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Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.

A simple and novel metal-free reduction of azides to amines in the presence of DBU is reported. This DBU-promoted transformation features good functional group tolerance and high chemo-selectivity.

A novel and efficient method for the synthesis of 3-thiocyanindoles from 2-alkynyl arylazides with KSCN is described. NBS (N-bromosuccinimide) plays an important role in this cascade bromination/cross-coupling reaction. This reaction provides the 3-thiocyanindole products in good to excellent yields under mild reaction conditions.

Seed germination is critical for successful crop production, and the sensitivity to pH and salt stress depends on the plant’s tolerance mechanisms. In view of the characteristics of calcium-rich and acidic soils in the karst areas of Guizhou Province, China, the effects of pH stress and calcium stress on the seed germination characteristics of three herbages were studied with the goal of exploring and revealing the mechanism of adaptation of the three herbages to an acidic soil environment and providing a theoretical basis for the selection and cultivation of acid-tolerant herbages in southwest China. In this study, six concentration gradients of CaCl2, including 0, 25 mmol/L, 50 mmol/L, 100 mmol/L, 150 mmol/L, and 200 mmol/L, and seven pH gradients, including 4.55, 5.35, 6.61, 7.03, 8.0, and 9.18 were established, respectively. The germination rate, germination potential and germination index of the seedlings were measured for each seed germination and seedling growth stage of orchardgrass, perennial ryegrass, and alfalfa, respectively. The results showed that when the concentration of salt stress began to change, the herbage seeds could adapt to salt stress at an appropriate pH condition. When only the pH value or CaCl2 concentration changes, the increase in pH and CaCl2 will inhibit the growth of shoots and roots. Weak acid can promote the growth of shoots and young roots, while alkaline conditions can inhibit their growth. The effect of a low concentration of CaCl2 was not apparent, while a high concentration of CaCl2 clearly inhibited the plants. The optimal pH and CaCl2 of the bud and root lengths changed after the interaction. In conclusion, there is a substantial difference between pH and calcium salt stress, and the interaction between pH and calcium salt concentration has a substantial influence on the salt and alkali tolerance of the three types of seeds.

Forage quality is a key property of grassland ecosystems. In this study, grassland forage qualities were measured at 373 sampling sites throughout Guizhou Province in the karst mountain region of Southwest China, and the factors affecting it were explored. The forage quality level of most plant species was categorized into four levels: (1) preferred forage species; (2) desirable forage species; (3) consumed but undesirable forage species; and (4) non-consumable or toxic forage species. High temperature and precipitation appeared to facilitate the growth of preferred forage species, but limited the growth of other plants. Increasing soil pH had a positive impact on the number and biomass of preferred forage plants, but a negative influence on other plants, especially non-consumable or toxic plants. Both GDP and population density had a positive correlation with the number and biomass of preferred forage species, while such correlations for other levels of forage species tended to be negative. Grazing could lead to a decrease in the preferred forage species. Therefore, it is suggested that by focusing on soil improvement in grassland and maintaining an appropriate grazing intensity, global warming and rapid economic growth in Guizhou Province will likely contribute to increase the forage quality of karst grasslands in Southwest China.

For a partially coherent Bessel–Gaussian (PCBG) vortex beam, information regarding the topological charge (TC) is hidden in the phase of the cross-spectral density (CSD) function. We theoretically and experimentally confirmed that during free-space propagation, the number of coherence singularities is equal to the magnitude of the TC. In contrast to the Laguerre–Gaussian vortex beam, this quantitative relationship only holds for the case with an off-axis reference point for the PCBG vortex beam. The phase winding direction is determined by the sign of the TC. We developed a scheme for CSD phase measurement of PCBG vortex beams and verified the aforementioned quantitative relationship at different propagation distances and coherence widths. The findings of this study may be useful for optical communications.

The sales of cultural and creative products can bring substantial profit for the museums. Facing the impact of the COVID-19 pandemic, higher sales of cultural and creative products are pivotal for the sustainable development of museums. This study, based on the decomposed Theory of Planned Behavior (TPB), constructed a model of factors influencing the intentions to purchase Museum’s Cultural and Creative Products and analyzed the 1,115 questionnaires returned. The empirical results showed good fit and explanatory power of the model and validated the decomposed TPB.

