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201.
Yijun Zuo 《Journal of theoretical biology》2010,262(4):576-583
Genomewide association studies (GWAS) are being conducted to unravel the genetic etiology of complex diseases, in which complex epistasis may play an important role. One-stage method in which interactions are tested using all samples at one time may be computationally problematic, may have low power as the number of markers tested increases and may not be cost-efficient. A common two-stage method may be a reasonable and powerful approach for detecting interacting genes using all samples in both two stages. In this study, we introduce an alternative two-stage method, in which some promising markers are selected using a proportion of samples in the first stage and interactions are then tested using the remaining samples in the second stage. This two-stage method is called mixed two-stage method. We then investigate the power of both one-stage method and mixed two-stage method to detect interacting disease loci for a range of two-locus epistatic models in a case-control study design. Our results suggest that mixed two-stage method may be more powerful than one-stage method if we choose about 30% of samples for single-locus tests in the first stage, and identify less than and equal to 1% of markers for follow-up interaction tests. In addition, we compare both two-stage methods and find that our two-stage method will lose power because we only use part of samples in both two stages. 相似文献
202.
Marcos Llope Priscilla Licandro Kung‐Sik Chan Nils Chr. Stenseth 《Global Change Biology》2012,18(1):106-117
Traditionally, marine ecosystem structure was thought to be bottom‐up controlled. In recent years, a number of studies have highlighted the importance of top‐down regulation. Evidence is accumulating that the type of trophic forcing varies temporally and spatially, and an integrated view – considering the interplay of both types of control – is emerging. Correlations between time series spanning several decades of the abundances of adjacent trophic levels are conventionally used to assess the type of control: bottom‐up if positive or top‐down if this is negative. This approach implies averaging periods which might show time‐varying dynamics and therefore can hide part of this temporal variability. Using spatially referenced plankton information extracted from the Continuous Plankton Recorder, this study addresses the potential dynamic character of the trophic structure at the planktonic level in the North Sea by assessing its variation over both temporal and spatial scales. Our results show that until the early‐1970s a bottom‐up control characterized the base of the food web across the whole North Sea, with diatoms having a positive and homogeneous effect on zooplankton filter‐feeders. Afterwards, different regional trophic dynamics were observed, in particular a negative relationship between total phytoplankton and zooplankton was detected off the west coast of Norway and the Skagerrak as opposed to a positive one in the southern reaches. Our results suggest that after the early 1970s diatoms remained the main food source for zooplankton filter‐feeders east of Orkney–Shetland and off Scotland, while in the east, from the Norwegian Trench to the German Bight, filter‐feeders were mainly sustained by dinoflagellates. 相似文献
203.
本文以干旱区植物为研究对象,探讨了自然降水资源的时空分布规律以及降水与固沙植物耗水之间的制约关系。通过扩展经典生态位理论的内涵,用数学抽象的方法定义植物水分生态位适宜度为其水分最适生态位点与现实生态位的贴近度,建立相应的数学模型,对固沙植物生态位适宜度进行了定量分析,并建立了生态位适宜度过程模拟方法。依据实验结果进行了有关计算与数值模拟,所做模拟结果与实际观测结果相吻合。结果表明,柠条与油嵩混播为实验条件下的最佳种植方式,密度为5000株／hm^2时其水分生态位适宜度最高,林木覆盖率也最大。文中进一步讨论了有限降水限制和沙地土壤水分亏缺胁迫下油篙和柠条对水分的竞争行为,混播下的生态位适宜度变化及稳定共存格局形成的机理。该结果为干旱区人工林的营建提供了定量依据。 相似文献
204.
205.
转基因动物在输血医学中的应用 总被引：2，自引：0，他引：2
转基因动物技术是在动物整体水平研究和表达目的基因的生物技术,其基本特点是：分子及细胞水平操作,组织及整体水平表达,是常规分子生物学理论和技术的拓展和延伸,也是现代生物高技术研究和开发的热点之一。本简述了转基因动物在输血医学领域的应用及其发展前景,包括利用转基因动物生物反应器制备人血浆蛋白和人血红蛋白、建立血传播病毒的感染模型和血液相关遗传模型以及转基因动物与输血医学的基础研究等。 相似文献
206.
