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We used cDNA microarrays containing -9,000 unigenes to identify 486 salt responsive expressed sequence tags （ESTs） （representing -450 unigenes） in shoots of the highly salt-tolerant rice variety, Nona Bokra （Oryza sativa L. ssp. Indica pv. Nona）. Some of the genes identified in this study had previously been associated with salt stress. However the majority were novel, indicating that there is a great number of genes that are induced by salt exposure. Analysis of the salt stress expression profile data of Nona provided clues regarding some putative cellular and molecular processes that are undertaken by this tolerant rice variety in response to salt stress. Namely, we found that multiple transcription factors were induced during the initial salt response of shoots. Many genes whose encoded proteins are implicated in detoxification, protectant and transport were rapidly induced. Genes supporting photosynthesis were repressed and those supporting carbohydrate metabolism were altered. Commonality among the genes induced by salt exposure with those induced during senescence and biotic stress responses suggests that there are shared signaling pathways among these processes. We further compared the transcriptome changes of the salt-sensitive cultivar, IR28, with that of Nona rice. Many genes that are salt responsive in Nona were found to be differentially regulated in IR28. This study identified a large number of candidate functional genes that appear to be involved in salt tolerance and further examination of these genes may enable the molecular basis of salt tolerance to be elucidated.

Background With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected assembly outcomes, and there was no consensus on how to approach an optimal solution by selecting software tool and suitable strategy based on the properties of RNA-Seq data. Results To reveal the performance of different programs for transcriptome assembly, this work analyzed some important factors, including k -mer values, genome complexity, coverage depth, directional reads, etc . Seven program conditions, four single k -mer assemblers (SK: SOAPdenovo, ABySS, Oases and Trinity) and three multiple k -mer methods (MK: SOAPdenovo-MK, trans-ABySS and Oases-MK) were tested. While small and large k -mer values performed better for reconstructing lowly and highly expressed transcripts, respectively, MK strategy worked well for almost all ranges of expression quintiles. Among SK tools, Trinity performed well across various conditions but took the longest running time. Oases consumed the most memory whereas SOAPdenovo required the shortest runtime but worked poorly to reconstruct full-length CDS. ABySS showed some good balance between resource usage and quality of assemblies. Conclusions Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly. Some practical guidelines for transcript reconstruction from short-read RNA-Seq data were proposed. De novo assembly of C. sinensis transcriptome was greatly improved using some optimized methods.

Single-walled carbon nanotubes of a single chirality can be produced with an abundance of more than 92 per cent when using tungsten-based bimetallic alloy nanocrystals as catalysts. A new route to single-walled carbon nanotubes Single-walled carbon nanotubes (SWNTs) have many outstanding material properties that depend sensitively on their exact structure. This structure–function relationship can be fully exploited only with access to structurally pure SWNTs, but producing just one tube type remains a considerable challenge. Here Feng Yang et al . describe a strategy to realize chirality-specific growth of a single SWNT type using solid tungsten–cobalt alloy nanoparticles as catalysts. The tungsten component ensures high-temperature stability for the catalyst structure and cobalt is an effective catalyst. Optimization of the strategy should boost selectivity further, to deliver structurally pure SWNT samples that may enable wider use and development of these unique materials for practical applications. Carbon nanotubes have many material properties that make them attractive for applications 1 , 2 . In the context of nanoelectronics 3 , interest has focused on single-walled carbon nanotubes 4 (SWNTs) because slight changes in tube diameter and wrapping angle, defined by the chirality indices ( n ,  m ), will shift their electrical conductivity from one characteristic of a metallic state to one characteristic of a semiconducting state, and will also change the bandgap. However, this structure–function relationship can be fully exploited only with structurally pure SWNTs. Solution-based separation methods 5 yield tubes within a narrow structure range, but the ultimate goal of producing just one type of SWNT by controlling its structure during growth has proved to be a considerable challenge over the last two decades 6 , 7 , 8 , 9 . Such efforts aim to optimize the composition 6 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 or shape 18 , 19 , 20 , 21 of the catalyst particles that are used in the chemical vapour deposition synthesis process to decompose the carbon feedstock and influence SWNT nucleation and growth 22 , 23 , 24 , 25 . This approach resulted in the highest reported proportion, 55 per cent, of single-chirality SWNTs in an as-grown sample 11 . Here we show that SWNTs of a single chirality, (12, 6), can be produced directly with an abundance higher than 92 per cent when using tungsten-based bimetallic alloy nanocrystals as catalysts. These, unlike other catalysts used so far, have such high melting points that they maintain their crystalline structure during the chemical vapour deposition process. This feature seems crucial because experiment and simulation both suggest that the highly selective growth of (12, 6) SWNTs is the result of a good structural match between the carbon atom arrangement around the nanotube circumference and the arrangement of the catalytically active atoms in one of the planes of the nanocrystal catalyst. We anticipate that using high-melting-point alloy nanocrystals with optimized structures as catalysts paves the way for total chirality control in SWNT growth and will thus promote the development of SWNT applications.

