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121.
181 Integrative analysis of gene expression and protein–protein interaction networks in Glioblastoma
Seema Mishra 《Journal of biomolecular structure & dynamics》2013,31(1):116-117
Glioblastoma multiforme (GBM) is the most malignant of all the brain tumors with very low median survival time of one year, as per Central Brain Tumor Registry of the USA, 2001. Efforts are ongoing to understand this disease pathogenesis in complete details. Global gene expression changes in GBM pathogenesis have been studied by several groups using microarray technology (e.g. Carro et al., 2010). One of the many approaches to ‘understand the control mechanisms underlying the observed changes in the activity of a biological process’ (Cline et al., 2007) is integration of gene expression and protein–protein interactions (PPI) datasets. Among several examples, aberrant activation of Wnt/β-catenin signaling pathway as well as sonic hedgehog (SHH) signaling pathway is reported in GBMs (Klaus & Birchmeier, 2008). Further, these two pathways are also involved in proliferation and clonogenicity of glioma cancer stem cells (Li et al., 2009), which are thought to play a role in glioma initiation, proliferation, and invasion, and are one of the important points of intervention. Hedgehog–Gli1 signaling is also found to regulate the expression of stemness genes. In this paper, analyses of the relationship between the significant differential expression of these and other genes and the connectivity as well as topological features of a PPI network would be discussed. This way, genes potentially overlooked when relying solely on expression profiles may be identified which can be biologically relevant as possible drug target/s or disease biomarker/s. 相似文献
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123.
Among five hairy root lines of Picrorhiza kurrooa that were established through Agrobacterium rhizogenes, one (H7) was selected for encapsulation due to high accumulation of picrotin and picrotoxinin (8.3 and 47.6 μg/g DW, respectively). Re-grown encapsulated roots induced adventitious shoots with 73 % frequency on MS medium supplemented with 0.1 μM 6-benzylaminopurine, following 6 months of storage at 25 °C. Regenerated plantlets had 85 % survival after 2 months. Regenerants were of similar morphotype having increased leaf number and branched root system as compared to non-transformed plants. The transformed nature of the plants was confirmed through PCR and Southern blot analysis. Genetic fidelity analysis of transformed plants using RAPD and ISSR showed 5.2 and 3.6 % polymorphism, respectively. Phytochemical analysis also showed that picrotin and picrotoxinin content were similar in hairy root line and its regenerants. 相似文献
124.
Siddhartha K. Mishra Neelam S. Sangwan Rajender S. Sangwan 《Acta Physiologiae Plantarum》2013,35(5):1439-1451
β-glucosidase from Withania somnifera (Solanaceae) leaf has been purified to homogeneity and characterized for its physico-kinetic properties. The enzyme purification was achieved through a sequence of gel filtration and ion-exchange column chromatography, and PAGE revealed the homogeneity purification status of the enzyme. The properties of the enzyme included an acidic pH optima (4.8), alkaline pI (8.7), meso-thermostabity, monomeric structure with subunit molecular weight of about 50 kDa, high affinity for substrate (K m) for pNPG (0.19 mM) and high (105,263 M?1 s?1) catalytic efficiency (K cat/K m). The mesostable enzyme had a stringent substrate specificity restricted only to β-linked gluco-conjugate. The enzyme is optimally active at 40 °C with 12.4 kcal Mol?1 activation energy, and was highly sensitive to d-gluconic acid lactone inhibition (94 % at 1 mM) with an apparent K i 0.21 mM. The enzyme could catalyze transglucosylation of geraniol with pNPG as glucosyl donor, but not with cellobiose. Some of the physico-kinetic properties were noted to be novel when comprehensively compared with its counterparts from plant, animal and microbial counterparts. Nevertheless, the catalytic and other features of the enzyme were relatively closer to Oryza sativa among plants and Talaromyces thermophillus among fungi. Significance of building-up of a library of novel plant β-glucosidases for structural investigation to understand naturally evolved mechanistics of catalysis has been indicated. 相似文献
125.
