Molecular cavities play a critical role in our understanding of molecular phenomena. Recently, a number of works on the visual analysis of protein cavity dynamics have been developed to allow experts and users to interactively research dynamic cavity data. However, previous explorations are limited to studying cavity-lining amino acids and they lack a consideration of the impact of the key amino acids, which are far away from the cavity but have an important impact on the cavity. When studying protein amino acids, biochemists use normal mode decomposition to analyze protein changes on a time scale. However, the high-dimensional parameter space generated via decomposition is too large to be analyzed in detail. We present a novel approach that combines cavity characterization and normal mode analysis (NMA) for cavity dynamics analysis to reduce and explore this vast space through interactive visualization. PNMAVis can analyze whether direct factors (cavity-lining amino acids) or indirect factors (key amino acids) affect cavity changes, through multiple linked 2D and 3D views. The visual analysis method we proposed is based on close cooperation with domain experts, aiming to meet their needs to explore the relationship between cavity stability and cavity-lining amino acids fluctuations and key amino acids fluctuations as much as possible, and also to help domain experts identify potential allosteric residues. The effectiveness of our new method is demonstrated by the case study conducted by cooperative protein experts on a biological field case and an open normal mode data set.
Summary Zoige wetland of Tibetan plateau is characterized by being located at a low latitude (33°56′N, 102°52′E) region and under the annual temperature around 1°C. Previous studies indicated that Zoige wetland was one of the CH 4 emission centres in Qinghai‐Tibetan plateau; in this study, the methanogen community in this low‐latitude wetland was analysed based on the homology of 16S rRNA and mcrA genes retrieved from the soil. The results indicated that members of Methanosarcinales and Methanomicrobiales constituted the majority of methanogens, and a novel uncultured methanogen cluster, Zoige cluster I (ZC‐I) affiliated to Methanosarcinales , could be dominant. Using quantitative polymerase chain reaction (qPCR) assay, ZC‐I methanogens were estimated to be 10 7 cells per gram of soil, accounting for about 30% of the total Archeae . By combining culturable enrichment with qPCR assay, the quantity of ZC‐I methanogens in the methanogenic enrichment with acetate, H2/CO 2 , methanol or trimethylamine was determined to increase to 10 8 cells ml −1 , but not with formate, which indicated that ZC‐I methanogens could use the four methanogenic substrates. The growth rates at 30°C and 15°C were not pronounced different, implying ZC‐I to be the cold‐adaptive methanogens. The broad substrate spectrum identified the ZC‐I methanogens to be a member of Methanosarcinaceae , and could represent a novel sub‐branch specifically inhabited in cold ecosystems. Fluorescence in situ hybridization (FISH) images also visualized ZC‐I methanogens the sarcina‐like aggregate of the spherical cells. The prevalence and flexibility in substrate utilization and growth temperature suggested ZC‐I methanogens to be an important player in the methanogenesis of Zoige wetland.
Patients with minor ischemic stroke (MIS) have substantial disability rates at 90 days. Our study aimed to explore the association between the systemic inflammation response index (SIRI) and 3-month functional outcomes in patients with MIS.
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