普定喀斯特次生林木本植物叶生活型比例和谱系多样性的驱动因素

为探讨喀斯特森林落叶阔叶植物(DBL)与常绿阔叶植物(EBL)比例和生物多样性差异及其驱动因素，该研究以贵州省普定县43个喀斯特次生林样地作为研究对象，采用广义线性回归模型、模型选择和Mantel检验的多元回归方法，分析地理距离、环境(包括地形和基岩类型)和人类活动等因素对样地内落叶阔叶植物和常绿阔叶植物所占比例以及谱系多样性的影响。结果表明：(1)普定喀斯特次生林样地内落叶阔叶植物与常绿阔叶植物虽在物种丰富度和个体多度上总体相当，但样地间差异较大；样地落叶与常绿阔叶植物谱系alpha多样性(即SES.MPD)无明显差异，但落叶阔叶植物谱系beta多样性(即SES.betaMPD)明显小于常绿阔叶植物。(2)落叶阔叶植物丰富度占比和相对多度随基岩类型改变而变化，均表现为泥灰岩森林高于石灰岩森林，而落叶阔叶植物丰富度占比随人类活动增强而上升。(3)样地落叶阔叶植物谱系alpha多样性随人类活动增强而升高，而常绿阔叶植物谱系alpha多样性受环境和人类活动等因素的作用不明显；落叶阔叶植物和常绿阔叶植物谱系beta多样性受不同因素调节，前者随基岩类型和人类活动等因素变化而升高，后者则随地理距...     

Homology‐dependent repair is involved in 45S rDNA loss in plant CAF‐1 mutants

Arabidopsis thaliana mutants in FAS1 and FAS2 subunits of chromatin assembly factor 1 (CAF1) show progressive loss of 45S rDNA copies and telomeres. We hypothesized that homology‐dependent DNA damage repair (HDR) may contribute to the loss of these repeats in fas mutants. To test this, we generated double mutants by crossing fas mutants with knock‐out mutants in RAD51B, one of the Rad51 paralogs of A. thaliana. Our results show that the absence of RAD51B decreases the rate of rDNA loss, confirming the implication of RAD51B‐dependent recombination in rDNA loss in the CAF1 mutants. Interestingly, this effect is not observed for telomeric repeat loss, which thus differs from that acting in rDNA loss. Involvement of DNA damage repair in rDNA dynamics in fas mutants is further supported by accumulation of double‐stranded breaks (measured as γ‐H2AX foci) in 45S rDNA. Occurrence of the foci is not specific for S‐phase, and is ATM‐independent. While the foci in fas mutants occur both in the transcribed (intranucleolar) and non‐transcribed (nucleoplasmic) fraction of rDNA, double fas rad51b mutants show a specific increase in the number of the intranucleolar foci. These results suggest that the repair of double‐stranded breaks present in the transcribed rDNA region is RAD51B dependent and that this contributes to rDNA repeat loss in fas mutants, presumably via the single‐stranded annealing recombination pathway. Our results also highlight the importance of proper chromatin assembly in the maintenance of genome stability.     

蔓地亚红豆杉3′-N-去苯甲酰-2-脱氧紫杉醇苯甲酰转移酶基因的克隆与序列分析

3′-N-去苯甲酰-2-脱氧紫杉醇苯甲酰转移酶(DBTNBT)是催化紫杉醇生物合成最后一步反应所需要的酶,负责将带有不完全侧链的紫杉醇前体催化形成紫杉醇。利用蔓地亚红豆杉的总DNA和总RNA为模板,采用PCR和RT-PCR技术克隆出DBTNBT基因的DNA序列和cDNA序列,测序结果显示长度分别为1465bp和1362bp,编码438个氨基酸的多肽。同源性比较分析结果表明,其碱基序列与已经报道的蔓地亚红豆杉的DBTNBT基因的一致性为99%,其氨基酸序列与已经报道的蔓地亚红豆杉的DBTNBT氨基酸序列的一致性为96%。DNA序列和cDNA序列比对发现该基因含有1个内含子。利用SWISS-PROT、DNAMAN等生物信息学工具对其蛋白序列进行了分析,为利用基因工程的方法生产紫杉醇或其前体物质提供了分子基础。     

