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Prasad Dinesh Shankaracharya Vidyarthi Ambarish Sharan 《World journal of microbiology & biotechnology》2011,27(9):2227-2230
A rapid, sensitive and cost-effective method was developed for detection of foodborne pathogens, particularly Salmonella species. The method utilizes single stranded DNA (ssDNA) probes and non-functionalized gold nanoparticles to provide a colorimetric
assay for the detection of PCR amplified DNA. Different food samples were tested with the PCR-based colorimetric assay parallel
with the conventional culture method. The sensitivity and specificity of colorimetric assay was 89.15 and 99.04% respectively
with reference to conventional culture method. The total time required to detect the Salmonella spp. present in food samples by the developed method is less than 8 h, including 6 h incubation. It was observed that the
colorimetric assay was 10 times more sensitive than gel-based detection with the same concentration of DNA used for analysis. 相似文献
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Present study was aimed at finding a better alternative to paclitaxel, an anticancer chemotherapeutic drug. Two targets, tubulin beta-1 chain and apoptosis regulator Bcl-2 protein (202F) were used in the study. Of these, structure of tubulin beta-1 chain is not known and that of Bcl-2 was taken from protein data bank with ID 202F. Tertiary structure model of tubulin beta-1 chain was predicted and validated. The validated 3D structure of tubulin beta-1 chain and Bcl-2 protein was taken to study their interaction with paclitaxel. Molecular docking of paclitaxel and its analogues was performed with these targets separately. Results showed that out of 84 analogues taken from PubChem, CID_44322802 had glide score of -9.62, as compared to -5.86 of paclitaxel with tubulin beta-1 chain. It was also observed that CID_9919057 had glide score of -9.0, as compared to -8.24 of paclitaxel with Bcl-2 protein. However, further experimental and clinical verification is needed to establish these analogues as drug. 相似文献
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Ramita Dewan Ruth Chia Jinhui Ding Richard A. Hickman Thor D. Stein Yevgeniya Abramzon Sarah Ahmed Marya S. Sabir Makayla K. Portley Arianna Tucci Kristina Ibáñez F.N.U. Shankaracharya Pamela Keagle Giacomina Rossi Paola Caroppo Fabrizio Tagliavini Maria L. Waldo Per M. Johansson Bryan J. Traynor 《Neuron》2021,109(3):448-460.e4
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Hong Li Gustavo Glusman Hao Hu Shankaracharya Juan Caballero Robert Hubley David Witherspoon Stephen L. Guthery Denise E. Mauldin Lynn B. Jorde Leroy Hood Jared C. Roach Chad D. Huff 《PLoS genetics》2014,10(1)
The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome sequencing (WGS) marks the final step in increasing genetic marker density by assaying all single-nucleotide variants (SNVs), and thus has the potential to further improve relationship detection by enabling more accurate detection of IBD segments and more precise resolution of IBD segment boundaries. However, WGS introduces new complexities that must be addressed in order to achieve these improvements in relationship detection. To evaluate these complexities, we estimated genetic relationships from WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as controls. We identified several genomic regions with excess pairwise IBD in both the pedigree and control datasets using three established IBD methods: GERMLINE, fastIBD, and ISCA. These spurious IBD segments produced a 10-fold increase in the rate of detected false-positive relationships among controls compared to high-density microarray datasets. To address this issue, we developed a new method to identify and mask genomic regions with excess IBD. This method, implemented in ERSA 2.0, fully resolved the inflated cryptic relationship detection rates while improving relationship estimation accuracy. ERSA 2.0 detected all 1st through 6th degree relationships, and 55% of 9th through 11th degree relationships in the 30 families. We estimate that WGS data provides a 5% to 15% increase in relationship detection power relative to high-density microarray data for distant relationships. Our results identify regions of the genome that are highly problematic for IBD mapping and introduce new software to accurately detect 1st through 9th degree relationships from whole-genome sequence data. 相似文献
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