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Pallikkara Pulikkal Babitha Mohammed Marunnan Sahila Srinivas Bandaru Anuraj Nayarisseri Sivanpillai Sureshkumar 《Bioinformation》2015,11(8):378-386
AbbreviationsAD - Alzheimer׳s Disease,
AChE - Acetyl Choline Estarase,
OPLS - Optimized Potentials for Liquid Simulations,
PDB - Protein Data Bank. 相似文献
2.
Jessica M. E. van den Oever Sahila Balkassmi Tim Segboer E. Joanne Verweij Pieter A. van der Velden Dick Oepkes Egbert Bakker Elles M. J. Boon 《PloS one》2013,8(12)
Objectives
RASSF1A has been described to be differentially methylated between fetal and maternal DNA and can therefore be used as a universal sex-independent marker to confirm the presence of fetal sequences in maternal plasma. However, this requires highly sensitive methods. We have previously shown that Pyrophosphorolysis-activated Polymerization (PAP) is a highly sensitive technique that can be used in noninvasive prenatal diagnosis. In this study, we have used PAP in combination with bisulfite conversion to develop a new universal methylation-based assay for the detection of fetal methylated RASSF1A sequences in maternal plasma.Methods
Bisulfite sequencing was performed on maternal genomic (g)DNA and fetal gDNA from chorionic villi to determine differentially methylated regions in the RASSF1A gene using bisulfite specific PCR primers. Methylation specific primers for PAP were designed for the detection of fetal methylated RASSF1A sequences after bisulfite conversion and validated.Results
Serial dilutions of fetal gDNA in a background of maternal gDNA show a relative percentage of ∼3% can be detected using this assay. Furthermore, fetal methylated RASSF1A sequences were detected both retrospectively as well as prospectively in all maternal plasma samples tested (n = 71). No methylated RASSF1A specific bands were observed in corresponding maternal gDNA. Specificity was further determined by testing anonymized plasma from non-pregnant females (n = 24) and males (n = 21). Also, no methylated RASSF1A sequences were detected here, showing this assay is very specific for methylated fetal DNA. Combining all samples and controls, we obtain an overall sensitivity and specificity of 100% (95% CI 98.4%–100%).Conclusions
Our data demonstrate that using a combination of bisulfite conversion and PAP fetal methylated RASSF1A sequences can be detected with extreme sensitivity in a universal and sex-independent manner. Therefore, this assay could be of great value as an addition to current techniques used in noninvasive prenatal diagnostics. 相似文献3.
Mohammed Marunnan Sahila Pallikkara Pulikkal Babitha Srinivas Bandaru Anuraj Nayarisseri Victor Arokia Doss 《Bioinformation》2015,11(6):280-289
The present antipsychotic drugs have known to show serious concerns like extra pyramidal side effects therefore, pursuit for novel
antipsychotic GABAnergic drugs has lately focused on the folkloric medicine from plant derivatives as better treatment option of
schizophrenia. The present study centers to identify potential inhibitors of plant origin for GABA receptor through in silico
approaches. Three compound datasets were undertaken in the study. The first set consisted of seven compounds which included
Magnolol, Honokiol and other plant derivatives. The second set consisted of 16 derivatives of N-diarylalkenyl-piperidinecarboxylic
acid synthesized by Zheng et al., 2006. The third dataset had thirty two compounds which were Magnolol and Honokiol analogues
synthesized by Fuchs et al., 2014. All the compounds were docked at the allosteric site of the GABA (A) receptor. The compounds
were further tested for ADMET and biological activity. We observed Honokiol and its derivatives demonstrated superior druglike
properties than any compound undertaken in the study. Further, compound 61 [2-(4-methoxyphenyl)-4-propylphenol] of dataset
three - a synthetic derivative of honokiol had better profile than its parent compound. In a possible attempt to identify compound
with even better efficacious compound than 61, virtual screening was performed, 135 compounds akin to compound 61 were
retrieved. Interestingly none of the 135 compounds showed better druggable properties than compound 61. Our in silico
pharmacological profiling of compounds is in coherence and is complemented by the findings of Fuchs et al, which also revealed
compound 61 to be the good potentiator of GABA receptor.
Abbreviations
GABA (A) R - Gamma Amino Butyric Acid Receptor, subtype A, GPCR - G Protein Coupled Receptor, OPLS - Optimized Potentials for Liquid Simulations, PDB - Protein Data Bank, PLP - Piece wise Linear Potential, T.E.S.T - Toxicity Estimation Software Tool, TCM - Traditional Chinese Medicine. 相似文献4.
Fantai Kong Chaoping Liang Luhua Wang Yongping Zheng Sahila Perananthan Roberto C. Longo John P. Ferraris Moon Kim Kyeongjae Cho 《Liver Transplantation》2019,9(2)
Capacity degradation by phase changes and oxygen evolution has been the largest obstacle for the ultimate commercialization of high‐capacity LiNiO2‐based cathode materials. The ultimate thermodynamic and kinetic reasons of these limitations are not yet systematically studied, and the fundamental mechanisms are still poorly understood. In this work, both phenomena are studied by density functional theory simulations and validation experiments. It is found that during delithiation of LiNiO2, decreased oxygen reduction induces a strong thermodynamic driving force for oxygen evolution in bulk. However, oxygen evolution is kinetically prohibited in the bulk phase due to a large oxygen migration kinetic barrier (2.4 eV). In contrast, surface regions provide a larger space for oxygen migration leading to facile oxygen evolution. These theoretical results are validated by experimental studies, and the kinetic stability of bulk LiNiO2 is clearly confirmed. Based on these findings, a rational design strategy for protective surface coating is proposed. 相似文献
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