Context Fine-scale spatial vegetation patterns are ubiquitous and can have profound impacts on large scale ecological processes including surface runoff, soil erosion, and livestock forage efficiency. However, we have limited knowledge of the fine-scale spatial vegetation patterns in humid grasslands.Objectives The objectives were to characterize the spatial vegetation patterns at centimeter scale in humid grasslands, quantify the vegetation patterns variation under different image pixel sizes and plant covers, and explore the potential ecological implications of the spatial vegetation patterns.Methods Seventy plots with plant covers ranging from 30.8–99.3% were selected from seven humid grasslands in southwest China and their spatial vegetation patterns quantified at image pixel sizes of 0.04, 0.25, 1, and 4 cm.Results With increasing pixel size, plant patch density and total edge density decreased, plant patch size increased, and the plant patch shape became more regular. At a plant cover level below 50%, increasing plant cover will result in increasing patch density and patch size, leading to greater spatial heterogeneity. At plant cover levels above 50%, increasing plant cover will cause the rapid expansion of patch size, along with a lower patch density, forming a more homogeneous landscape dominated by plant patches. The small stems, branches, and leaves of grasses fragmented non-plant patches into smaller patches with increasing plant cover; this fragmentation resembles road-induced landscape fragmentation processes.Conclusions Medium plant cover has the highest heterogeneity of spatial vegetation pattern at the fine scale, which may have significant implications on ecological processes and related management practices.

Southwest China is an important route for invasive species. In this study, 49 invasive plants of 15 families and 41 genera were found within 373 grassland sampling sites of Guizhou Province, a typical karst mountainous region with a high invasion risk located in Southwest China. Invasive plants could be found within over 90% of the grassland sampling sites, and malignant invasive species were found in 60% of the sites. In about 30% of the sampling sites, more than one malignant species coexisted. The malignant invasive species were mainly distributed in the southwestern part of Guizhou Province. Their distribution patterns were affected by environmental and traffic factors; they preferred areas with low elevation, high temperature, high rainfall, high soil nutrient content, and traffic accessibility and could adversely affect plant cover and biomass. Conversely, seriously invasive species and other low-level invasive species had a positive or neutral effect on grassland communities. Therefore, the focus of invasive plant control measures should be on malignant invasive species. Specific control policies and practices, especially in areas with resource-rich environments and well-developed traffic networks, should be carried out to facilitate grassland ecosystem sustainability and to prevent the spread of invasive species to inland China.

Post-operative nausea and vomiting (PONV) is an event of multifactorial origin with an incidence of 30% in the general population. Opioids such as fentanyl are being used as adjuvant to local anesthetic for its antiemetic effect. In this context, with this study we aimed to evaluate the impact of spinal fentanyl as an adjuvant on the incidence of PONV compared with a placebo, and shivering. A systematic search of randomized controlled trials that evaluated the use of spinal fentanyl in the prevention of PONV and shivering was conducted in different databases, of which 32 studies met the inclusion criteria. A total of 2116 patients scheduled for various surgeries, including cesarean section, orthopedic surgery in the lower limb, hysterectomy, and transurethral resection of the prostate, were included in the final analysis. The meta-analysis estimated the relative risk of incidence of PONV in the first 24 hours after surgery and secondary outcomes included the shivering symptom. The use of intrathecal fentanyl was associated with lower incidence of PONV, but not statistically significant when compared to the placebo (RR: 0.74 CI95%: 0.55-1.01

