DNA barcoding of invasive plants in China: A resource for identifying invasive plants

Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH‐psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra‐ and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH‐psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS + matK performed best and provided 91.03% discriminatory power, followed by ITS2 + matK (85.78%). For identifying unknown individuals, ITS + matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2 + matK (91.67%). Thus, we propose ITS/ITS2 + matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.     

Alien invasive plants in China: risk assessment and spatial patterns

With a wide range of habitats and exploding development of international trade, China is facing escalating risk of the plant invasion. Research on the risk assessment of alien invasive plants may help us manage the invasive with priority, and is imperatively needed in China. However, until now, few studies have been conducted for the risk of alien invasive plants and its spatial patterns in China, especially with a regard to ecosystem conservation and biodiversity protection. In this paper, we assessed the risk of invasive plants and its spatial patterns. We focused on the following basic questions: Which alien invasive plants are the most noxious, and which of them are mild? How are the spatial patterns of alien invasive plants at different risk ranks? In the present study, the risk of 100 major alien invasive plants in China was assessed based on a revised risk assessment system and an extensive consult with literatures. The results indicated that there were 18 species of rank 1st, 29 of rank 2nd, 33 of rank 3rd and 20 of rank 4th. Although, there was high richness of alien invasive plants in South China, most of them were of low risk. By contrast, low richness of alien invasive plants was observed in North China and the regions in high altitude, but most of the invasive were of high risk. Compared with previous studies, our study appears to have delivered credible results and may play an early warning function, and also further our understanding of the risk of invasive plants and its spatial patterns in China, though we acknowledged that the risk assessment may have some potential weakness, and appealed timely and further investigations in future.     

温州外来入侵植物风险评价体系研究——以黑荆为例

以现有生物入侵风险评价体系为基础,根据温州地区的自然环境和外来入侵植物调查结果,建立了区域性较强的"温州外来入侵植物风险评价体系",并以外来植物黑荆(Acacia mearnsii De Wild. )为例对这一评价体系进行了验证.整个评价体系由境内外重视程度、地理分布、入侵途径、传播与繁殖方式、危害性和影响以及防除处理难度6个一级指标和15个二级指标组成,并采用"层次分析法"(analytic hierarchy process,AHP)确定各指标的权重,按不同的权重赋予各指标不同的分值(评价总分为100分),各指标的得分总和即为最终的评价得分(R值).使用该评价体系对黑荆进行风险评价和赋值,结果显示,在温州地区,黑荆的风险评估得分R值为64分,风险程度中等,要加以一定程度的监控管理.温州外来入侵植物风险评价体系具有区域可行性,可以为温州外来入侵植物的科学管理提供依据.     

PCR to predict risk of airborne disease

Plant, animal and human diseases spread by microscopic airborne particles have had major economic and social impacts during history. Special air-sampling devices have been used to collect such particles since the 19th century but it has often been impossible to identify them accurately. Exciting new opportunities to combine air sampling with quantitative PCR to identify and count these particles are reviewed, using crop pathogen examples. These methods can be used to predict the risk of unexpected outbreaks of airborne diseases by identifying increases in pathogen inoculum or genetic changes in pathogen populations that render control ineffective. The predictions can provide guidance to policymakers, health professionals or the agricultural industry for the development of strategies to minimise the risk of severe pandemics.     

Development of a high-throughput yeast two-hybrid screening system to study protein-protein interactions in plants

We have developed a high-throughput yeast two-hybrid screening system (HTP-YTH) that incorporates yeast gap-repair cloning, multiple positive ( ADE2, HIS3, lacZ) and negative ( URA3-based) selection schemes to reduce the incidence of negative and false positive clones, and automation of laboratory procedures to increase throughput. This HTP-YTH system has been applied to the study of protein-protein interactions that are involved in rice defense signal transduction pathways. More than 100 genes involved in plant defense responses were selected from DuPont's rice expressed sequence tag (EST) databases as baits for HTP-YTH screening. Results from YTH screening of eight of these rice genes are presented in this paper. Not only have we identified known protein-protein interactions, but we have also discovered novel interactions, which may ultimately reveal the regulatory network of host defense signal transduction pathways. We have demonstrated that our HTP-YTH method can be used to map protein-protein interaction networks and signal transduction pathways in any system. In combination with other approaches, such efficient YTH screens can help us systemically to study the functions of known and unknown genes in the genomics era.     

