山西省重点保护野生植物资源及区系特征研究

以《国家重点保护野生植物名录(第一批)》和《山西省重点保护野生植物名录(第一批)》为依据,建立山西省重点保护野生植物名录。共记录57种保护植物,隶属于38科45属（其中国家Ⅰ级保护2种,国家Ⅱ级保护6种,省级保护49种）。分析结果得出,山西省重点保护野生植物在全省的分布不集中,零散分布于全省61个县区境内,且绝大多数物种的分布范围很狭窄。山西省重点保护野生植物区系具有复杂多样、起源古老、孑遗植物和单种属多等特点,科、属植物区系成分以温带分布型占优势,同时也有较明显的热带性质,过渡性特征比较明显,有其独特的地理优势和保护价值。本研究旨在对山西省重点保护野生植物资源现状及区系特征进行初步研究,从而为野生植物资源的保护和合理有效地利用提供科学的理论依据与参考。     

松褐天牛产卵刻痕在黑松树干上分布规律的研究

调查和分析了松褐天牛Monochamus alternatusHope的产卵刻槽在寄主植物黑松上的分布情况,结果表明：产卵刻槽分布与寄主胸径和树高有一定的相关关系,黑松树干胸径在9～15 cm之间,树高在4～7 m之间最适合天牛产卵危害,其中在胸径9～13 cm范围内产卵刻槽数量最多,在此范围的寄主受天牛为害最重。天牛在胸径＞17 cm或树高＞7 m时,没有产卵刻槽分布。产卵刻槽集中分布于树干1～2 m位置,3 m以上很少有刻槽分布,同时,天牛产卵多在光线充足的地方,其中南面产卵刻槽数量最多。     

Integrating multi-platform genomic data using hierarchical Bayesian relevance vector machines

Background

Recent advances in genome technologies and the subsequent collection of genomic information at various molecular resolutions hold promise to accelerate the discovery of new therapeutic targets. A critical step in achieving these goals is to develop efficient clinical prediction models that integrate these diverse sources of high-throughput data. This step is challenging due to the presence of high-dimensionality and complex interactions in the data. For predicting relevant clinical outcomes, we propose a flexible statistical machine learning approach that acknowledges and models the interaction between platform-specific measurements through nonlinear kernel machines and borrows information within and between platforms through a hierarchical Bayesian framework. Our model has parameters with direct interpretations in terms of the effects of platforms and data interactions within and across platforms. The parameter estimation algorithm in our model uses a computationally efficient variational Bayes approach that scales well to large high-throughput datasets.

Results

We apply our methods of integrating gene/mRNA expression and microRNA profiles for predicting patient survival times to The Cancer Genome Atlas (TCGA) based glioblastoma multiforme (GBM) dataset. In terms of prediction accuracy, we show that our non-linear and interaction-based integrative methods perform better than linear alternatives and non-integrative methods that do not account for interactions between the platforms. We also find several prognostic mRNAs and microRNAs that are related to tumor invasion and are known to drive tumor metastasis and severe inflammatory response in GBM. In addition, our analysis reveals several interesting mRNA and microRNA interactions that have known implications in the etiology of GBM.

Conclusions

Our approach gains its flexibility and power by modeling the non-linear interaction structures between and within the platforms. Our framework is a useful tool for biomedical researchers, since clinical prediction using multi-platform genomic information is an important step towards personalized treatment of many cancers. We have a freely available software at: http://odin.mdacc.tmc.edu/~vbaladan.

     

Research Symposium—Aberdeen

ABSTRACT

Background: Climate change may increase the risk of biological invasions. However, current knowledge of this interaction is limited.

Aims: We aimed to quantify (1) the effect of climate change on the potential distribution of invasive plant species in Spain, (2) the importance of the area of origin of such species and (3) the vulnerability of different biogeographic provinces to future changes in climatic suitability for invaders.

Methods: We applied six methods of species distribution modelling to assess the variation of climatically suitable areas for 40 alien plants. We developed a Potential Area Change Index and used it as the response variable in modelling for three future emissions scenarios and three global circulation models over three time periods. The area of origin and biogeographic province in Spain were also considered.

Results: We found a highly specific response for each plant species rather than a clear trend for the entire set of species. Predicted climate suitability increased over higher emission scenarios and longer projected time lags. Neotropical species showed the greatest potential climatic range expansion. We detected a strong interaction between the geographic origin of a species and the biogeographic province.