Accelerating the healing of bone fractures in the presence of infection is a serious challenge that has increased hopes for reducing this challenge by using nanotechnology. This study tried to effectively reduce bacterial infection by producing alendronate (An)-maghemite nanosphere-hydroxyapatite (An-MNS-HA) through co-precipitation, in addition to increasing the rate of proliferation and differentiation of human primary osteoblasts cells. After production of An-MNS-HA, their physicochemical properties were investigated by TEM, DLS and FTIR methods as well as the level of An release. The toxicity of An-MNS-HA was determined by MTT assay and the antibacterial activities of An-MNS-HA were also performed on both Gram-negative and Gram-positive bacteria. In addition, cell differentiation markers including ALP, OC, ODF, OPG and RANKL genes were analyzed by real time PCR technique. The results revealed that An-MNS-HA is spherical with a rough surface with a size of around 105.5 ± 2.08 nm. Also, DLS and FTIR results confirmed the potential loading of HA and An on MNS with a drug loading efficiency of 55.39 ± 4.68% and a drug release rate of 80.93 ± 5.28% from An-MNS-HA. The antibacterial activity of An-MNS-HA on both Gram-negative and Gram-positive bacteria exhibited a significant reduction in infection, despite a greater effect on Gram-negative bacteria. Also, cell proliferation and differentiation in the presence of An-MNS-HA were observed which were associated with an increase in the expression of the ALP, OC, ODF and OPG mRNA as well as decreased expression of RANKL gene. Finally, An-MNS-HA with high biological compatibility, antibacterial activity and induction of ossification, has a good ability to accelerate and repair bone defects.

Physical exercise-induced enhancement of learning and memory and alleviation of age-related cognitive decline in humans have been widely acknowledged. However, the mechanistic relationship between exercise and cognitive improvement remains largely unknown. In this study, we found that exercise-elicited cognitive benefits were accompanied by adaptive hippocampal proteasome activation. Voluntary wheel running increased hippocampal proteasome activity in adult and middle-aged mice, contributing to an acceleration of neurogenesis that could be reversed by intrahippocampal injection of the proteasome inhibitor MG132. We further found that increased levels of insulin-like growth factor-1 (IGF-1) in both serum and hippocampus may be essential for exercise-induced proteasome activation. Our in vitro study demonstrated that IGF-1 stimulated proteasome activity in cultured adult neural progenitor cells (NPCs) by promoting nuclear translocation of nuclear factor erythroid 2-related factor 2 (Nrf2), followed by elevated expressions of proteasome subunits such as PSMB5. In contrast, pretreating adult mice with the selective IGF-1R inhibitor picropodophyllin diminished exercise-induced neurogenesis, concurrent with reduced Nrf2 nuclear translocation and proteasome activity. Likewise, lowering Nrf2 expression by RNA interference with bilateral intrahippocampal injections of recombinant adeno-associated viral particles significantly suppressed exercise-induced proteasome activation and attenuated cognitive function. Collectively, our work demonstrates that proteasome activation in hippocampus through IGF-1/Nrf2 signaling is a key adaptive mechanism underlying exercise-related neurogenesis, which may serve as a potential targetable pathway in neurodegeneration.

Overcoming the Rayleigh diffraction limit has been a longstanding focus in optical field. In this paper, a complex Gaussian-correlated beam was used as the illumination source, which renders the minimum resolution distance of four symmetrical pinholes at least 0.05 times the Rayleigh diffraction limit. In addition, the method was applied in displacement measurements, which can measure a displacement below the Rayleigh diffraction limit. The theoretical results show that the complex Gaussian-correlated beam has a great potential to realize sub-diffraction-limit and micro-displacement measurements.

Global warming will stimulate primary production, which is likely to drive shifts in litter production and lead to an increase in carbon (C) inputs to soil. However, the effects of such changes on soil C cycling in subtropical forests remain largely unknown. In a typical subtropical evergreen broadleaved forest in Southwestern China we conducted a controlled experiment that included addition and removal of litter, and trenching. Annual soil respiration in control, trenching, litter addition, and litter removal treatments were 1083.47, 521.50, 1363.30, and 896.15 g C m–2 y–1, respectively. Soil respiration was significantly related to temperature in all treatments, but was independent of soil moisture, except in control plots. Q10 values in control, trenching, litter addition, and litter removal treatments were 3.46, 6.36, 2.72, and 4.85, respectively. Litter addition reduced Q10, but litter removal and trenching increased it. Average heterotrophic soil respiration produced C in the amount equivalent to 48% of the efflux from the soil. Soil respiration in the litter addition treatment was 25% higher than in the control treatment; this increase is about 8% larger than the 17% decrease in soil respiration caused by litter removal. This implies a priming effect on soil respiration. Our results suggest that increases in litter production in response to human disturbances and global warming could have rapid and important consequences on soil respiration in subtropical evergreen broadleaved forests.