Synapses are the basic units of information transmission, processing and integration in the nervous system. Dysfunction of the synaptic development has been recognized as one of the main reasons for mental dementia and psychiatric diseases such as Alzheimer’s disease and autism. However, the underlying mechanisms of the synapse formation are far from clear. Here we report that phospholipase D1 (PLD1) promotes the development of dendritic spines in hippocampal neurons. We found that overexpressing PLD1 increases both the density and the area of dendritic spines. On the contrary, loss of function of PLD1, including overexpression of the catalytically-inactive PLD1 (PLD1ci) or knocking down PLD1 by siRNAs, leads to reduction in the spine density and the spine area. Moreover, we found that PLD1 promotes the dendritic spine development via regulating the membrane level of N-cadherin. Further studies showed that the regulation of surface N-cadherin by PLD1 is related with the cleavage of N-cadherin by a member of the disintegrin and metalloprotease family-ADAM10. Taking together, our results indicate a positive role of PLD1 in synaptogenesis by inhibiting the ADAM10 mediated N-cadherin cleavage and provide new therapeutic clues for some neurological diseases.

Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with features that vary by ethnicity. A systematic characterization of the genomic landscape of Chinese ccRCC is lacking, and features of ccRCC associated with tumor thrombus (ccRCC-TT) remain poorly understood. Here, we applied whole-exome sequencing on 110 normal-tumor pairs and 42 normal-tumor-thrombus triples, and transcriptome sequencing on 61 tumor-normal pairs and 30 primary-thrombus pairs from 152 Chinese patients with ccRCC. Our analysis reveals that a mutational signature associated with aristolochic acid (AA) exposure is widespread in Chinese ccRCC. Tumors from patients with ccRCC-TT show a higher mutational burden and genomic instability; in addition, mutations in BAP1 and SETD2 are highly enriched in patients with ccRCC-TT. Moreover, patients with/without TT show distinct molecular characteristics. We reported the integrative genomic sequencing of Chinese ccRCC and identified the features associated with tumor thrombus, which may facilitate ccRCC diagnosis, prognosis and treatment. The genomic heterogeneity of clear cell renal cell carcinoma (ccRCC) across populations is poorly understood. Here, the authors analyse a cohort of Chinese ccRCC cases revealing a mutational signature associated with aristolochic acid exposure, and higher mutational burden and enrichment for BAP1 and SETD2 mutations in ccRCC cases associated with tumor thrombus.

Stochastic neural network has the characteristics of good global convergence and fast gradient-based learning ability. It can be applied to multidimensional nonlinear systems, but its generalization ability is poor. In this paper, combined with rule base, through the PCA method, an improved multimodal variable-structure random-vector neural network algorithm (MM-P-VSRVNN) is proposed for coagulant dosing, which is a key production process in water purification process. Ensuring for qualified water, how to control coagulation dosage effectively, obtain valid production cost, and increase more profits is a focus in the water treatment plan. Different with the normal neural network mode, PCA is used to optimize hidden-layer nodes and update the neural network structure at every computation. This method rectifies coagulant dosage effectively while keeping valid coagulation performance. By the way, the MM-P-VSRVNN algorithm can decrease computation time and avoid overfitting learning ability. Finally, the method is proved feasible through the experiment and analyzed by the simulation result.

Xiangdong Fu and colleagues report characterization of a major rice grain yield QTL at the DEP1 locus. Grain yield is controlled by quantitative trait loci (QTLs) derived from natural variations in many crop plants. Here we report the molecular characterization of a major rice grain yield QTL that acts through the determination of panicle architecture. The dominant allele at the DEP1 locus is a gain-of-function mutation causing truncation of a phosphatidylethanolamine-binding protein-like domain protein. The effect of this allele is to enhance meristematic activity, resulting in a reduced length of the inflorescence internode, an increased number of grains per panicle and a consequent increase in grain yield. This allele is common to many Chinese high-yielding rice varieties and likely represents a relatively recent introduction into the cultivated rice gene pool. We also show that a functionally equivalent allele is present in the temperate cereals and seems to have arisen before the divergence of the wheat and barley lineages.

