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111.
Karthik Hullahalli Marinelle Rodrigues Brendan D. Schmidt Xiang Li Pooja Bhardwaj Kelli L. Palmer 《PloS one》2015,10(9)
Clustered, Regularly Interspaced Short Palindromic Repeats and their associated Cas proteins (CRISPR-Cas) provide prokaryotes with a mechanism for defense against mobile genetic elements (MGEs). A CRISPR locus is a molecular memory of MGE encounters. It contains an array of short sequences, called spacers, that generally have sequence identity to MGEs. Three different CRISPR loci have been identified among strains of the opportunistic pathogen Enterococcus faecalis. CRISPR1 and CRISPR3 are associated with the cas genes necessary for blocking MGEs, but these loci are present in only a subset of E. faecalis strains. The orphan CRISPR2 lacks cas genes and is ubiquitous in E. faecalis, although its spacer content varies from strain to strain. Because CRISPR2 is a variable locus occurring in all E. faecalis, comparative analysis of CRISPR2 sequences may provide information about the clonality of E. faecalis strains. We examined CRISPR2 sequences from 228 E. faecalis genomes in relationship to subspecies phylogenetic lineages (sequence types; STs) determined by multilocus sequence typing (MLST), and to a genome phylogeny generated for a representative 71 genomes. We found that specific CRISPR2 sequences are associated with specific STs and with specific branches on the genome tree. To explore possible applications of CRISPR2 analysis, we evaluated 14 E. faecalis bloodstream isolates using CRISPR2 analysis and MLST. CRISPR2 analysis identified two groups of clonal strains among the 14 isolates, an assessment that was confirmed by MLST. CRISPR2 analysis was also used to accurately predict the ST of a subset of isolates. We conclude that CRISPR2 analysis, while not a replacement for MLST, is an inexpensive method to assess clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs. 相似文献
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Mahendra Awale Vivek Kumar Parameswaran Saravanan C. Gopi Mohan 《Journal of molecular modeling》2010,16(3):475-488
The current therapy for leishmaniasis is not sufficient and it has two severe drawbacks, host-toxicity and drug resistance.
The substantial knowledge of parasite biology is not yet translating into novel drugs for leishmaniasis. Based on this observation,
a 3D structural model of Leishmania mitogen-activated protein kinase (MAPK) homologue has been developed, for the first time, by homology modeling and molecular
dynamics simulation techniques. The model provided clear insight in its structure features, i.e. ATP binding pocket, phosphorylation lip, and common docking site. Sequence-structure homology recognition identified Leishmania CRK3 (LCRK3) as a distant member of the MAPK superfamily. Multiple sequence alignment and 3D structure model provided the
putative ATP binding pocket of Leishmania with respect to human ERK2 and LCRK3. This analysis was helpful in identifying the binding sites and molecular function of
the Leishmania specific MAPK homologue. Molecular docking study was performed on this 3D structural model, using different classes of competitive
ATP inhibitors of LCRK3, to check whether they exhibit affinity and could be identified as Leishmania MAPK specific inhibitors. It is well known that MAP kinases are extracellular signal regulated kinases ERK1 and ERK2, which
are components of the Ras-MAPK signal transduction pathway which is complexed with HDAC4 protein, and their inhibition is
of significant therapeutic interest in cancer biology. In order to understand the mechanism of action, docking of indirubin
class of molecules to the active site of histone deacetylase 4 (HDAC4) protein is performed, and the binding affinity of the
protein-ligand interaction was computed. The new structural insights obtained from this study are all consistent with the
available experimental data, suggesting that the homology model of the Leishmania MAPK and its ligand interaction modes are reasonable. Further the comparative molecular electrostatic potential and cavity
depth analysis of Leishmania MAPK and human ERK2 suggested several important differences in its ATP binding pocket. Such differences could be exploited
in the future for designing Leishmania specific MAPK inhibitors. 相似文献
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Murali kannan Maruthamuthu Vidhya Selvamani Saravanan Prabhu Nadarajan Hyungdon Yun You-Kwan Oh Gyeong Tae Eom Soon Ho Hong 《Journal of industrial microbiology & biotechnology》2018,45(1):31-41
