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The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated) approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters)-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity c in RO((N + nm) log n), where N is the size of the output patterns and (n x m) is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1) The method recovers states previously obtained by visually analyzing free energy surfaces. (2) It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3) The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the choice of reaction coordinates. (An abstract version of this work was presented at the 2005 Asia Pacific Bioinformatics Conference [1].). 相似文献
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64.
Margaret M. Mullins Leonard I. Kleinman Paul T. Russell Laxmi S. Srivastava 《Life sciences》1982,31(24):2751-2755
Plasma aldosterone concentrations were found to be higher in the newborn, presumably prehypertensive, spontaneously hypertensive rat at 5, 10 and 20 days of age compared to age-matched normotensive Wistar-Kyoto (WKY). In addition, plasma aldosterone concentrations were seen to rise in newborn WKY in contrast to findings in Wistar rats and other mammalian species. 相似文献
65.
Hao Yang Peng Luo Jun Wang Chengxiang Mou Li Mo Zhiyuan Wang Yao Fu Honghui Lin Yongping Yang Laxmi Dutt Bhatta 《PloS one》2015,10(8)
Climate and human-driven changes play an important role in regional droughts. Northwest Yunnan Province is a key region for biodiversity conservation in China, and it has experienced severe droughts since the beginning of this century; however, the extent of the contributions from climate and human-driven changes remains unclear. We calculated the ecosystem evapotranspiration (ET) and water yield (WY) of northwest Yunnan Province, China from 2001 to 2013 using meteorological and remote sensing observation data and a Surface Energy Balance System (SEBS) model. Multivariate regression analyses were used to differentiate the contribution of climate and vegetation coverage to ET. The results showed that the annual average vegetation coverage significantly increased over time with a mean of 0.69 in spite of the precipitation fluctuation. Afforestation/reforestation and other management efforts attributed to vegetation coverage increase in NW Yunnan. Both ET and WY considerably fluctuated with the climate factors, which ranged from 623.29 mm to 893.8 mm and –51.88 mm to 384.40 mm over the time period. Spatially, ET in the southeast of NW Yunnan (mainly in Lijiang) increased significantly, which was in line with the spatial trend of vegetation coverage. Multivariate linear regression analysis indicated that climatic factors accounted for 85.18% of the ET variation, while vegetation coverage explained 14.82%. On the other hand, precipitation accounted for 67.5% of the WY. We conclude that the continuous droughts in northwest Yunnan were primarily climatically driven; however, man-made land cover and vegetation changes also increased the vulnerability of local populations to drought. Because of the high proportion of the water yield consumed for subsistence and poor infrastructure for water management, local populations have been highly vulnerable to climate drought conditions. We suggest that conservation of native vegetation and development of water-conserving agricultural practices should be implemented as adaptive strategies to mitigate climate change. 相似文献
66.
Plants, being sessile organisms, are more exposed to the hazards of constantly changing environmental conditions globally. During the lifetime of a plant, the root system encounters various challenges such as obstacles, pathogens, high salinity, water logging, nutrient scarcity etc. The developmental plasticity of the root system provides brilliant adaptability to plants to counter the changes exerted by both external as well as internal cues and achieve an optimized growth status. Phytohormones are one of the major intrinsic factors regulating all aspects of plant growth and development both independently as well as through complex signal integrations at multiple levels. We have previously shown that glucose (Glc) and brassinosteroid (BR) signalings interact extensively to regulate lateral root (LR) development in Arabidopsis.1 Auxin efflux as well as influx and downstream signaling components are also involved in Glc-BR regulation of LR emergence. Here, we provide evidence for involvement of ethylene signaling machinery downstream to Glc and BR in regulation of LR emergence. 相似文献
67.