Cytotoxic T lymphocyte antigen 4 (CTLA-4) genetic polymorphisms are implicated to be associated with susceptibility to bone sarcomas, but published studies have reported inconclusive results. The objective of our study was to conduct a meta-analysis investigating the associations between CTLA-4 gene polymorphisms and risk of bone sarcomas. PubMed and Embase databases were searched for all articles published up to June 2, 2013. Odds ratio (OR) with a 95 % confidence interval (95 % CI) was used to assess the association. Finally, 11 individual studies with a total of 2,951 cases with bone sarcomas and 3,396 controls were included in the meta-analysis. There were four studies on the CTLA-4 49G/A polymorphism, three studies on CTLA-4 318C/T polymorphism, two studies on CTLA-4 1661A/G polymorphism, and two studies on CTLA-4 60A/G polymorphism. Overall, CTLA-4 49G/A polymorphism was obviously associated with risk of bone sarcomas (A vs. G: OR = 1.36, 95 % CI = 1.20–1.54; AA vs. GG: OR = 2.24, 95 % CI = 1.67–2.99; AA vs. AG/GG: OR = 2.00, 95 % CI = 1.53–2.62; AA/GA vs. GG: OR = 1.35, 95 % CI = 1.14–1.61). However, CTLA-4 318C/T, 1661A/G, and 60A/G polymorphisms were not associated with risk of bone sarcomas. The current meta-analysis suggests that CTLA-4 49G/A polymorphism is obviously associated with risk of bone sarcomas. More studies are needed to further evaluate the associations between CTLA-4 polymorphisms and risk of bone sarcomas.

Interleukin-1β (IL-1β) has a significant role in osteo - arthritis (OA). The purinergic receptor, P2X4, has previously been implicated in IL‑1β secretion. The NLRP1 inflam- masome mediates the production of IL‑1β in inflammatory disorders. However, it is unknown whether P2X4 modulates NLRP1‑mediated IL‑1β release. In the present study, the corre- lation between the P2X4 receptor and NLRP1 was investigated in OA fibroblast‑like synoviocytes (OAFLS). The expression of P2X4 and NLRP1 was detected in the OAFLS. The OAFLS were stimulated with P2X4 and the levels of IL‑1β and matrix metalloproteinases (MMPs) were measured. To determine whether P2X4 is involved in NLRP1‑triggered IL‑1β produc- tion, NLRP1 small interfering RNA (siRNA) was used. In the OAFLS, a markedly higher expression of P2X4 and NLRP1 was revealed compared with that in the normal FLS. OAFLS stimulated by P2X4 resulted in concentration‑dependent increases in the production of IL‑1β, MMP‑3 and MMP‑9. Furthermore, P2X4‑mediated IL‑1β production was attenuated by the NLRP1 siRNA. The results of the present study indicate that P2X4 induced IL‑1β, MMP‑3 and MMP‑9 production in the OAFLS. IL‑1β induced by P2X4 is mediated via NLRP1. P2X4/NLRP1 may be important in the pathogenesis of OA and may represent a novel therapeutic target.

RNA interference (RNAi) is one of the most popular and effective molecular technologies for knocking down the expression of an individual gene of interest in living organisms. Yet the technology still faces the major issue of nonspecific gene silencing, which can compromise gene functional characterization and the interpretation of phenotypes associated with individual gene knockdown. Designing an effective and target-specific small interfering RNA (siRNA) for induction of RNAi is therefore the major challenge in RNAi-based gene silencing. A 'good' siRNA molecule must possess three key features: (a) the ability to specifically silence an individual gene of interest, (b) little or no effect on the expressions of unintended siRNA gene targets (off-target genes), and (c) no cell toxicity. Although several siRNA design and analysis algorithms have been developed, only a few of them are specifically focused on gene silencing in plants. Furthermore, current algorithms lack a comprehensive consideration of siRNA specificity, efficacy, and nontoxicity in siRNA design, mainly due to lack of integration of all known rules that govern different steps in the RNAi pathway. In this review, we first describe popular RNAi methods that have been used for gene silencing in plants and their serious limitations regarding gene-silencing potency and specificity. We then present novel, rationale-based strategies in combination with computational and experimental approaches to induce potent, specific, and nontoxic gene silencing in plants.