深圳市入侵植物区系与风险分布

外来植物入侵现象随着城市化的推进在各地愈演愈烈,严重影响城市的生态系统稳定和社会经济发展。在深圳陆域优势植被普查的基础上开展,对深圳全市的入侵植物分布、来源、入侵途径、风险等进行调查分析,为深圳的入侵植物防治提供技术支撑。基础数据采用高分辨率遥感影像与地面实地观察结合的方法普查得到;并通过文献分析法对植物种类基础数据按研究要求进行筛选、提取、分析;创新性的引入斑块入侵风险计算方法和入侵植物种群风险计算方法,经计算得出深圳市范围内的入侵植物风险分布现状与高风险入侵植物种群。结果表明：(1)参照《中国外来入侵植物名录》标准,深圳市陆域群落优势植物共有入侵植物63科200属258种,且以豆科、菊科、禾本科植物为主;其中36种为林业部门、生态环境部门、农业农村部和海关明确的官方认定且需要严格管控的入侵物种;(2)单种科和少种科占比较高,共占比87.3%,大型科虽然占比仅4.8%,却包含了共计106种,占入侵植物总种数41.1%;单种属在深圳入侵植物区系中占绝对优势,占比83.5%,远高于其他类型之和;中型属中,属种比为1∶6;(3)热带区系属性非常明显,热带分布科共计35科,占总科数的92.1...     

A screening model to predict microalgae biomass growth in photobioreactors and raceway ponds

A microalgae biomass growth model was developed for screening novel strains for their potential to exhibit high biomass productivities under nutrient‐replete conditions in photobioreactors or outdoor ponds. Growth is modeled by first estimating the light attenuation by biomass according to Beer‐Lambert's Law, and then calculating the specific growth rate in discretized culture volume slices that receive declining light intensities due to attenuation. The model uses only two physical and two species‐specific biological input parameters, all of which are relatively easy to determine: incident light intensity, culture depth, as well as the biomass light absorption coefficient and the specific growth rate as a function of light intensity. Roux bottle culture experiments were performed with Nannochloropsis salina at constant temperature (23°C) at six different incident light intensities (10, 25, 50, 100, 250, and 850 µmol/m² s) to determine both the specific growth rate under non‐shading conditions and the biomass light absorption coefficient as a function of light intensity. The model was successful in predicting the biomass growth rate in these Roux bottle batch cultures during the light‐limited linear phase at different incident light intensities. Model predictions were moderately sensitive to minor variations in the values of input parameters. The model was also successful in predicting the growth performance of Chlorella sp. cultured in LED‐lighted 800 L raceway ponds operated in batch mode at constant temperature (30°C) and constant light intensity (1,650 µmol/m² s). Measurements of oxygen concentrations as a function of time demonstrated that following exposure to darkness, it takes at least 5 s for cells to initiate dark respiration. As a result, biomass loss due to dark respiration in the aphotic zone of a culture is unlikely to occur in highly mixed small‐scale photobioreactors where cells move rapidly in and out of the light. By contrast, as supported also by the growth model, biomass loss due to dark respiration occurs in the dark zones of the relatively less well‐mixed pond cultures. In addition to screening novel microalgae strains for high biomass productivities, the model can also be used for optimizing the pond design and operation. Additional research is needed to validate the biomass growth model for other microalgae species and for the more realistic case of fluctuating temperatures and light intensities observed in outdoor pond cultures. Biotechnol. Bioeng. 2013; 110: 1583–1594. © 2012 Wiley Periodicals, Inc.     

