基于结构方程模型的吴起县农业生态经济系统耦合关系

基于2008年吴起县农户调查资料,利用结构方程模型对吴起县农业生态经济系统耦合关系进行了分析.结果表明：具有相关关系的农业资源和产业态势对系统耦合有一定影响,其影响系数分别为0.14和1.00;农业资源与产业态势之间的相关系数为-0.11,说明吴起县的产业发展并非建立在对农业资源有效利用基础之上,农业资源对经济效益的变化没有直接作用;产业的发展主要建立在对农业资源之外的能量和物质的开发利用上,导致产业态势对经济效益的直接路径系数为-2.95,总的路径系数仅为0.23.从农业生态系统与经济系统的关系及其耦合的角度看,目前研究区农业系统建立在不稳定的、较少依赖于本系统资源的耦合态势下,即在农业生态经济系统良性耦合机制的建立与形成过程中潜伏了较大危机.为此,需要提高牧草等农业资源的利用率,发展林草及其相关产业.     

中高纬度地区TRMM卫星降雨数据的精度评价

卫星降雨产品在降雨空间格局分析中扮演着重要角色,其中TRMM 3B42（3B42）是重要的产品之一,具有适宜的空间和时间尺度,已成为生态、气候、水文模型的重要驱动因子.当前对3B42 V7新版本数据的精度和误差认识仍然有限,尤其缺少中高纬度地区的数据精度评价研究,制约其在生态、气候和水文等领域的应用.本文基于内蒙古自治区1998—2012年3B42 V7产品和53个气象站点数据,评估其在中高纬度地区的精度,揭示了各精度评价指标的空间分布特征及其影响因子.总体精度评价结果表明： 3B42在年、月、日尺度上均高估降雨量,且误差随时间尺度增大而增加,日降雨量的平均误差和平均绝对误差分别为-0.06和0.88 mm;降雨事件侦测能力表现良好,公正预兆评分达到0.23,但对降雨事件总频率存在微弱高估.数据精度受海拔和多年平均降雨量影响,随海拔升高,降雨绝对误差减小,降雨事件探测能力减弱,多年平均降雨量对数据精度的影响则相反.     

Standard survey designs drive bias in the mapping of upland swamp communities

Vegetation maps are critical biodiversity planning instruments, but the classification of vegetation for mapping can be strongly biased by survey design. Standardization of survey design across different vegetation types is therefore increasingly recommended for vegetation mapping programs. However, some vegetation types have complex small‐scale vegetation patterns that are important in characterizing these vegetation types, and standard designs will often not capture these patterns. The objective of this paper was to investigate the magnitude of potential map bias that results from survey design standardization and recommend approaches to deal with this bias. We surveyed upland swamps of the Greater Blue Mountains World Heritage Area Australia using two contrasting survey designs, including the standard 400 m² single quadrat design recommended and used by authorities. We then derived a classification for these swamps and tested the effect of survey design on this classification, species richness and the type of species detected (obligate or facultative swamp species). Species richness and species type were not significantly different among survey techniques. However, more than 40% of swamps clustered differently among survey designs. Thus, one of the 10 derived communities (which is floristically consistent with a previously mapped endangered community) was indistinct, and some individual swamps misclassified using the standard survey design. An effect of landscape position on swamp floristic patterns and a significant trend for high similarity scores among swamps surveyed with multiple small quadrats compared to the standard survey design was also determined. Australian upland swamps are classified at the global scale as shrub‐dominated wetlands, and complex floristic patterns have been recorded in shrub‐dominated wetlands in both northern and southern hemispheres. We therefore advocate either multiple survey designs or different survey standards for upland swamp communities and other vegetation types that have complex floristic patterns at small scales.     

