Recent advances in clustering methods for protein interaction networks

The increasing availability of large-scale protein-protein interaction data has made it possible to understand the basic components and organization of cell machinery from the network level. The arising challenge is how to analyze such complex interacting data to reveal the principles of cellular organization, processes and functions. Many studies have shown that clustering protein interaction network is an effective approach for identifying protein complexes or functional modules, which has become a major research topic in systems biology. In this review, recent advances in clustering methods for protein interaction networks will be presented in detail. The predictions of protein functions and interactions based on modules will be covered. Finally, the performance of different clustering methods will be compared and the directions for future research will be discussed

Hybridising Minjian Religion in South China: Participants, Rituals, and Architecture

This study focuses on the ongoing hybridisation of minjian (folk or popular, literally “among the people”) religious activities in rural areas of south China. It demonstrates recent changes in religious hybridisation through extensive fieldwork in two villages. It also investigates intellectual debate on the concept of minjian religion and presents the relationship between state power and the religious revival in contemporary Chinese society. It then draws on fieldwork data to examine the hybrid nature of Chinese minjian religion from three aspects: the diversification of participants, the performative hybridisation of rituals, and the blending of spatial layouts. The main argument is that the revival of minjian religion involves the hybridisation of mystical and secular elements and of traditional and modern elements through the complex interactions between rural communities and official authorities

Carnitine metabolites and cognitive improvement in patients with schizophrenia treated with olanzapine: a prospective longitudinal study

Objective: Cognitive impairment is one of the core symptoms of schizophrenia, which is stable and lifelong. L-carnitine has been shown to improve cognitive function and decrease the rate of cognitive deterioration in patients with Alzheimer’s disease. However, it remains unclear regarding the role of L-carnitine and its metabolites in cognitive functions in schizophrenia after treatment with olanzapine. The purpose of this study was to evaluate the relationship between changes in plasma levels of L-carnitine metabolites and cognitive improvement after olanzapine treatment.Methods: This was a prospective longitudinal study. In this study, we recruited 25 female patients with first episode schizophrenia (FES) who were drug naïve at baseline and received 4 weeks of olanzapine monotherapy. Cognitive function was assessed at baseline and 4-week follow-up using the RBANS. Plasma L-carnitine metabolite levels were determined by a metabolomics technology based on untargeted ultra-performance liquid chromatography-mass spectrometry (UPLC-MS).Results: We found that the immediate memory index, delayed memory index and RBANS composite score were significantly increased at the 4-week follow-up after treatment. A total of 7 differential L-carnitine metabolites were identified in FES patients after olanzapine monotherapy. In addition, we found that changes in butyrylcarnitine were positively correlated with improvements in language index and RBANS composite score. Further regression analyses confirmed the association between reduced butyrylcarnitine levels and cognitive improvement after olanzapine monotherapy in FES patients.Conclusion: Our study shows that cognitive improvement after olanzapine treatment was associated with changes in L-carnitine metabolite levels in patients with FES, suggesting a key role of L-carnitine in cognition in schizophrenia

Comparing the Salt Tolerance of Three Landscape Plants Using a Near-Continuous Gradient Dosing System

Screening salinity-tolerant plants is usually time intensive and only applicable to a limited number of salinity levels. A near-continuous gradient dosing (NCGD) system allows researchers to evaluate a large number of plants for salinity tolerance with multiple treatments, more flexibility, and reduced efforts of irrigation. Rose of sharon (Hibiscus syriacus), ninebark (Physocarpus opulifolius), and japanese spirea (Spiraea japonica) were irrigated using an NCGD system with eight electrical conductivity (EC) levels ranging from 0.9 to 6.5 dS·m–1. At 11 weeks after irrigation was initiated, there were no significant differences among EC levels in terms of visual score, growth index [(Height + Width 1 + Width 2)/3], stem diameter, number of inflorescences, and shoot dry weight (DW) of rose of sharon. However, the root DW, relative chlorophyll content (SPAD), and net photosynthesis rate (Pn) of rose of sharon decreased linearly as EC levels increased. Ninebark and japanese spirea had increased foliar salt damage with increasing EC levels. The growth index, stem diameter, number of inflorescences, shoot and root DW, SPAD, and Pn of ninebark decreased linearly as EC levels increased. The growth index and SPAD of japanese spirea decreased quadratically with increasing EC levels, but its stem diameter, number of inflorescences, shoot and root DW, and Pn decreased linearly with increasing EC levels. The salinity threshold (50% loss of shoot DW) was 5.4 and 4.6 dS·m–1, respectively, for ninebark and japanese spirea. We were not able to define the salinity threshold for rose of sharon in this study. However, rose of sharon was the most salinity-tolerant species among the three landscape plants

