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1.
This paper describes a method for the rapid isolation of phycobilisomes using a cationic detergent, CTAB (cetyltrimethylammonium bromide). The method has distinct advantages over those currently in use in that (i) release of intact phycobilisomes from cells in the presence of CTAB occurs in 40 s (as compared to 40-60 min of incubation required with Triton X-100), thereby reducing the chances of proteolysis of the component phycobiliproteins; and (ii) these phycobilisome preparations have reduced chlorophyll contamination in the initial stages. In addition this method also helps retain the structural and functional properties, as evidenced by spectroscopy and sodium dodecyl sulfate-polyacrylamide gel analysis. 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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Erin L. Landguth Brenna R. Forester Andrew J. Eckert Andrew J. Shirk Mitra Menon Amy Whipple Casey C. Day Samuel A. Cushman 《Molecular ecology resources》2020,20(2):605-615
We implemented multilocus selection in a spatially‐explicit, individual‐based framework that enables multivariate environmental gradients to drive selection in many loci as a new module for the landscape genetics programs, CDPOP and CDMetaPOP. Our module simulates multilocus selection using a linear additive model, providing a flexible platform to evaluate a wide range of genotype‐environment associations. Importantly, the module allows simulation of selection in any number of loci under the influence of any number of environmental variables. We validated the module with individual‐based selection simulations under Wright‐Fisher assumptions. We then evaluated results for simulations under a simple landscape selection model. Next, we simulated individual‐based multilocus selection across a complex selection landscape with three loci linked to three different environmental variables. Finally, we demonstrated how the program can be used to simulate multilocus selection under varying selection strengths across different levels of gene flow in a landscape genetics framework. This new module provides a valuable addition to the study of landscape genetics, allowing for explicit evaluation of the contributions and interactions between gene flow and selection‐driven processes across complex, multivariate environmental and landscape conditions. 相似文献
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Ramya Krishnan Rahul Ravikumar Menon Naoto Tanaka Hans-Jürgen Busse Srinivasan Krishnamurthi Natarajan Rameshkumar 《PloS one》2016,11(3)
A novel yellow colony-forming bacterium, strain P3B162T was isolated from the pokkali rice rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abilities to promote plant growth under saline conditions. The novel strain P3B162T possesses plant growth beneficial traits such as positive growth on 1-aminocyclopropane-1-carboxylic acid (ACC), production of indole acetic acid (IAA) and siderophore. In addition, it also showed important phenotypic characters such as ability to form biofilm and utilization of various components of plant root exudates (sugars, amino acids and organic acids), clearly indicating its lifestyle as a plant rhizosphere associated bacterium. Taxonomically, the novel strain P3B162T was affiliated to the genus Arthrobacter based on the collective results of phenotypic, genotypic and chemotaxonomic analyses. Moreover, molecular analysis using 16S rRNA gene showed Arthrobacter globiformis NBRC 12137T, Arthrobacter pascens DSM 20545T and Arthrobacter liuii DSXY973T as the closely related phylogenetic neighbours, showing more than 98% 16S rRNA similarity values, whereas the recA gene analysis displayed Arthrobacter liuii JCM 19864T as the nearest neighbour with 94.7% sequence similarity and only 91.7% to Arthrobacter globiformis LMG 3813T and 88.7% to Arthrobacter pascens LMG 16255T. However, the DNA-DNA hybridization values between strain P3B162T, Arthrobacter globiformis LMG 3813T, Arthrobacter pascens LMG 16255T and Arthrobacter liuii JCM 19864T was below 50%. In addition, the novel strain P3B162T can be distinguished from its closely related type strains by several phenotypic characters such as colony pigment, tolerance to NaCl, motility, reduction of nitrate, hydrolysis of DNA, acid from sucrose, cell wall sugars and cell wall peptidoglycan structure. In conclusion, the combined results of this study support the classification of strain P3B162T as a novel Arthrobacter species and we propose Arthrobacter pokkalii sp.nov.as its name. The type strain is P3B162T (= KCTC 29498T = MTCC 12358T). 相似文献
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