To alleviate the contradiction in healthcare resources, the Chinese government formally established the framework of a hierarchical medical system in 2015, which contains the following brief generalities: \" separate treatment of emergencies and slows, first-contact care at the primary, two-way referral, and upper and lower linkage, \". This study systematically summarizes and models the connotations of China's hierarchical medical system and a sample of 11,200 chronic disease patients in Tianjin, the largest port city in northern China, was selected for the empirical study to investigate the relationship between chronic disease patients' policy perceptions of the hierarchical medical system and their preference for healthcare. We found that under the strategy of separate treatment, improving the healthcare accessibility, drug supply, and lowering the cost of medical care would have a positive impact on increasing the preference of patients with chronic diseases to go to the primary hospitals. Under the two-way triage strategy, improving the level of physician services, referral convenience and treatment Standards have a positive impact on chronic disease patients' preference for primary care; The impact of the hierarchical medical system on the preference for healthcare differed between groups, focusing on differences in health literacy level, age and household type; The role of \" upper and lower linkage \" is crucial in the hierarchical medical system and it plays a part in mediating the influence of the \" separate treatment of emergencies and slows\" design and the \"two-way referral \" order on the treatment preferences of chronic disease patients. The results of the study provide a reference for the further development of a scientific and rational hierarchical medical system in the future.

Single-crystal metal foils are valuable for their surface properties that allow for synthesis of materials like graphene. Jin et al. present a strategy for creating colossal single-crystal metal foils called “contact-free annealing” (see the Perspective by Rollett). The method relies on hanging and heating commercially available, inexpensive, cold-rolled metal foils. Almost as if by magic, the polycrystalline grains rotate and anneal into a large single-crystal sheet with a specific crystal orientation. The strategy allows for the creation of much larger and much cheaper single-crystal metal foils. Science , this issue p. 1021 ; see also p. 996 Contact-free annealing allows for the synthesis of large single-crystal metal foils. Single-crystal metals have distinctive properties owing to the absence of grain boundaries and strong anisotropy. Commercial single-crystal metals are usually synthesized by bulk crystal growth or by deposition of thin films onto substrates, and they are expensive and small. We prepared extremely large single-crystal metal foils by “contact-free annealing” from commercial polycrystalline foils. The colossal grain growth (up to 32 square centimeters) is achieved by minimizing contact stresses, resulting in a preferred in-plane and out-of-plane crystal orientation, and is driven by surface energy minimization during the rotation of the crystal lattice followed by “consumption” of neighboring grains. Industrial-scale production of single-crystal metal foils is possible as a result of this discovery.

Accumulating evidence suggests AKT1 and DRD2-AKT-GSK3 signaling involvement in schizophrenia. AKT1 activity is also required for lithium, a GSK3 inhibitor, to modulate mood-related behaviors. Notably, GSK3 inhibitor significantly alleviates behavioral deficits in Akt1 −/− female mice, whereas typical/atypical antipsychotics have no effect. In agreement with adjunctive therapy with lithium in treating schizophrenia, our data mining indicated that the average utilization rates of lithium in the Taiwan National Health Insurance Research Database from 2002 to 2013 are 10.9% and 6.63% in inpatients and outpatients with schizophrenia, respectively. Given that lithium is commonly used in clinical practice, it is of great interest to evaluate the effect of lithium on alleviating Akt1-related deficits. Taking advantage of Akt1 +/− mice to mimic genetic deficiency in patients, behavioral impairments were replicated in female Akt1 +/− mice but were alleviated by subchronic lithium treatment for 13 days. Lithium also effectively alleviated the observed reduction in phosphorylated GSK3α/β expression in the brains of Akt1 +/− mice. Furthermore, inhibition of Akt expression using an Akt1/2 inhibitor significantly reduced neurite length in P19 cells and primary hippocampal cell cultures, which was also ameliorated by lithium. Collectively, our findings implied the therapeutic potential of lithium and the importance of the AKT1-GSK3 signaling pathway.