Growth, Gas Exchange, and Mineral Nutrients of Ornamental Grasses Irrigated with Saline Water

Ornamental grasses are commonly used in urban landscapes in Utah and the Intermountain West of the United States. The relative salt tolerance of Eragrostis spectabilis (Pursh) Steud. (purple love grass), Miscanthus sinensis Andersson ‘Gracillimus’ (maiden grass), Panicum virgatum L. ‘Northwind’ (switchgrass), and Schizachyrium scoparium (Michx.) Nash (little bluestem) were evaluated in a greenhouse. Plants were irrigated with a nutrient solution at an electrical conductivity (EC) of 1.2 dS·m–1 (control), or saline solution at an EC of 5.0 or 10.0 dS·m–1. At harvest (65 days after the initiation of treatment), P. virgatum and S. scoparium exhibited no foliar salt damage, and E. spectabilis and M. sinensis had minimal foliar salt damage when irrigated with saline solution at an EC of 5.0 dS·m–1. At an EC of 10.0 dS·m–1, P. virgatum and S. scoparium still had no foliar salt damage, but E. spectabilis and M. sinensis displayed slight foliar salt damage, with visual scores greater than 3 (0 = dead; 5 = excellent). Compared with the control, saline solution at an EC of 5.0 and 10.0 dS·m–1 reduced the shoot dry weight of all ornamental grasses by 25% and 46%, respectively. The leaf sodium (Na+) concentration of E. spectabilis, M. sinensis, P. virgatum, and S. scoparium irrigated with saline solution at an EC of 10.0 dS·m–1 increased 14.3, 52.6, 5.3, and 1.7 times, respectively, and the chloride (Cl–) concentration increased by 9.4, 11.1, 2.8, and 2.7 times, respectively. As a result of the salt-induced water deficit, plant height, leaf area, number of inflorescences and tillers, net photosynthesis rate (Pn), stomatal conductance (gS), and transpiration rate of four tested ornamental grasses decreased to some extent. Although high Na+ and Cl– accumulated in the leaf tissue, all ornamental grass species still had a good visual quality, with average visual scores greater than 3. In conclusion, all ornamental grasses showed a very strong tolerance to the salinity levels used in this research

Detection of Energy Cutoffs in Flare-accelerated Electrons

Energy cutoffs in electron distribution define the lower and upper limits on the energy range of energetic electrons accelerated in solar flares. They are crucial parameters for understanding particle acceleration processes and energy budgets. Their signatures have been reported in studies of flattened flare X-ray spectra, i.e., the impulsive emission of nonthermal bremsstrahlung from energetic electrons impacting ambient, thermal plasma. However, these observations have not provided unambiguous constraints on the cutoffs. Moreover, other processes may result in similar spectral features. Even the existence and necessity of cutoffs as physical parameters of energetic electrons have been under debate. Here we report a search for their signatures in flare-accelerated electrons with two approaches, i.e., in both X-ray spectra and solar energetic particle (SEP) events. These represent two different electron populations, but may contain information of the same acceleration process. By studying a special group of late impulsive flares, and a group of selected SEP events, we found evidence of cutoffs revealed in both X-ray spectra and SEP electron distributions. In particular, we found for the first time consistent low- and high-energy cutoffs in both hard X-ray-producing and escaping electrons in two events. We also showed the importance of high-energy cutoff in studies of spectral shapes. These results provide evidence of cutoffs in flare-accelerated energetic electrons and new clues for constraining electron distribution parameters and particle acceleration models