Native range climate is insufficient to predict anuran invasive potential

Niche conservatism explains biological invasions worldwide. However, a plethora of ecological processes may lead invasive species to occupy environments that are different from those found within native ranges. Here, we assess the potential invadable areas of  the world’s most pervasive invasive amphibians: the cane toad, Rhinella marina?+?R. horribilis, and the North American bullfrog, Lithobates catesbeianus. The uncontrolled spread of such voracious, large-bodied, and disease-tolerant anurans has been documented to impact native faunas worldwide. To disentangle their invasion-related niche dynamics, we compared the predictive ability and distributional forecasts of ecological niche models calibrated with information from native, invaded and pooled (native?+?invaded) ranges. We found that including occurrences from invaded ranges improved model accuracy for both studied species. Non-native occurrences also accounted for 54% and 61% increase in the total area of potential distribution of the cane toad and bullfrog, respectively. Besides, the latter species occupied locations with climatic conditions that are more extreme than those found within its native range. Our results indicate that the occupancy of environments different from those found in native ranges increases the overall potential distribution of the studied invasive anuran species. Therefore, climate information on native ranges alone is insufficient to explain and anticipate the distributional patterns of invasion of cane toads and bullfrogs, underestimating predictions of potential invadable distribution. Moreover, such an observed expansion of realized niches towards occupancy of climates not found within native ranges also has clear implications for invasion risk assessments based on climate modelling worldwide.

     

A fast-track for invasion: invasive plants promote the performance of an invasive herbivore

With the greater frequency of biological invasions worldwide there is an increased likelihood that exotic species will interact with each other, and such interactions could enhance one another??s invasion potential. Although direct and indirect interactions between exotic species have been well documented for plant-herbivore interactions, the majority of studies have focused on a single interaction and on plant rather than herbivore performance. In this study we investigated whether invasive exotic plants could contribute to the invasion of California by an exotic generalist herbivore (Epiphyas postvittana). We tested this expectation in the greenhouse by monitoring the performance of larval and pupal stages of E. postvittana on six pairs of congeneric invasive and native plants. Larval survivorship and pupal weight of E. postvittana were both greater on the invasive species, and larval development time was shorter on the invasive plant species for two of the plant genera. Our results suggest that prior invasion of exotic plants could function as a catalyst for the subsequent invasion of an exotic insect herbivore, at least in the case where they have shared some history, thereby accelerating the invasion process and expansion of its novel geographic range.     

Heterogeneous response of circumboreal wildfire risk to climate change since the early 1900s

We investigated changes in wildfire risk over the 1901?2002 (ad ) period with an analysis of broad‐scale patterns of July monthly drought code (MDC) variability on 28 forested ecoregions of the North American and Eurasian continents. The MDC is an estimate of the net effect of changes in evapotranspiration and precipitation on cumulative moisture depletion in soils, and is well correlated with annual fire statistics across the circumboreal (explaining 25–61% of the variance in regional area burned). We used linear trend and regime shift analyses to investigate (multi‐) decadal changes in MDC and percentage area affected by drought, and kernel function for analysis of temporal changes in the occurrence rates of extreme drought years. Our analyses did not reveal widespread patterns of linear increases in dryness through time as a response to rising Northern Hemisphere land temperatures. Instead, we found heterogeneous patterns of drought severity changes that were inherent to the nonuniformly distributed impacts of climate change on dryness. Notably, significant trends toward increasing summer moisture in southeastern and southwestern boreal Canada were detected. The diminishing wildfire risk in these regions is coherent with widely reported decreases in area burned since about 1850, as reconstructed by dendrochronological dating of forest stands. Conversely, we found evidence for increasing percentage area affected by extreme droughts in Eurasia (+0.57% per decade; P<0.05) and occurrence rates of extreme drought years in Eurasian taiga (centered principally on the Okhotsk–Manchurian taiga, P=0.07). Although not statistically significant, temporal changes in occurrence rates are sufficiently important spatially to be paid further attention. The absence of a linear trend in MDC severity, in conjunction with the presence of an increase in the occurrence rate of extreme drought years, suggest that fire disturbance regimes in the Eurasian taiga could be shifting toward being increasingly pulse dependent.     