In a cell-surface display (CSD) system, successful display of a protein or peptide is highly dependent on the anchoring motif and the position of the display in that anchoring motif. In this study, a recombinant bacterial CSD system for manganese (Mn) and cobalt (Co) recovery was developed by employing OmpC as an anchoring motif on three different external loops. A portion of Cap43 protein (TRSRSHTSEG)3 was employed as a manganese and cobalt binding peptide (MCBP), which was fused with OmpC at three different external loops. The fusions were made at the loop 2 [fusion protein-2 (FP2)], loop 6 (FP6), and loop 8 (FP8) of OmpC, respectively. The efficacy of the three recombinant strains in the recovery of Mn and Co was evaluated by varying the concentration of the respective metal. Molecular modeling studies showed that the short trimeric repeats of peptide probably form a secondary structure with OmpC, thereby giving rise to a difference in metal recovery among the three recombinant strains. Among the three recombinant strains, FP6 showed increased metal recovery with both Mn and Co, at 1235.14 (1 mM) and 379.68 (0.2 mM) µmol/g dry cell weight (DCW), respectively. 相似文献
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Sanyog Jain Pooja Yadav Rajan Swami Nitin Kumar Swarnakar Varun Kushwah Sameer S. Katiyar 《AAPS PharmSciTech》2018,19(4):1699-1711
Implication of different dietary specific lipids such as phytantriol (PT) and glyceryl monooleate (GMO) on enhancing the oral bioavailability of amphotericin B (AmB) was examined. Liquid crystalline nanoparticles (LCNPs) were prepared using hydrotrope method, followed by in vitro characterization, Caco-2 cell monolayer uptake, and in vivo pharmacokinetic and toxicity evaluation. Optimized AmB-LCNPs displayed small particle size (<?210 nm) with a narrow distribution (~?0.2), sustained drug release and high gastrointestinal stability, and reduced hemolytic toxicity. PLCNPs presented slower release, i.e., ~?80% as compared to ~?90% release in case of GLCNPs after 120 h. Significantly higher uptake in Caco-2 monolayer substantiated the role of LCNPs in increasing the intestinal permeability followed by increased drug titer in plasma. Pharmacokinetic studies demonstrated potential of PT in enhancing the bioavailability (approximately sixfold) w.r.t. of its native counterpart with reduced nephrotoxicity as presented by reduced nephrotoxicity biomarkers and histology studies. These studies established usefulness of PLCNPs over GLCNPs and plain drug. It can be concluded that acid-resistant lipid, PT, can be utilized efficiently as an alternate lipid for the preparation of LCNPs to enhance bioavailability and to reduce nephrotoxicity of the drug as compared to other frequently used lipid, i.e., GMO. 相似文献
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Maryam Ahmadian Sihao Liu Shannon M. Reilly Nasun Hah Weiwei Fan Eiji Yoshihara Pooja Jha C. Daniel De Magalhaes Filho Sandra Jacinto Andrew V. Gomez Yang Dai Ruth T. Yu Christopher Liddle Annette R. Atkins Johan Auwerx Alan R. Saltiel Michael Downes Ronald M. Evans 《Cell reports》2018,22(11):2849-2859
119.
Purvi M. Rakhashiya Pooja P. Patel Bhavisha P. Sheth Jigna G. Tank 《Archives Of Phytopathology And Plant Protection》2016,49(1-4):64-73
Plant pathogenic organisms are known to infect host cell using various range of secretory proteins. Amongst all other secretion systems, type III secretion system (T3SS) is a key mechanism for bacterial pathogenesis for establishing and maintaining infection into the host. Expression levels of seven genes viz. avrXacE1, avrXacE2, hpaA and hrpG along with bacterial endogenous control lrp (leucine-responsive protein) were studied. The pathogenic organisms selected for the present study includes Enterobacter cloacae, Enterobacter spp., Pantoea ananatis, Xanthomonas campestris pv. Citri, Pantoea agglomerans, Ochrobactrum anthropi and Erwinia chrysanthemi. P. agglomerans and Enterobacter spp. gave high expression of above-mentioned virulence genes compared to Xanthomonas, while E. cloacae and P. ananatis showed similar expression with that of Xanthomonas. The detailed relationship of the expression profiles with respect to the selected organisms is discussed. 相似文献
120.
Ravindranath MH Muthugounder S Presser N Selvan SR Santin AD Bellone S Saravanan TS Morton DL 《Biochemical and biophysical research communications》2007,353(2):251-258
Ganglioside signatures of four poorly and three moderately differentiated ovarian epithelial cancer (OEC) cell lines reveal the presence of GM3, GM2, GD2, O-AcGD2, GD1a and GM1b. The expression of GM3, presence of GD1a and GM1b in the ascitic fluid and plasma, together with a positive correlation in the total-gangliosides levels between ascitic fluid and plasma of OEC patients support the earlier contention that the tumor-gangliosides may be released (or shed) into the tumor-microenvironment. The immunogenicity of OEC-gangliosides is determined by comparing anti-ganglioside-IgM titers in ascitic fluid (n = 14) and plasma (n = 23) of OEC-patients and age-matched healthy (n = 14). The titers were measured by ELISA. Strikingly, the level of anti-GD1a-IgM is significantly higher in ascitic fluid and plasma of patients than in the plasma of healthy volunteers. Paired sample analysis of ascitic fluid and plasma from the same patients confirmed the significant expression of anti-GD1a IgM in OEC patients, while no such difference was observed with other anti-ganglioside IgMs among different groups. The significance of the endogenous IgM response to GD1a may be to eliminate this immunosuppressive-ganglioside from the tumor-microenvironment. 相似文献