Yushu TangLei Wang Jianwei JiaYanli Li Wenquan ZhangHongli Wang Ying Sun 《Ecological Engineering》2011,37(11):1638-1646
To clarify the effects of artifical disturbances on the soil microbial respiration (SMR) of existed tidal wetlands, the SMR of three typical areas in Chongming Dongtan and Jiuduansha of the Yangtze River Estuary, China, were evaluated. The causes of the differences in the SMR were also evaluated by analyzing the microbial activity factors and community structure, as well as the physical-chemical characteristics of the different wetland soils. The results showed that the SMR of the existed wetlands in the area of siltation promotion was significantly higher (P < 0.01) than that of the natural area. Different agricultural practices on the inner land also affected the SMR of the tidal wetlands. Overall, the results indicated that the difference in soil microbial characteristics between the artificially disturbed and natural tidal wetlands may be the primary cause of their different SMR. Path analysis indicated that the correlation between soil bacterial diversity and SMR were especially strong. Phylogenetic analysis showed that the bacterial microbial community structure in wetland soil that had been subject to artificial disturbance was changed due to the alteration of the soil physicochemical characteristics, and Pseudomonas sp., Bacillus sp., Uncultured Lactococcus sp. and Streptococcus sp., which have high heterotrophic metabolism or stress tolerance capability, became the dominant bacterial flora in the artificially disturbed wetland soil, ultimately strengthening the SMR. This may be the essential cause of the higher SMR in wetland soils that have been subjected to artificial disturbance, resulting in a low organic carbon accumulation capability. 相似文献
207.
Morgan M. Sparks;Claire E. Schraidt;Xiaoshen Yin;Lisa W. Seeb;Mark R. Christie; 《Molecular ecology》2024,33(20):e17121
Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72—a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation. 相似文献
208.
The Epidemiology Work Group at the Workshop on Future Research for Improving Risk Assessment Methods, Of Mice, Men, and Models, held August 16 to 18, 2000, at Snowmass Village, Aspen, Colorado, concluded that in order to improve the utility of epidemiologic studies for risk assessment, methodologic research is needed in the following areas: (1) aspects of epidemiologic study designs that affect doseresponse estimation; (2) alternative methods for estimating dose in human studies; and (3) refined methods for dose-response modeling for epidemiologic data. Needed research in aspects of epidemiologic study design includes recognition and control of study biases, identification of susceptible subpopulations, choice of exposure metrics, and choice of epidemiologic risk parameters. Much of this research can be done with existing data. Research needed to improve determinants of dose in human studies includes additional individual-level data (e.g., diet, co-morbidity), development of more extensive human data for physiologically based pharmacokinetic (PBPK) dose modeling, tissue registries to increase the availability of tissue for studies of exposure/dose and susceptibility biomarkers, and biomarker data to assess exposures in humans and animals. Research needed on dose-response modeling of human studies includes more widespread application of flexible statistical methods (e.g., general additive models), development of methods to compensate for epidemiologic bias in dose-response models, improved biological models using human data, and evaluation of the benchmark dose using human data. There was consensus among the Work Group that, whereas most prior risk assessments have focused on cancer, there is a growing need for applications to other health outcomes. Developmental and reproductive effects, injuries, respiratory disease, and cardiovascular disease were identified as especially high priorities for research. It was also a consensus view that epidemiologists, industrial hygienists, and other scientists focusing on human data need to play a stronger role throughout the risk assessment process. Finally, the group agreed that there was a need to improve risk communication, particularly on uncertainty inherent in risk assessments that use epidemiologic data. 相似文献
209.