The recognition that multigene mechanisms control the pathways determining the aging process renders gene screening a necessary skill for biogerontologists. In the past few years, this task has become much more accessible, with the advent of DNA chip technology. Most commercially available microarrays are designed with prefixed templates of genes of general interest, allowing investigators little freedom of choice in attempting to focus gene screening on a particular thematic pathway of interest. This report describes our "designer microarray" approach as a next generation of DNA chips, allowing individual investigators to engage in gene screening with a user friendly, do-it-yourself approach, from designing the probe templates to data mining. The end result is the ability to use microarrays as a platform for versatile gene discovery.

Climate change is generally predicted to increase net primary production, which could lead to additional C input to soil. In arid central Asia, precipitation has increased and is predicted to increase further. To assess the combined effects of these changes on soil CO2 efflux in arid land, a two factorial manipulation experiment in the shrubland of an arid region in northwest China was conducted. The experiment used a nested design with fresh organic matter and water as the two controlled parameters. It was found that both fresh organic matter and water enhanced soil respiration, and there was a synergistic effect of these two treatments on soil respiration increase. Water addition not only enhanced soil C emission, but also regulated soil C sequestration by fresh organic matter addition. The results indicated that the soil CO2 flux of the shrubland is likely to increase with climate change, and precipitation played a dominant role in regulating soil C balance in the shrubland of an arid region.

Assessing oil pollution using traditional field-based methods over large areas is difficult and expensive. Remote sensing technologies with good spatial and temporal coverage might provide an alternative for monitoring oil pollution by recording the spectral signals of plants growing in polluted soils. Total petroleum hydrocarbon concentrations of soils and the hyperspectral canopy reflectance were measured in wetlands dominated by reeds (Phragmites australis) around oil wells that have been producing oil for approximately 10 years in the Yellow River Delta, eastern China to evaluate the potential of vegetation indices and red edge parameters to estimate soil oil pollution. The detrimental effect of oil pollution on reed communities was confirmed by the evidence that the aboveground biomass decreased from 1076.5 g m(-2) to 5.3 g m(-2) with increasing total petroleum hydrocarbon concentrations ranging from 9.45 mg kg(-1) to 652 mg kg(-1). The modified chlorophyll absorption ratio index (MCARI) best estimated soil TPH concentration among 20 vegetation indices. The linear model involving MCARI had the highest coefficient of determination (R(2) = 0.73) and accuracy of prediction (RMSE = 104.2 mg kg(-1)). For other vegetation indices and red edge parameters, the R(2) and RMSE values ranged from 0.64 to 0.71 and from 120.2 mg kg(-1) to 106.8 mg kg(-1) respectively. The traditional broadband normalized difference vegetation index (NDVI), one of the broadband multispectral vegetation indices (BMVIs), produced a prediction (R(2) = 0.70 and RMSE = 110.1 mg kg(-1)) similar to that of MCARI. These results corroborated the potential of remote sensing for assessing soil oil pollution in large areas. Traditional BMVIs are still of great value in monitoring soil oil pollution when hyperspectral data are unavailable.

This paper presented a novel approach to search and optimize path points for anti-ship missile path planning. We utilized the method of MAKLINK graph to construct free space, and then, a global state connected graph is built up for searching for all possible routes. Genetic Algorithm is used to search and optimize path points severally in these local routes. According to flight rules and technique characteristics of anti-ship missile, a coding measure and the fitness function are proposed. By introducing constraints selection strategy, the method in this paper guaranteed that all paths resulted could satisfy constraints. The results by simulation revealed that the method proposed in this paper is effective in solving the path planning problem with constraints.