两种滨藜甜菜碱醛脱氢酶基因的克隆及序列分析

甜菜碱醛脱氢酶(Betaine aldehyde dehydrogenase,BADH)对非生物胁迫下植物渗透调节物质的合成和积累具有重要作用。分别从异苞滨藜和鞑靼滨藜两种盐生植物中分离到了BADH基因。序列分析表明,BADH全长均为1 507bp,编码501个氨基酸,两种BADH序列具有较高的相似性。甜菜碱醛脱氢酶的克隆为植物的基因转化及其功能分析奠定了基础。     

Fragment-HMM: a new approach to protein structure prediction

We designed a simple position-specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly, clustering, target selection, refinement, and consensus, all in one process. Our initial implementation of this theory converges to within 6 A of the native structures for 100% of decoys on all six standard benchmark proteins used in ROSETTA (discussed by Simons and colleagues in a recent paper), which achieved only 14%-94% for the same data. The qualities of the best decoys and the final decoys our theory converges to are also notably better.     

Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11?kb), single molecule,real-time sequencing

The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.     

Short-Term Temporal Effects on Community Structure of Lepidoptera in Restored and Remnant Tallgrass Prairies

Understanding the degree to which species assemblages naturally vary over time will be critically important when assessing whether direct management effects or contingency is responsible for species gain or loss. In this study, we tested three predictions related to short‐term variation in prairie moth communities: (1) communities would only exhibit significant temporal variation in newly restored sites (1–3 years old); (2) prairie size and age would positively influence community reassembly, with larger, older restorations sampling a greater proportion of the regional species pool; and (3) older restorations (7–10 years old) would have yet to converge on the community composition of prairie remnants. Moths were sampled from 13 Tallgrass prairie restorations and remnants in central Iowa in 2004–2005. Repeated measures analysis of variance revealed significant effects of sampling year on moth species richness and abundance as well as on the richness of two functional groups, but difference among prairie types was only observed in 2005. Rarefaction analysis revealed that older restorations and prairie remnants supported higher species richness compared to recently planted sites, and nonmetric, multidimensional scaling ordination indicated that restorations older than 7 years were clearly converging on the species composition of remnants. These results suggest that moth communities in restorations and remnants are highly variable in time but that as restorations age, they appear to reaccumulate moth species found in prairie remnants. The long‐term persistence of a particular species assemblage within a given site, however, might be a difficult endpoint to attain in central Iowa prairies because of significant annual variation in species occurrence.     

The partitioning of diversity: showing Theseus a way out of the labyrinth

A methodology for partitioning of biodiversity into α, β and γ components has long been debated, resulting in different mathematical frameworks. Recently, use of the Rao quadratic entropy index has been advocated since it allows comparison of various facets of diversity (e.g. taxonomic, phylogenetic and functional) within the same mathematical framework. However, if not well implemented, the Rao index can easily yield biologically meaningless results and lead into a mathematical labyrinth. As a practical guideline for ecologists, we present a critical synthesis of diverging implementations of the index in the recent literature and a new extension of the index for measuring β‐diversity. First, we detail correct computation of the index that needs to be applied in order not to obtain negative β‐diversity values, which are ecologically unacceptable, and elucidate the main approaches to calculate the Rao quadratic entropy at different spatial scales. Then, we emphasize that, similar to other entropy measures, the Rao index often produces lower‐than‐expected β‐diversity values. To solve this, we extend a correction based on equivalent numbers, as proposed by Jost (2007), to the Rao index. We further show that this correction can be applied to additive partitioning of diversity and not only its multiplicative form. These developments around the Rao index open up an exciting avenue to develop an estimator of turnover diversity across different environmental and temporal scales, allowing meaningful comparisons of partitioning across species, phylogenetic and functional diversities within the same mathematical framework. We also propose a set of R functions, based on existing developments, which perform different key computations to apply this framework in biodiversity science.