A risk signature-based on metastasis-associated genes to predict survival of patients with osteosarcoma

Osteosarcoma (OS) is the most common primary solid malignant bone tumor, and its metastasis is a prominent cause of high mortality in patients. In this study, a prognosis risk signature was constructed based on metastasis-associated genes. Four microarrays datasets with clinical information were downloaded from Gene Expression Omnibus, and 256 metastasis-associated genes were identified by limma package. Further, a protein-protein interaction network was constructed, and survival analysis was performed using data from the Therapeutically Applicable Research to Generate Effective Treatments data matrix, identifying 19 genes correlated with prognosis. Six genes were selected by the least absolute shrinkage and selection operator regression for multivariate cox analysis. Finally, a three-gene (MYC, CPE, and LY86) risk signature was constructed, and datasets GSE21257 and GSE16091 were used to validate the prediction efficiency of the signature. The survival times of low- and high-risk groups were significantly different in the training set and validation set. Additionally, gene set enrichment analysis revealed that the genes in the signature may affect the cell cycle, gap junctions, and interleukin-6 production. Therefore, the three-gene survival risk signature could potentially predict the prognosis of patients with OS. Further, proteins encoded by CPE and LY86 may provide novel insights into the prediction of OS prognosis and therapeutic targets.     

入侵植物筛选方法在我国口岸防控中的应用建议

入侵植物是生物入侵中数量最多的类群,给全世界造成了重大的经济和环境影响。植物入侵的预测研究是口岸防控工作中的重要技术环节之一。本文介绍了入侵植物筛选方法的概念,简述了与之相关的基础理论、研究情况以及3种植物入侵的预测方法。综合来看,入侵植物筛选方法主要采用植物自身的生物生态学特性作为评估指标来筛选外来植物,能快速可靠地将外来植物评判为严重入侵植物、非入侵植物以及介于二者之间的一般入侵植物,因此该方法能为我国口岸防范外来植物入侵的管理提供基础技术支撑。当前我国入侵植物筛选方法的研究和应用尚处起步阶段,通过本文的简述期望引起相关人员对此问题进行探讨,并为我国口岸入侵植物防控工作提供理论参考。     

Design of forest management planning DSS for wildfire risk reduction

Forest management planning is generally a complicated task. The amount of data, information and knowledge involved in the management process is often overwhelming. Decision support systems can help forest managers make well documented decisions concerning forest management planning. These systems include a wide variety of components, depending on the management goals of the forested land. Although an increased growth of decision support systems in specific domains of forest management planning exists, there is no special design model for the deployment of forest management planning. To this direction, this paper has the following objectives: Firstly, to propose a conceptual design model for developing goal-driven forest management planning decision support systems. Secondly, to apply the design model for a particular case of these systems, the wildfire risk reduction decision support systems. Thirdly, to present the deployment of a wildfire risk reduction decision support system as well as its results for a specific forest area.     