Motivation: Membrane transport proteins play a crucial role in the import and export of ions, small molecules or macromolecules across biological membranes. Currently, there are a limited number of published computational tools which enable the systematic discovery and categorization of transporters prior to costly experimental validation. To approach this problem, we utilized a nearest neighbor method which seamlessly integrates homologous search and topological analysis into a machine-learning framework. Results: Our approach satisfactorily distinguished 484 transporter families in the Transporter Classification Database, a curated and representative database for transporters. A five-fold cross-validation on the database achieved a positive classification rate of 72.3% on average. Furthermore, this method successfully detected transporters in seven model and four non-model organisms, ranging from archaean to mammalian species. A preliminary literature-based validation has cross-validated 65.8% of our predictions on the 11 organisms, including 55.9% of our predictions overlapping with 83.6% of the predicted transporters in TransportDB. Availability and Supplementary information: http://bioinfo.noble.org/manuscript-support/transporter/ Contact: pzhao@noble.org

Objective Eldecalcitol (ELD) is an active form of vitamin D analog that has been approved for the treatment of osteoporosis in Japan. Over recent years, a number of multicenter, randomized controlled clinical trials have been conducted. Our goal is to comprehensively summarize the results from these studies. Methods We searched the databases MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials up to February 28, 2015. Each database was searched using search terms “Eldecalcitol” and “ED-71” and the results were combined. The retrieved data from three independent clinical trials included a total of 1,332 patients with osteoporosis. After the data were pooled from three trials, RevMan software was used to conduct meta-analyses to determine the effects of ELD on bone mineral density (BMD) and bone turnover marker (BTM) type I collagen amino-terminal telopeptide (NTX). Effects of ELD on some of the bone formation and bone resorption parameters, incidence of vertebral fractures at the lower spine, and health-related quality of life (HRQOL) in patients with osteoporosis were also summarized. Results With a test for overall effectZ=6.35, ELD could increase lumbar BMD (P

Background Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence tag (EST) database developed from nine cDNA libraries representing tissues from different plant organs, developmental stages, and abiotic stress factors. The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported. Results A total of 41,516 ESTs were generated from nine cDNA libraries of tall fescue representing tissues from different plant organs, developmental stages, and abiotic stress conditions. The Festuca Gene Index (FaGI) has been established. To date, this represents the first publicly available tall fescue EST database. In silico gene expression studies using these ESTs were performed to understand stress responses in tall fescue. A large number of ESTs of known stress response gene were identified from stressed tissue libraries. These ESTs represent gene homologues of heat-shock and oxidative stress proteins, and various transcription factor protein families. Highly expressed ESTs representing genes of unknown functions were also identified in the stressed tissue libraries. Conclusion FaGI provides a useful resource for genomics studies of tall fescue and other closely related forage and turf grass species. Comparative genomic analyses between tall fescue and other grass species, including ryegrasses (Lolium sp.), meadow fescue (F. pratensis) and tetraploid fescue (F. arundinacea var glaucescens) will benefit from this database. These ESTs are an excellent resource for the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) PCR-based molecular markers.

The advance of high-throughput experimental technologies poses continuous challenges to computational data analysis in functional and comparative genomics studies. Gene ontology (GO) annotation and transcriptional profiling using gene expression array have been two of the major approaches for system-wide analysis of gene functions and gene interactions. In the literature, extensive studies have been reported in each aspect. Yet there is a lack of efficient algorithm that discover associative patterns across these two data domains. We proposed a mixture model associative artificial neural network to tackle this deficiency. The algorithm inherits the theoretical foundation of adaptive resonance associative map (ARAM), with essential redefinition of pattern similarity measures and learning functions. The proposed algorithm is capable of clustering data based on both GO semantic similarity and expressional correlation, for the purpose of systematically discovering genome-wide, highly correlated gene groups, which in turn suggest similar or closely related functions. We applied the proposed algorithm to the analysis of the Saccharomyces cerevisiae (yeast) dataset and obtained satisfactory results.