Conclusions: Special attention should be given to the areas where aridification of climate is projected and where introduced neotropical species are likely to expand their range. Future work should develop accurate species-specific approaches that allow the management invasive plant species.     

Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks

The ensemble modeling (EM) approach has shown promise in capturing kinetic and regulatory effects in the modeling of metabolic networks. Efficacy of the EM procedure relies on the identification of model parameterizations that adequately describe all observed metabolic phenotypes upon perturbation. In this study, we propose an optimization-based algorithm for the systematic identification of genetic/enzyme perturbations to maximally reduce the number of models retained in the ensemble after each round of model screening. The key premise here is to design perturbations that will maximally scatter the predicted steady-state fluxes over the ensemble parameterizations. We demonstrate the applicability of this procedure for an Escherichia coli metabolic model of central metabolism by successively identifying single, double, and triple enzyme perturbations that cause the maximum degree of flux separation between models in the ensemble. Results revealed that optimal perturbations are not always located close to reaction(s) whose fluxes are measured, especially when multiple perturbations are considered. In addition, there appears to be a maximum number of simultaneous perturbations beyond which no appreciable increase in the divergence of flux predictions is achieved. Overall, this study provides a systematic way of optimally designing genetic perturbations for populating the ensemble of models with relevant model parameterizations.     

Population structure and morphology of South African deep-water parapagurid hermit crabs

The parapagurid hermit crabs Sympagurus dimorphus (Studer, 1883) and Parapagurus bouvieri (Stebbing, 1910) form dominant components of South African deeper-water benthic invertebrate communities and, as adults, forego the use of “traditional” gastropod shells in favour of symbiotically associated Epizoanthus carcinoecia. A total of 1,122 adult S. dimorphus and 549 adult P. bouvieri derived from demersal research trawl surveys were examined to investigate parameters of population structure, carcinoecia association and morphology. S. dimorphus had a female-biased sex ratio of 1:1.5, and P. bouvieri an equal sex ratio of 1:1. The proportion of males of both species increased with cephalothoracic shield length (CL). The lengths of the major right chelipeds of both S. dimorphus males and females, and P. bouvieri males were positively allometric, and negatively allometric in P. bouvieri females. All P. bouvieri inhabited carcinoecia, while 3.39% (n = 38) of S. dimorphus specimens occupied gastropod shells. There was a positive relationship between S. dimorphus CL and rate of gastropod shell occupation (r² = 0.96). In S. dimorphus, number of zoanthid polyps forming the carcinoecia pseudoshell increased with both total shell volume (R² = 0.73) and colony height (R² = 0.61), but no such relationships were found for P. bouvieri. Euspira napus was the most common original shell around which carcinoecia developed in both S. dimorphus (45.45%) and P. bouvieri (39.00%). We speculate that these hermit species exist along an evolutionary continuum of carcinoecia use. Sympagurus dimorphus retains the ability to occupy both gastropod shells and pseudoshells and, like most other hermit crabs, continue to use shells/carcinoecia as shelters to protect the entire body. In contrast, adult P. bouvieri appear to be totally reliant on carcinoecia, which they use more as a brood pouch covering only the abdomen, rather than as a shelter into which they can fully retract to escape predation.     

台湾和日本拟步甲在纬度分布上的比较研究

台湾和日本处在不同的地理纬度上,同属岛屿海洋性气候,前者地域面积远小于后者,拟步甲的物种多样性却大于后者。为弄清楚这些科学问题,作者采用G-F指数对从台湾到日本不同纬度梯度上的拟步甲多样性分布格局进行了比较分析,得到如下初步结论：(1) G-F指数从大到小依次是：台湾(21°N-25°N)(0．826)>日本(24°N-45°N)(0．824)>日本Ⅱ纬度区(30°N-35°N)(0．792)>日本Ⅰ纬度区(24°N-30°N)(0．765)>日本Ⅲ纬度区(35°N-40°N)(0．761)>日本Ⅳ纬度区(40°N-45°N)(0．603);(2)台湾拟步甲属的多样性(DG)、族的多样性(DF)和G-F指数(DG-F)均最高,分别是4．263、24．464和0．826;(3)各纬度上拟步甲的物种分布情况：台湾(21°N-25°N)(541种)>日本(24°N-45°N)(489种)>日本Ⅰ纬度区(24°N-30°N)(257种)>日本Ⅱ纬度区(30° N-35° N)(231种)>日本Ⅲ纬度区(35° N-40° N)(172种)>日本Ⅳ纬度区(40° N-45° N)(60种)。研究数据显示, G-F指数能较好地反映台湾和日本各地拟步甲族、属的多样性。其物种多样性在纬度上的分布表现为从南向北递减的趋势,并对其基本原因进行分析。作者首次基于台湾和日本两个岛屿拟步甲物种多样性的比较分析,对现有岛屿生物多样性的有关理论提出个人看法,认为岛屿生物地理学的“物种-面积关系理论”中的“岛屿面积越大,物种数量就越多”可能存在一定的局限性,不一定能客观地反映种类众多的现生岛屿昆虫物种多样性的实际情况。     