Sébastien Lavergne Wilfried Thuiller James Molina Max Debussche 《Journal of Biogeography》2005,32(5):799-811
Aim Assessing whether environmental and human factors influenced the spatial distribution and the dynamics of regionally rare plant species since the late nineteenth century, and whether these spatial and temporal patterns of rare species occurrences differ according to their chorology (level of endemism and biogeographic affinity). Location An area extending over 6250 km2 in the French Mediterranean Region. Methods We used two botanical surveys achieved in 1886 and in 2001, and considered species rare if occurring in only one or two sites in the study area. Each rare species was assigned to a group of endemism level (restricted endemic, non‐endemic), and of biogeographic affinity (Mediterranean, South/Central European, Mountain, Eurosiberian). A 1 × 1 km grid was applied to the study zone. Generalized linear models were developed to study the spatial distribution and the fate of rare species occurrences (local extinction vs. local persistence between 1886 and 2001), as a function of environmental and human variables. Multivariate analyses were used to test whether the spatial distribution and the fate of rare species occurrences differed according to their chorology. Results In 2001, rare species as a whole tended to occur at higher altitude, in zones dominated by semi‐natural open habitats, and where cultivated area had decreased in the last 30 years. Between 1886 and 2001, rare species were the most prone to local extinction in zones where human population density, cultivated area and livestock density had increased the most. Between 1886 and 2001, rare species had a higher probability of local persistence in zones of high altitude and steep slope, on basic bedrocks and with low cultivated area. Rare species with Mountain and Eurosiberian affinities occurred in marginal habitats in the study region, i.e. on gneiss‐micaschist bedrocks and at high altitudes, whereas Mediterranean and South/Central European rare species occupied more varied environmental conditions. Between 1886 and 2001, Eurosiberian rare species showed high rates of local extinction whereas Mediterranean rare species had a significantly higher probability of local persistence. Restricted endemic species mostly occurred in zones of high slope, low human population density, and where cultivated area had decreased in the last 30 years. Occurrences of restricted endemics remained significantly stable between 1886 and 2001. Main conclusions Environmental and land‐use changes that occurred over the twentieth century in the Mediterranean Basin had significant impacts on the spatial distribution and on the long‐term dynamics of rare species occurrences. Urbanization and recent agriculture intensification, occurring mainly in coastal plains and littoral zones, caused most local extinctions of rare species from 1886 to 2001. Local populations of Eurosiberian species, which reach their range limits in marginal zones of the Mediterranean, also appear to be highly vulnerable. Conversely, most restricted endemic species occur in habitats with harsh topography and low human disturbance and have a higher potential of local persistence. 相似文献
210.
Alexander V. Semenov Jan Dirk van Elsas Debora C. M. Glandorf Menno Schilthuizen Willem F. de Boer 《Ecology and evolution》2013,3(8):2739-2750
To fulfill existing guidelines, applicants that aim to place their genetically modified (GM) insect‐resistant crop plants on the market are required to provide data from field experiments that address the potential impacts of the GM plants on nontarget organisms (NTO's). Such data may be based on varied experimental designs. The recent EFSA guidance document for environmental risk assessment (2010) does not provide clear and structured suggestions that address the statistics of field trials on effects on NTO's. This review examines existing practices in GM plant field testing such as the way of randomization, replication, and pseudoreplication. Emphasis is placed on the importance of design features used for the field trials in which effects on NTO's are assessed. The importance of statistical power and the positive and negative aspects of various statistical models are discussed. Equivalence and difference testing are compared, and the importance of checking the distribution of experimental data is stressed to decide on the selection of the proper statistical model. While for continuous data (e.g., pH and temperature) classical statistical approaches – for example, analysis of variance (ANOVA) – are appropriate, for discontinuous data (counts) only generalized linear models (GLM) are shown to be efficient. There is no golden rule as to which statistical test is the most appropriate for any experimental situation. In particular, in experiments in which block designs are used and covariates play a role GLMs should be used. Generic advice is offered that will help in both the setting up of field testing and the interpretation and data analysis of the data obtained in this testing. The combination of decision trees and a checklist for field trials, which are provided, will help in the interpretation of the statistical analyses of field trials and to assess whether such analyses were correctly applied. 相似文献