Background BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Results Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. Conclusion PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.

Computational prediction of transcription factor's binding sites and regulatory target genes has great value to the biological studies of cellular process. Existing practices either look into first-hand gene expression data which could be costly for large scale analysis, or apply statistical or heuristic learning methods to discover potential binding sites which have limited accuracy due to the complexity of the data. Based on well-studied information retrieval theories, this paper proposes a novel systematic approach for transcription factor target gene prediction. The key of the approach is to model the prediction problem as a classification task by representing the features of the sequential data into vector data points in a higher-order domain. The proposed approach has produced satisfactory results in our controlled experiment on Auxin Response Factor (ARF) target gene prediction in Arabidopsis.

A current and significant limitation to metabolomics is the large-scale, high-throughput conversion of raw chromatographically coupled mass spectrometry datasets into organized data matrices necessary for further statistical processing and data visualization. This article describes a new data extraction tool, MET-IDEA (Metabolomics Ion-based Data Extraction Algorithm) which surmounts this void. MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude. The functionality of MET-IDEA is illustrated using metabolomics data obtained for elicited cell culture exudates from the model legume, Medicago truncatula. The results indicate that MET-IDEA is capable of rapidly extracting semiquantitative data from raw data files, which allows for more rapid biological insight. MET-IDEA is freely available to academic users upon request.

The goal of this study was to identify age-related changes in the expression of estrogen target genes in mouse uterus. We developed a novel 'estrogen response element (ERE) Chip' microarray bearing 297 genes including both known estrogen target genes and genes identified by searching the mouse genome database to have EREs, AP-1 sites, and Sp1 sites, all targets of estrogen receptor (ER) regulation. 400-500 bp PCR products of these 297 genes were printed onto nylon membranes creating the 'ERE Chip' microarray. This microarray is unique because it is the first estrogen-responsive gene-specific microarray to identify changes in uterine gene expression in young versus old mice. Using this ERE microarray we identified 10 uterine genes whose expression was up-regulated in old mice, e.g. beta-actin, calcium binding protein 45a, Sp1, and COUP-TFII. In contrast, the expression of only 4 uterine genes, i.e., complement C3, lactoferrin, Muc-1, and 17-beta-hydroxysteroid dehydrogenase 8 (H2-Ke6) was down-regulated in old mice. These changes may reflect an increase in stromal and a decrease in glandular epithelial gene expression, and may be associated with age-related changes in these tissue compartments within the uterus, possibly leading to the decline in reproductive function in C57Bl/6 mice.

In this study we aimed to determine whether a sequential distribution pattern along an aridity gradient is related to seed germination and seedling emergence of three Caragana species. The study tested the adaptive abilities of these species to major sandy environment factors including soil water potential, precipitation amount, and sand burial depth. The rank order of tolerance to drought and sand burial of the three species is C. korshinskii>C. intermedia>C. microphylla. The amount of precipitation and sand burial depth appear to be the main selective forces responsible for the geographical distribution of these species., Environmental tolerance of a species has been shown to correlate positively with its geographical range. On the Ordos Plateau, three Caragana species are distributed sequentially along the precipitation gradient. We hypothesized that this geographical distribution pattern is related to environmental tolerances of the three Caragana species during seed germination and seedling emergence stages. To test this hypothesis, we examined seed germination under different temperature, light and water potentials, and monitored seedling emergence for seeds buried at eight sand depths and given different amounts of water. Seeds of C. korshinskii germinated to high percentages at 5 : 15 to 25 : 35 °C in both light and darkness, while those of C. intermedia and C. microphylla did so only at 15 : 25 and 25 : 35 °C, respectively. Nearly 30 % of the C. korshinskii seeds germinated at −1.4 MPa at 20 and 25 °C, while no seeds of the other two species did so. Under the same treatments, seedling emergence percentages of C. korshinskii were higher than those of the other two species. The rank order of tolerance to drought and sand burial of the three species is C. korshinskii > C. intermedia > C. microphylla. The amount of precipitation and sand burial depth appear to be the main selective forces responsible for the geographical distribution of these species.