Suman Kundu Talat Roome Ashish Bhattacharjee Kevin A. Carnevale Valentin P. Yakubenko Renliang Zhang Sung Hee Hwang Bruce D. Hammock Martha K. Cathcart 《Journal of lipid research》2013,54(2):436-447
Monocyte chemoattractant protein-1 (MCP-1)-induced monocyte chemotaxis is a major event in inflammatory disease. Our prior studies have demonstrated that MCP-1-dependent chemotaxis requires release of arachidonic acid (AA) by activated cytosolic phospholipase A2 (cPLA2). Here we investigated the involvement of AA metabolites in chemotaxis. Neither cyclooxygenase nor lipoxygenase pathways were required, whereas pharmacologic inhibitors of both the cytochrome-P450 (CYP) and the soluble epoxide hydrolase (sEH) pathways blocked monocyte chemotaxis to MCP-1. To verify specificity, we demonstrated that the CYP and sEH products epoxyeiscosatrienoic acids (EETs) and dihydroxyeicosatrienoic acids (DHETs), respectively, restored chemotaxis in the presence of the inhibitors, indicating that sEH-derived products are essential for MCP-1-driven chemotaxis. Importantly, DHETs also rescued chemotaxis in cPLA2-deficient monocytes and monocytes with blocked Erk1/2 activity, because Erk controls cPLA2 activation. The in vitro findings regarding the involvement of CYP/sEH pathways were further validated in vivo using two complementary approaches measuring MCP-1-dependent chemotaxis in mice. These observations reveal the importance of sEH in MCP-1-regulated monocyte chemotaxis and may explain the observed therapeutic value of sEH inhibitors in treatment of inflammatory diseases, cardiovascular diseases, pain, and even carcinogenesis. Their effectiveness, often attributed to increasing EET levels, is probably influenced by the impairment of DHET formation and inhibition of chemotaxis. 相似文献
126.
Sandhya Mishra Ram Sanmukh Upadhyay Chandra Shekhar Nautiyal 《Applied microbiology and biotechnology》2013,97(13):5659-5668
The field of allelopathy is one of the most fascinating but controversial processes in plant ecology that offers an exciting, interdisciplinary, complex, and challenging study. In spite of the established role of soil microbes in plant health, their role has also been consolidated in studies of allelopathy. Moreover, allelopathy can be better understood by incorporating soil microbial ecology that determines the relevance of allelopathy phenomenon. Therefore, while discussing the role of allelochemicals in plant–plant interactions, the dynamic nature of soil microbes should not be overlooked. The occurrence and toxicity of allelochemicals in soil depend on various factors, but the type of microflora in the surroundings plays a crucial role because it can interfere with its allelopathic nature. Such microbes could be of prime importance for biological control management of weeds reducing the cost and ill effects of chemical herbicides. Among microbes, our main focus is on bacteria—as they are dominant among other microbes and are being used for enhancing crop production for decades—and fungi. Hence, to refer to both bacteria and fungi, we have used the term microbes. This review discusses the beneficial role of microbes in reducing the allelopathic effects of weeds. The review is mainly focused on various functions of bacteria in (1) reducing allelopathic inhibition caused by weeds to reduce crop yield loss, (2) building inherent defense capacity in plants against allelopathic weed, and (3) deciphering beneficial rhizospheric process such as chemotaxis/biofilm, degradation of toxic allelochemicals, and induced gene expression. 相似文献
127.
David F. Stowe Ashish K. Gadicherla Yifan Zhou Mohammed Aldakkak Qunli Cheng Wai-Meng Kwok Ming Tao Jiang James S. Heisner MeiYing Yang Amadou K.S. Camara 《生物化学与生物物理学报:生物膜》2013,1828(2):427-442
We tested if small conductance, Ca2 +‐sensitive K+ channels (SKCa) precondition hearts against ischemia reperfusion (IR) injury by improving mitochondrial (m) bioenergetics, if O2‐derived free radicals are required to initiate protection via SKCa channels, and, importantly, if SKCa channels are present in cardiac cell inner mitochondrial membrane (IMM). NADH and FAD, superoxide (O2?), and m[Ca2 +] were measured in guinea pig isolated hearts by fluorescence spectrophotometry. SKCa and IKCa channel opener DCEBIO (DCEB) was given for 10 min and ended 20 min before IR. Either TBAP, a dismutator of O2?, NS8593, an antagonist of SKCa isoforms, or other KCa and KATP channel antagonists, were given before DCEB and before ischemia. DCEB treatment resulted in a 2-fold increase in LV pressure on reperfusion and a 2.5 fold decrease in infarct size vs. non-treated hearts associated with reduced O2? and m[Ca2 +], and more normalized NADH and FAD during IR. Only NS8593 and TBAP antagonized protection by DCEB. Localization of SKCa channels to mitochondria and IMM was evidenced by a) identification of purified mSKCa protein by Western blotting, immuno-histochemical staining, confocal microscopy, and immuno-gold electron microscopy, b) 2-D gel electrophoresis and mass spectroscopy of IMM protein, c) [Ca2 +]‐dependence of mSKCa channels in planar lipid bilayers, and d) matrix K+ influx induced by DCEB and blocked by SKCa antagonist UCL1684. This study shows that 1) SKCa channels are located and functional in IMM, 2) mSKCa channel opening by DCEB leads to protection that is O2? dependent, and 3) protection by DCEB is evident beginning during ischemia. 相似文献
128.
