (PCR-RFLP) technique for the early detection and identification of Mycobacterium tuberculosis directly from clinical samples. PCR-RFLP of hsp65 was applied to the DNA... more
We attempted to apply the PCR-restriction fragment length polymorphism (PCR-RFLP) technique for the early detection and identification of Mycobacterium tuberculosis directly from clinical samples. PCR-RFLP of hsp65 was applied to the DNA extracted directly from sputum samples (n = 226) collected from 226 patients. We could detect and identify M. tuberculosis in 84.5% of the acid-fast bacillus (AFB) smear-positive samples (n = 149) and 11% of the AFB smear-negative samples (n = 18) obtained from patients with clinical and radiological evidence of tuberculosis. Sputum samples (n = 59) obtained from patients suffering from respiratory diseases other than tuberculosis were included as negative controls. To test the sensitivity of the assay, we spiked a smear-negative sample with serial dilutions of H37Rv. The protocol could detect down to 10 organisms/microl. PCR-RFLP was found to be a simple and reproducible method for early detection of M. tuberculosis from sputum samples. The present...
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The aim of this study was to ascertain the incidence of drug resistance of Mycobacterium tuberculosis isolates from patients in Delhi, India, being treated with DOTS and in private clinics, since a large proportion of patients with... more
The aim of this study was to ascertain the incidence of drug resistance of Mycobacterium tuberculosis isolates from patients in Delhi, India, being treated with DOTS and in private clinics, since a large proportion of patients with tuberculosis in India seek help from private healthcare sectors. Sputum samples were collected from 60 cases of tuberculosis attending a DOTS center and 42 patients from private clinics. Of these, 35 patients from the DOTS center and 12 patients from private clinics had a second sputum sample collected following two months of therapy. The isolated M. tuberculosis strains were assayed for isoniazid (INH), rifampicin (RIF), streptomycin (SM) and ethambutol (EMB) susceptibility by the proportion method. The frequencies of multidrug resistance (MDR) in the M. tuberculosis strains obtained from those treated with DOTS and in private centers were 12.7% and 5% (p > 0.5), respectively. Isolates obtained after two months of therapy showed a similar rate of MDR ...
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Spt6 is a multifunctional histone chaperone involved in the maintenance of chromatin structure during elongation by RNA polymerase II (Pol II). Spt6 has a tandem SH2 (tSH2) domain within its C terminus that recognizes Pol II C-terminal... more
Spt6 is a multifunctional histone chaperone involved in the maintenance of chromatin structure during elongation by RNA polymerase II (Pol II). Spt6 has a tandem SH2 (tSH2) domain within its C terminus that recognizes Pol II C-terminal domain (CTD) peptides phosphorylated on Ser2, Ser5, or Try1 in vitro. Deleting the tSH2 domain, however, only has a partial effect on Spt6 occupancy in vivo, suggesting that more complex mechanisms are involved in the Spt6 recruitment. Our results show that the Ser2 kinases Bur1 and Ctk1, but not the Ser5 kinase Kin28, cooperate in recruiting Spt6, genome-wide. Interestingly, the Ser2 kinases promote the association of Spt6 in early transcribed regions and not toward the 3' ends of genes, where phosphorylated Ser2 reaches its maximum level. In addition, our results uncover an unexpected role for histone deacetylases (Rpd3 and Hos2) in promoting Spt6 interaction with elongating Pol II. Finally, our data suggest that phosphorylation of the Pol II CT...
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Lipoproteins are known to be effective immunogens and affect both innate and adaptive immunity. The lprN gene of Mycobacterium tuberculosis has been predicted to encode for a putative lipoprotein in silico. Here, we studied its function... more
Lipoproteins are known to be effective immunogens and affect both innate and adaptive immunity. The lprN gene of Mycobacterium tuberculosis has been predicted to encode for a putative lipoprotein in silico. Here, we studied its function as an immunogen by in vivo studies in mice. The recombinant LprN protein, expressed and purified in Escherichia coli, triggered a cell-mediated immune response in BALB/c mice. This was observed by significantly higher T-cell proliferation and increased production of TNF-α and IFN-γ cytokines. However, pre-exposure to LprN protein failed to provide protection in mice after challenge with a virulent strain of M. tuberculosis. Histological examination showed an increase in tissue destruction in experimental animals, indicating an immunogenic potential for LprN protein that enhanced the virulence of bacilli.
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ABSTRACT Determination of lipid content of any biological sample is essential for various kinds of studies related to pathogenicity and drug development. Thus, reliable methods for the quantitative extraction of lipids are of critical... more
ABSTRACT Determination of lipid content of any biological sample is essential for various kinds of studies related to pathogenicity and drug development. Thus, reliable methods for the quantitative extraction of lipids are of critical importance. The mycobacterial cell wall is largely composed of lipids. Commonly used methods to extract lipids, such as the Bligh and Dyer method or the Folch method, yield a low amount of lipids when applied to mycobacterial cells. This study presents an efficient modification of Chandramauli’s method, a less known method developed at this institute earlier that is able to yield a considerably higher concentration of mycobacterial lipids.