Salt Tolerance of Sego SupremeTM Plants

Sego SupremeTM is a designated plant breeding and introduction program at the Utah State University Botanical Center and the Center for Water Efficient Landscaping. This plant selection program introduces native and adapted plants to the arid West for aesthetic landscaping and water conservation. The plants are evaluated for characteristics such as color, flowering, ease of propagation, market demand, disease/pest resistance, and drought tolerance. However, salt tolerance has not been considered during the evaluation processes. Four Sego SupremeTM plants [Aquilegia barnebyi (oil shale columbine), Clematis fruticosa (Mongolian gold clematis), Epilobium septentrionale (northern willowherb), and Tetraneuris acaulis var. arizonica (Arizona four-nerve daisy)] were evaluated for salt tolerance in a greenhouse. Uniform plants were irrigated weekly with a nutrient solution at an electrical conductivity (EC) of 1.25 dS·m−1 as control or a saline solution at an EC of 2.5, 5.0, 7.5, or 10.0 dS·m−1 for 8 weeks. After 8 weeks of irrigation, A. barnebyi irrigated with saline solution at an EC of 5.0 dS·m−1 had slight foliar salt damage with an average visual score of 3.7 (0 = dead; 5 = excellent), and more than 50% of the plants were dead when irrigated with saline solutions at an EC of 7.5 and 10.0 dS·m−1. However, C. fruticosa, E. septentrionale, and T. acaulis had no or minimal foliar salt damage with visual scores of 4.2, 4.1, and 4.3, respectively, when irrigated with saline solution at an EC of 10.0 dS·m−1. As the salinity levels of treatment solutions increased, plant height, leaf area, and shoot dry weight of C. fruticosa and T. acaulis decreased linearly; plant height of A. barnebyi and E. septentrionale also declined linearly, but their leaf area and shoot dry weight decreased quadratically. Compared with the control, the shoot dry weights of A. barnebyi, C. fruticosa, E. septentrionale, and T. acaulis decreased by 71.3%, 56.3%, 69.7%, and 48.1%, respectively, when irrigated with saline solution at an EC of 10.0 dS·m−1. Aquilegia barnebyi and C. fruticosa did not bloom during the experiment at all treatments. Elevated salinity reduced the number of flowers in E. septentrionale and T. acaulis. Elevated salinity also reduced the number of shoots in all four species. Among the four species, sodium (Na+) and chloride (Cl–) concentration increased the most in A. barnebyi by 53 and 48 times, respectively, when irrigated with saline solution at an EC of 10.0 dS·m−1. In this study, C. fruticosa and T. acaulis had minimal foliar salt damage and less reduction in shoot dry weight, indicating that they are more tolerant to salinity. Epilobium septentrionale was moderately tolerant to saline solution irrigation with less foliar damage, although it had more reduction in shoot dry weight. On the other hand, A. barnebyi was the least tolerant with severe foliar damage, more reduction in shoot dry weight, and a greater concentration of Na+ and Cl–

Reconstruct gene regulatory network using slice pattern model

<p>Abstract</p> <p>Background</p> <p>Gene expression time series array data has become a useful resource for investigating gene functions and the interactions between genes. However, the gene expression arrays are always mixed with noise, and many nonlinear regulatory relationships have been omitted in many linear models. Because of those practical limitations, inference of gene regulatory model from expression data is still far from satisfactory.</p> <p>Results</p> <p>In this study, we present a model-based computational approach, Slice Pattern Model (SPM), to identify gene regulatory network from time series gene expression array data. In order to estimate performances of stability and reliability of our model, an artificial gene network is tested by the traditional linear model and SPM. SPM can handle the multiple transcriptional time lags and more accurately reconstruct the gene network. Using SPM, a 17 time-series gene expression data in yeast cell cycle is retrieved to reconstruct the regulatory network. Under the reliability threshold, <it>θ </it>= 55%, 18 relationships between genes are identified and transcriptional regulatory network is reconstructed. Results from previous studies demonstrate that most of gene relationships identified by SPM are correct.</p> <p>Conclusion</p> <p>With the help of pattern recognition and similarity analysis, the effect of noise has been limited in SPM method. At the same time, genetic algorithm is introduced to optimize parameters of gene network model, which is performed based on a statistic method in our experiments. The results of experiments demonstrate that the gene regulatory model reconstructed using SPM is more stable and reliable than those models coming from traditional linear model.</p