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  1. Article ; Online: The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics

    Akanksha Pandey / Edward L. Braun

    Biophysica, Vol 1, Iss 8, Pp 87-

    A Case Study Focused on Early Animal Divergences

    2021  Volume 105

    Abstract: Despite the long history of using protein sequences to infer the tree of life, the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic ... ...

    Abstract Despite the long history of using protein sequences to infer the tree of life, the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure. We test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments: buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies, whereas solvent-exposed and helix sites had unequal numbers of sites, supporting the minority topologies. This suggests that the relatively slowly evolving buried, sheet, and coil sites are giving an accurate picture of the true species tree and the amount of conflict among gene trees. Taken as a whole, this study indicates that phylogenetic analyses using sites in different structural environments can yield different topologies for the deepest branches in the animal tree of life and that analyzing larger numbers of taxa eliminates this conflict. More broadly, our results highlight the desirability of incorporating information about protein structure into phylogenomic analyses.
    Keywords protein structure ; relative solvent accessibility ; secondary structure ; phylogeny ; models of sequence evolution ; gene tree–species tree discordance ; Biology (General) ; QH301-705.5
    Subject code 500
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root

    Akanksha Pandey / Edward L. Braun

    Biology, Vol 9, Iss 4, p

    2020  Volume 64

    Abstract: Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in ... ...

    Abstract Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. We focused on a dataset that appeared to have a mixture of signals and we found that the most striking difference in phylogenetic signal reflected relative solvent accessibility. Analyses of exposed sites (residues located on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge+ctenophore clade. These differences in phylogenetic signal were not ameliorated when we conducted analyses using a set of maximum-likelihood profile mixture models. These models are very similar to the Bayesian CAT model, which has been used in many analyses of deep metazoan phylogeny. In contrast, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acid trees estimated using the exposed and buried site both supported placement of ctenophores sister to all other animals. Although the central conclusion of our analyses is that sites in different structural environments yield distinct trees when analyzed using models of protein evolution, our amino acid recoding analyses also have implications for metazoan evolution. ...
    Keywords protein structure ; relative solvent accessibility ; non-stationary models ; RY coding ; heteropecilly ; metazoan phylogeny ; Biology (General) ; QH301-705.5
    Subject code 612 ; 572
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Pharmaceutical characterization and exploration of Arkeshwara rasa in MDA-MB-231 cells

    Remya Jayakumar / Manoj Kumar Dash / Pankaj Kumar / Shiwakshi Sharma / Saumya Gulati / Akanksha Pandey / Kaushavi Cholke / Zeeshan Fatima / S.K. Trigun / Namrata Joshi

    Journal of Ayurveda and Integrative Medicine, Vol 15, Iss 1, Pp 100823- (2024)

    2024  

    Abstract: Background: The diverse specificity mode of cancer treatment targets and chemo resistance demands the necessity of drug entities which can address the devastating dynamicity of the disease. Objectives: To check the anti-tumour potential of traditional ... ...

    Abstract Background: The diverse specificity mode of cancer treatment targets and chemo resistance demands the necessity of drug entities which can address the devastating dynamicity of the disease. Objectives: To check the anti-tumour potential of traditional medicine rich in polyherbal components and metal nanoparticle namely Arkeshwara rasa (AR). Material methods: The AR was prepared in a modified version with reference from Rasaratna Samuchaya and characterized using sophisticated instrumental analysis including XRD, SEM-EDAX, TEM, TGA-DSC, and LC-MS and tested against the MDA-MB-231 cell line to screen cell viability and the cytotoxicity with MTT, SRB and the AO assay. Results: XRD pattern shows cubic tetrahedrite structure with Sb, Cu, S peaks and trace elements like Fe, Mg, etc. The particle size of AR ranges between 20 and 30 nm. The TGA points thermal decomposition at 210 °C and the metal sulphide peaks in DSC. LC-MS analysis reveals the components of the formulation more on the flavonoid portion. The IC50 value of MTT and SRB are 25.28 μg/mL and 31.7 μg/mL respectively. The AO colorimeter substantiated the cell viability and the apoptosis figures of the same cell line. The AR exhibits cytotoxicity and reaffirms the apoptosis fraction with SRB assay. Conclusions: The Hesperidine, Neohesperidin, Rutin components in the phytochemical pool can synergize the anti-tumour potential with either influencing cellular pathways or decreasing chemo resistance to conventional treatment. AR need to be further experimented with reverse transcription, flow cytometry, western blotting, etc.
    Keywords Traditional medicine ; Cancer ; IC50 value ; Hesperidin ; In-vitro ; Arkeshwara rasa ; Miscellaneous systems and treatments ; RZ409.7-999
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Whole genome phylogeny of Gallus

    George P. Tiley / Akanksha Pandey / Rebecca T. Kimball / Edward L. Braun / J. Gordon Burleigh

    Avian Research, Vol 11, Iss 1, Pp 1-

    introgression and data-type effects

    2020  Volume 15

    Abstract: Abstract Background Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, ... ...

    Abstract Abstract Background Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data. Methods We generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus (a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus. Results All of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent. Conclusions Overall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets (both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.
    Keywords Galliformes ; Incomplete lineage sorting ; Junglefowl ; Multispecies coalescent ; Phasianidae ; Phylogenomics ; Zoology ; QL1-991
    Subject code 333
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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