Manasi Mishra Rakesh S. Joshi Sushama Gaikwad Vidya S. Gupta Ashok P. Giri 《Biochemical and biophysical research communications》2013,430(3):1060-1065
Pin-II protease inhibitors (PIs) are the focus of research interest because of their large structural–functional diversity and relevance in plant defense. Two representative Capsicum annuum PI genes (CanPI-15 and -7) comprising one and four inhibitory repeat domains, respectively, were expressed and recombinant proteins were characterized. β-Sheet and unordered structure was found predominant in CanPI-15 while -7 also displayed the signatures of polyproline fold, as revealed by circular dichroism studies. Inhibition kinetics against bovine trypsin indicated three times higher potency of CanPI-7 (Ki ~ 57 μM) than -15 (~184 μM). Activity and structural stability of these CanPIs were revealed under various conditions of pH, temperature and denaturing agent. Structure prediction, docking studies with proteases and mass spectroscopy revealed the organization of multiple reactive site loops of multi domain PIs in space as well as the steric hindrances imposed while binding to proteases due to their close proximity. 相似文献
129.
Om P. Mishra Nicholas Simmons Sonia Tyagi Ralph Pietrofesa Vladimir V. Shuvaev Roman A. Valiulin Philipp Heretsch K.C. Nicolaou Melpo Christofidou-Solomidou 《Bioorganic & medicinal chemistry letters》2013,23(19):5325-5328
Secoisolariciresinol diglucosides (SDGs) (S,S)-SDG-1 (major isomer in flaxseed) and (R,R)-SDG-2 (minor isomer in flaxseed) were synthesized from vanillin via secoisolariciresinol (6) and glucosyl donor 7 through a concise route that involved chromatographic separation of diastereomeric diglucoside derivatives (S,S)-8 and (R,R)-9. Synthetic (S,S)-SDG-1 and (R,R)-SDG-2 exhibited potent antioxidant properties (EC50 = 292.17 ± 27.71 μM and 331.94 ± 21.21 μM, respectively), which compared well with that of natural (S,S)-SDG-1 (EC50 = 275.24 ± 13.15 μM). These values are significantly lower than those of ascorbic acid (EC50 = 1129.32 ± 88.79 μM) and α-tocopherol (EC50 = 944.62 ± 148.00 μM). Compounds (S,S)-SDG-1 and (R,R)-SDG-2 also demonstrated powerful scavenging activities against hydroxyl [natural (S,S)-SDG-1: 3.68 ± 0.27; synthetic (S,S)-SDG-1: 2.09 ± 0.16; synthetic (R,R)-SDG-2: 1.96 ± 0.27], peroxyl [natural (S,S)-SDG-1: 2.55 ± 0.11; synthetic (S,S)-SDG-1: 2.20 ± 0.10; synthetic (R,R)-SDG-2: 3.03 ± 0.04] and DPPH [natural (S,S)-SDG-1: EC50 = 83.94 ± 2.80 μM; synthetic (S,S)-SDG-1: EC50 = 157.54 ± 21.30 μM; synthetic (R,R)-SDG-2: EC50 = 123.63 ± 8.67 μM] radicals. These results confirm previous studies with naturally occurring (S,S)-SDG-1 and establish both (S,S)-SDG-1 and (R,R)-SDG-2 as potent antioxidants and free radical scavengers for potential in vivo use. 相似文献
130.
Chandra Bhushan Mishra Dimpy Sharma Amresh Prakash Namrata Kumari Nitin Kumar Pratibha Mehta Luthra 《Bioorganic & medicinal chemistry》2013,21(19):6077-6083
Novel 2-thioxothiazole derivatives (6–19) as potential adenosine A2A receptor (A2AR) antagonists were synthesized. The strong interaction of the compounds (6–19) with A2AR in docking study was confirmed by high binding affinity with human A2AR expressed in HEK293T cells using radioligand-binding assay. The compound 19 demonstrated very high selectivity for A2AR as compared to standard A2AR antagonist SCH58261. Decrease in A2AR-coupled release of endogenous cAMP in treated HEK293T cells demonstrated in vitro A2AR antagonist potential of the compound 19. Attenuation in haloperidol-induced impairment (catalepsy) in Swiss albino male mice pre-treated with compound 19 is evocative to explore its prospective in therapy of PD. 相似文献