Testing for effects of climate change on competitive relationships and coexistence between two bird species

Climate change is expected to have profound ecological effects, yet shifts in competitive abilities among species are rarely studied in this context. Blue tits (Cyanistes caeruleus) and great tits (Parus major) compete for food and roosting sites, yet coexist across much of their range. Climate change might thus change the competitive relationships and coexistence between these two species. Analysing four of the highest-quality, long-term datasets available on these species across Europe, we extend the textbook example of coexistence between competing species to include the dynamic effects of long-term climate variation. Using threshold time-series statistical modelling, we demonstrate that long-term climate variation affects species demography through different influences on density-dependent and density-independent processes. The competitive interaction between blue tits and great tits has shifted in one of the studied sites, creating conditions that alter the relative equilibrium densities between the two species, potentially disrupting long-term coexistence. Our analyses show that long-term climate change can, but does not always, generate local differences in the equilibrium conditions of spatially structured species assemblages. We demonstrate how long-term data can be used to better understand whether (and how), for instance, climate change might change the relationships between coexisting species. However, the studied populations are rather robust against competitive exclusion.     

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it is not clear how many biological replicates are needed to ensure valid biological interpretation of the results or which statistical tools are best for analyzing the data. An RNA-seq experiment with 48 biological replicates in each of two conditions was performed to answer these questions and provide guidelines for experimental design. With three biological replicates, nine of the 11 tools evaluated found only 20%–40% of the significantly differentially expressed (SDE) genes identified with the full set of 42 clean replicates. This rises to >85% for the subset of SDE genes changing in expression by more than fourfold. To achieve >85% for all SDE genes regardless of fold change requires more than 20 biological replicates. The same nine tools successfully control their false discovery rate at ≲5% for all numbers of replicates, while the remaining two tools fail to control their FDR adequately, particularly for low numbers of replicates. For future RNA-seq experiments, these results suggest that at least six biological replicates should be used, rising to at least 12 when it is important to identify SDE genes for all fold changes. If fewer than 12 replicates are used, a superior combination of true positive and false positive performances makes edgeR and DESeq2 the leading tools. For higher replicate numbers, minimizing false positives is more important and DESeq marginally outperforms the other tools.     

Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores

We compared the exon/intron organization of vertebrate genes belonging to different isochore classes, as predicted by their GC content at third codon position. Two main features have emerged from the analysis of sequences published in GenBank: (1) genes coding for long proteins (i.e., 500 aa) are almost two times more frequent in GC-poor than in GC-rich isochores; (2) intervening sequences (=sum of introns) are on average three times longer in GC-poor than in GC-rich isochores. These patterns are observed among human, mouse, rat, cow, and even chicken genes and are therefore likely to be common to all warm-blooded vertebrates. Analysis of Xenopus sequences suggests that the same patterns exist in cold-blooded vertebrates. It could be argued that such results do not reflect the reality because sequence databases are not representative of entire genomes. However, analysis of biases in GenBank revealed that the observed discrepancies between GC-rich and GC-poor isochores are not artifactual, and are probably largely underestimated. We investigated the distribution of microsatellites and interspersed repeats in introns of human and mouse genes from different isochores. This analysis confirmed previous studies showing that Ll repeats are almost absent from GC-rich isochores. Microsatellites and SINES (Alu, B1, B2) are found at roughly equal frequencies in introns from all isochore classes. Globally, the presence of repeated sequences does not account for the increased intron length in GC-poor isochores. The relationships between gene structure and global genome organization and evolution are discussed.     

Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests

Species pairs that differ primarily in characters involved in mating interactions and are largely sympatric raise intriguing questions about the mode of speciation. When species divergence is relatively recent, the footprint of the demographic history during speciation might be preserved and used to reconstruct the biogeography of species divergence. In this study, patterns of genetic variation were examined throughout the geographical range of two cryptic sister taxa of field crickets, Gryllus texensis and G. rubens; mitochondrial cytochrome oxidase I (COI) was sequenced in 365 individuals sampled from 48 localities. Despite significant molecular divergence between the species, they were not reciprocally monophyletic. We devised several analyses to statistically explore what historical processes might have given rise to this genealogical structure. The analyses indicated that the biogeographical pattern of genetic variation does not support a model of recent gene flow between species. Instead, coalescent simulations suggested that the genealogical structure within G. texensis, namely a deep split between two geographically overlapping clades, reflects historical substructure within G. texensis. Additional tests that consider the concentration of G. rubens haplotypes in one of the two G. texensis genetic clusters suggest a model of speciation in which G. rubens was derived from one lineage of a geographically subdivided ancestor. These results indicate that, despite the contemporary sympatry of G. texensis and G. rubens, the data are indicative of an peripatric origin in which G. rubens was derived from one of the two historical partitions in the species currently recognized as G. texensis. This proposed model of species divergence suggests how the interplay of geography and selection may give rise to new species, although this requires testing with multilocus data. Specifically, the model highlights how that geographical partitioning of ancestral variation in the past may augment the selectively driven divergence of characters involved in the reproductive isolation of the species today.     