Papapetrou EP Lee G Malani N Setty M Riviere I Tirunagari LM Kadota K Roth SL Giardina P Viale A Leslie C Bushman FD Studer L Sadelain M 《Nature biotechnology》2011,29(1):73-78
Realizing the therapeutic potential of human induced pluripotent stem (iPS) cells will require robust, precise and safe strategies for genetic modification, as cell therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify human iPS cells at 'safe harbor' sites in the genome, which fulfill five criteria based on their position relative to contiguous coding genes, microRNAs and ultraconserved regions. We demonstrate that ~10% of integrations of a lentivirally encoded β-globin transgene in β-thalassemia-patient iPS cell clones meet our safe harbor criteria and permit high-level β-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. This approach, combining bioinformatics and functional analyses, should be broadly applicable to introducing therapeutic or suicide genes into patient-specific iPS cells for use in cell therapy. 相似文献
68.
Root architecture is developmentally plastic and affected by many intrinsic factors (e.g. plant hormones) and extrinsic factors (e.g. touch, gravity) in order to maximize nutrient and water acquisition. We have recently shown that asymmetrical exposure of cytokinin (CK) at the root tip causes root growth directional changes that is dependent on ethylene signaling and is potentiated by glucose signaling. Auxin homeostasis as maintained by auxin signaling and transport is also involved in CK-induced root cell elongation and differential growth. The signaling pathways eventually converge at actin filament organization since actin filament organization inhibitor latrunculin B (Lat B) can also induce similar growth. We, show that CK can actually alter actin filament organization as seen in actin binding protein 35S::GFP-ABD2-GFP transgenic lines as is also altered by auxin polar transport inhibitor 1-N-naphthylphthalamic acid (NPA) and Lat B in different manners. 相似文献
69.
Laxmi Rawat Y. Singh N. Shukla J. Kumar 《Archives Of Phytopathology And Plant Protection》2013,46(12):1442-1467
The antagonistic potential of salinity tolerant (ST) Trichoderma (Th) isolates against Fusarium oxysporum f.sp. ciceri (foc) was tested, along with their capability to induce relative salt stress tolerance in chickpea with the aim to exploit their use as biological agents in reducing deleterious effects of salinity and controlling Fusarium wilt of chickpea under saline soil conditions. Under laboratory conditions, salt stress was created by supplementing nutrient medium with different concentrations of NaCl viz. 0, 70, 150 and 240?mM NaCl and a pot experiment was conducted using natural saline soil (EC – 6.6 dS?m?1). Out of 45 Th isolates studied, only five isolates viz. Th-13, Th-14, Th-19, Th-33 and Th-50 were selected to be ST as these were able to grow and sporulate in growth medium containing up to 240?mM NaCl. In saline medium, ST isolates greatly surpassed salinity sensitive (SS) isolate with respect to growth rate, mycelial dry weight, sporulation and biological proficiency against foc. Out of five ST isolates that retained their tolerance to different salt stress levels, Th-14 and Th-19 showed maximum antagonism against foc. Under greenhouse conditions, chickpea plants obtained from seeds bioprimed with Th-14 and Th-19 performed well both at germination and seedling stage in comparison to control in saline soil. As compared to untreated plants, characterisation of Th treated plants confirmed that they had reinforced contents of proline along with relatively higher levels of total phenols, membrane stability index and superoxide dismutase activity while lower accumulation of hydrogen peroxide and malondealdehyde contents. ST isolates, Th-14 and Th-19 significantly reduced foc-induced wilt disease incidence in chickpea plants. The population density of both the Th isolates in rhizosphere far exceeded that of foc under both saline and non-saline soils. However, Th-14 was found more efficient in increasing relative salt stress tolerance in chickpea and reducing the foc growth in rhizosphere under present materials and conditions. These findings provide a novel paradigm for developing alternative, environmentally safe strategy to alleviate salt stress and manage fungal diseases such as foc that aggravates under saline soils. 相似文献
70.
Keshab Deuba Anna Mia Ekstr?m Rachana Shrestha George Ionita Laxmi Bhatta Deepak Kumar Karki 《PloS one》2013,8(3)