Using MODIS satellite imagery to predict hantavirus risk

Aims Sin Nombre virus (SNV), a strain of hantavirus, causes hantavirus pulmonary syndrome (HPS) in humans, a deadly disease with high mortality rate (> 50%). The primary virus host is the deer mouse, and greater abundance of deer mice has been shown to increase the human risk of HPS. Our aim is to identify and compare vegetation indices and associated time lags for predicting hantavirus risk using remotely sensed imagery. Location Utah, USA. Methods A 5‐year time‐series of moderate‐resolution imaging spectroradiometer (MODIS) satellite imagery and corresponding field data was utilized to compare various vegetation indices that measure productivity with the goal of indirectly estimating mouse abundance and SNV prevalence. Relationships between the vegetation indices and deer mouse density, SNV prevalence and the number of infected deer mice at various time lags were examined to assess which indices and associated time lags might be valuable in predicting SNV outbreaks. Results The results reveal varying levels of positive correlation between the vegetation indices and deer mouse density as well as the number of infected deer mice. Among the vegetation indices, the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI) produced the highest correlations with deer mouse density and the number of infected deer mice using a time lag of 1.0 to 1.3 years for May and June imagery. Main conclusions This study demonstrates the potential for using MODIS time‐series satellite imagery in estimating deer mouse abundance and predicting hantavirus risk. The 1‐year time lag provides a great opportunity to apply satellite imagery to predict upcoming SNV outbreaks, allowing preventive strategies to be adopted. Analysis of different predictive indices and lags could also be valuable in identifying the time windows for data collection for practical uses in monitoring rodent abundance and subsequent disease risk to humans.     

中国外来植物入侵风险评估研究

对外来植物开展入侵风险评估是防止外来植物入侵最经济有效的措施,能够极大的节约外来种管理的经济和时间成本。研究简述了国内外入侵风险评估系统,从外来物种基础信息缺乏、外来植物的适生区分析不完善、风险评估体系构建不客观、对新近外来种的关注度不够4个方面阐述了我国外来植物风险评估存在的主要问题。并针对存在的问题提出了以下建议：（1）构建外来植物基础信息数据库是风险评估的基础,加强外来植物本底资料的调查与考证,并将外来植物表型数据的积累和分析纳入数据库,使得风险评估有据可依。（2）运用生态位模型进行生态风险分析是风险评估的重点,并将人类活动指标纳入预测模型,揭示人类活动对入侵植物分布格局的影响。（3）建立科学的风险评估系统是核心,包括通过选择风险指标和设置权重来提高评估系统的科学性、构建特定区域或特定生态类型的风险评估体系、根据评估对象的生物学与生态学特征建立符合实际要求的评估标准,实行差别化的风险评估等。（4）加强新近外来植物的管理是关键,应定期野外监测新近外来种的种群动态,定期审查风险评估结果,对高风险的新近外来种进行预警研究将为中国外来植物风险评估体系构建提供重要参考,为入侵植物防控措施的制定提供理论依据。     

Noninvasive fluorescent screening of microinjected bovine embryos to predict transgene integration

Most transgenic domestic animals are generated by direct microinjection of DNA fragments into zygote pronuclei. It has generally been assumed that the majority of integration events should occur prior to the first round of chromosomal DNA replication. The aim of this study was to investigate the expression of GFP in bovine preimplantation embryos by using a gfp reporter gene consisting of chicken beta-actin promoter, the CMV-IE enhancer, gfp cDNA (EGFP) (732 bp) and rabbit beta-globin polyadenylation sequences. In five experiments 302 bovine zygotes were injected while 75 served as a control. The fluorescence intensity was detected at 72 and 168 h following fertilization in bovine embryos injected with 3 ng/microl in experiments 1-3, and injected with 5 ng/microl in experiments 4-5. Eight embryos were considered as expressing green fluorescence protein; 2 of them were 100% fluorescent after microinjection of a higher dose of the DNA; one was 75%, two--50%, and three 25% transgenic. The mosaicism was assumed to be at 75%. The results indicated that the fluorescence could be analyzed at any time of bovine embryo development. It was therefore concluded, that chicken beta-actin promoter together with the CMV-IE enhancer would confer a strong expression of the gfp reporter gene in preimplantation bovine embryos. Therefore, using GFP that could be simply detected in live bovine (transgenic) embryos would be very promising in establishing transgenic lines of domestic animals producing in their fluids human therapeutic proteins.