Synonymous codon usage bias and overexpression of a synthetic gene encoding Interferon α2b in yeast

To achieve higher level expression of Interferon α2b (IFN-α2b) in methylotrophic yeast (Pichia pastoris), a cDNA fragment coding for the mature IFN-α2b was designed and synthesized based on the synonymous codon bias of P. pastoris and optimized G+C content. The synthetic IFN-α2b was inserted into the secreted expression vector pPICZαA, and then integrated into P. pastoris GS115 genome by electroporation. Multi-copy integrants in the Mut⁺ recombinant P. pastoris strain were screened by high concentrations of Zeocin. 120 hours culturing allowed expression of the IFN-α2b transformant up to 810 mg/L as detected by SDS-PAGE and quantitative methods. In addition, Western blot analysis showed that the recombinant proteins had immunogenicity. The significant antiviral activity of the recombinant IFN-α2b protein was verified by WISH/ VSV system, which was 3.3×10⁵ IU/mL. Foundation items: The National ‘973’ Basic Research Program (2002CB111302); The National Natural Science Foundation of China (30370807)     

Impact of mate availability, population size, and spatial aggregation of morphs on sexual reproduction in a distylous, aquatic plant

In distylous, self-incompatible plants, clonal propagation, unbalanced floral morph frequencies, and reduced population size can interfere with the functioning of distyly by compromising legitimate intermorph pollinations, resulting in reduced reproductive output. Here, we examined the mating system and the impact of mate availability, population size, and spatial aggregation of morphs on reproductive output in the distylous, clonal, aquatic plant Hottonia palustris. Controlled pollinations under greenhouse conditions detected no spontaneous selfing without the action of a pollen vector (autonomous autogamy) and demonstrated very low fruit and seed development after self-pollination. Intermorph (legitimate) crossings resulted in high reproductive output in both floral morphs (long- and short-styled individuals), whereas intramorph (illegitimate) crossings decreased fruit and seed development by more than 50%, indicating that the species has partial intramorph-incompatibility. In natural populations, small population size and increasing deviation of floral morph frequencies negatively affected reproductive outcome. Individuals of the majority morph type developed significantly fewer fruit and seeds than individuals of the minority morph type. This rapid decline in fecundity was symmetrical, indicating that regardless of which morph was in the majority, the same patterns of negative frequency-dependent mating occurred. Increasing spatial isolation between compatible morphs significantly reduced fruit and seed set in both morphs similarly. This study provides clear indications of frequency- and context-dependent mating in natural populations of a distylous plant species.     

Simplified method to obtain enhanced expression of tau protein from E. coli and one-step purification by direct boiling

Tau is an intrinsically disordered protein responsible for maintaining the structure and stability of axonal microtubules. However, in certain disease conditions including Alzheimer’s disease, tau protein may undergo biochemical and structural changes to form intracellular aggregates. Since tau is a proline- and arginine-rich eukaryotic protein, heterologous expression in Escherichia coli often results in poor yield and has been a major technical challenge. In the current work, we have improved the expressed yield of tau by overcoming codon bias problem and established a simplified protocol for efficient extraction. The reported method has two distinct features: (i) enhanced tau expression (upto eightfold) by supplementing deficient tRNAs that aid in rapid translation and (ii) direct boiling of expressed E. coli cells to extract tau with no separate cell lysis step. We further demonstrate that tau extracted by the direct boiling method is similar to tau purified by size-exclusion chromatography exhibiting similar structural and biophysical characteristics including aggregation propensity. Since morphologies and in vitro toxicity of fibrillar tau aggregates were also similar, tau extracted by the one-step direct boiling method can be used for tau aggregation assays without any additional purification.