A new scheme for femur shape recovery from volumetric images using deformable models was proposed. First, prior 3D deformable femur models are created as templates using point distribution models technology. Second, active contour models are employed to segment the magnetic resonance imaging (MRI) volumetric images of the tibial and femoral joint and the deformable models are initialized based on the segmentation results. Finally, the objective function is minimized to give the optimal results constraining the surface of shapes.

The variation of different ecosystems on the terrestrial carbon balance is predicted to be large. We investigated a typical arid region with widespread saline/alkaline soils, and evaluated soil respiration of different agricultural and natural ecosystems. Soil respiration for five ecosystems together with soil temperature, soil moisture, soil pH, soil electric conductivity and soil organic carbon content were investigated in the field. Comparing with the natural ecosystems, the mean seasonal soil respiration rates of the agricultural ecosystems were 96%-386% higher and agricultural ecosystems exhibited lower CO(2) absorption by the saline/alkaline soil. Soil temperature and moisture together explained 48%, 86%, 84%, 54% and 54% of the seasonal variations of soil respiration in the five ecosystems, respectively. There was a significant negative relationship between soil respiration and soil electrical conductivity, but a weak correlation between soil respiration and soil pH or soil organic carbon content. Our results showed that soil CO(2) emissions were significantly different among different agricultural and natural ecosystems, although we caution that this was an observational, not manipulative, study. Temperature at the soil surface and electric conductivity were the main driving factors of soil respiration across the five ecosystems. Care should be taken when converting native vegetation into cropland from the point of view of greenhouse gas emissions.

With industrial production and application of oil,oil pollution has become a worldwide and serious environmental problem.Ecological effects of oil pollution on soil,plant individuals,plant community and ecosystem are summed up systematically in this paper.There are many toxicants such as BTEX(benzene,toluene,ethylbenzene,and xylene) and PAHs(polycyclic aromatic hydrocarbons) in oils and petrochemicals.These oil pollutants transfer into the soil-plant system and affect the quality of underground water.Thus,oil pollution affects not only soil-plant system(including its composition,structure,function and service),but also human health through food chain.Oil pollution affects soil water condition,porosity and other physical properties;as well as soil carbon,nutrient and other chemical properties.It influences the composition and diversity of soil microbial community,soil enzymes and other biological properties.In most cases,oils pose oxidative stress to plants.Cell membranes are damaged by penetration of hydrocarbon molecules,leading to the leakage of cell contents.Oils usually reduce photosynthesis rates by destroying chloroplast membranes.Oil pollution often inhibits plant germination,growth,flowering and fruiting.However,low dose of oils may promote the growth of some plants.The effects of oil pollution on plant individuals can be classified into four categories: Promoting,no effect,sublethal and lethal.Correspondingly,plant responds in three ways(adaptation,tolerance and death).Thus,there are three basic patterns in which oil pollution affects plant community and finally reduces its biomass,species diversity and vegetation cover.The combination of the changes of plant community and the alternation of soil environment reduces the productivity,stability and health of ecosystem.Finally,functions and services of ecosystem are decreased by oil pollution.Oil pollutants can be biologically remediated and degraded by microorganisms,plants and mycorrhizae.These biological processes can be enhanced by nutrient addition and aeration.Vegetation indices,red edge effect and other remote sensing technologies are potential methods to monitor ecological effects of oil pollution.Overall,indices of different hierarchical levels in the soil-plant system respond to oil pollutants acutely or chronically.Linking these responses with ecological effects of oil pollution is one of the important and difficult issues in future researches.Therefore,multi-scaled and systematic researches should be carried out,and these researches should integrate indoor controlled experiments,outdoor controlled experiments and field investigations.With these researches,the system of hierarchical indices for ecological effects of oil pollution should be established to quantify the relationships between oil pollutants and indices of ecological effects.Then the ecological effects of oil pollution could be mechanically interpreted with simulations of some models,and the effects of oil pollution on soil-plant system could be comprehensively understood.These efforts will provide theoretical foundation and practical guidelines for ecological risk assessment,remediation and control of oil pollution.