A framework for estimating the sensitivity of eDNA surveys

Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species‐specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.     

Bioenergy harvest,climate change,and forest carbon in the Oregon Coast Range

Forests provide important ecological, economic, and social services, and recent interest has emerged in the potential for using residue from timber harvest as a source of renewable woody bioenergy. The long‐term consequences of such intensive harvest are unclear, particularly as forests face novel climatic conditions over the next century. We used a simulation model to project the long‐term effects of management and climate change on above‐ and belowground forest carbon storage in a watershed in northwestern Oregon. The multi‐ownership watershed has a diverse range of current management practices, including little‐to‐no harvesting on federal lands, short‐rotation clear‐cutting on industrial land, and a mix of practices on private nonindustrial land. We simulated multiple management scenarios, varying the rate and intensity of harvest, combined with projections of climate change. Our simulations project a wide range of total ecosystem carbon storage with varying harvest rate, ranging from a 45% increase to a 16% decrease in carbon compared to current levels. Increasing the intensity of harvest for bioenergy caused a 2–3% decrease in ecosystem carbon relative to conventional harvest practices. Soil carbon was relatively insensitive to harvest rotation and intensity, and accumulated slowly regardless of harvest regime. Climate change reduced carbon accumulation in soil and detrital pools due to increasing heterotrophic respiration, and had small but variable effects on aboveground live carbon and total ecosystem carbon. Overall, we conclude that current levels of ecosystem carbon storage are maintained in part due to substantial portions of the landscape (federal and some private lands) remaining unharvested or lightly managed. Increasing the intensity of harvest for bioenergy on currently harvested land, however, led to a relatively small reduction in the ability of forests to store carbon. Climate change is unlikely to substantially alter carbon storage in these forests, absent shifts in disturbance regimes.     

Theoretical study of electron transfer process between fullerenes and neurotransmitters; acetylcholine,dopamine, serotonin and epinephrine in nanostructures [neurotransmitters].C<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> complexes

Neurotransmitters are the compounds which allow the transmission of signals from one neuron to the next across synapses. They are the brain chemicals that communicate information throughout brain and body. Fullerenes are a family of carbonallotropes, molecules composed entirely of carbon, that take the forms of spheres, ellipsoids, and cylinders. Various empty carbon fullerenes (C_n) with different carbon atoms have been obtained and investigated. Topological indices have been successfully used to construct effective and useful mathematical methods to establish clear relationships between structural data and the physical properties of these materials. In this study, the number of carbon atoms in the fullerenes was used as an index to establish a relationship between the structures of neurotransmitters (NTs) acetylcholine (AC) 1, dopamine (DP) 2, serotonin (SE) 3, and epinephrine (EP) 4 as the well-known redox systems and fullerenes C_n (n = 60, 70, 76, 82, and 86) which create [NT].C_n; A-1 to A-5 up to D-1 to D-5. The relationship between the number of carbon atoms and the free energy of electron transfer (ΔG_et(n); n = 1–4) is assessed using the Rehm-Weller equation for A-1 to A-5 up to D-1 to D-5 supramolecular [NT].C_n complexes. The calculations are presented for the four reduction potentials (^Red.E₁ to ^Red.E₄) of fullerenes C_n. The results were used to calculate the four free energy values of electron transfer (ΔG_et(1) to ΔG_et(4)) of the supramolecular complexes A-1 to A-8 up to D-1 to D-8 for fullerenes C₆₀ to C₁₂₀. The first to fourth free activation energy values of electron transfer and the maximum wavelength of the electron transfers, ΔG^#_et(n) and λ_et (n = 1–4), respectively, were also calculated in this study for A-1 to A-8 up to D-1 to D-8 in accordance with the Marcus theory.