Ecological perspectives on the sequenced genome collection

Our complete genome collection is one of our most valuable biological resources. A key challenge for the future is the interpretation of these genomes from an ecological perspective. In this review, we discuss current work at this increasingly important interface. In particular, we review ongoing work aimed at developing high quality data sets that combine ecological, environmental, evolutionary and genomic information. Such data will help to identify biases in the sequence collection and facilitate future discoveries about the nature of ecological adaptation at the genome level. These efforts will be greatly enhanced by the contributions of ecologists.     

Reappraisal of the ill-defined Liassic pteridosperm Dichopteris using an ultrastructural approach

This review of the genus Dichopteris De Zigno is based on the original fossil specimens collected from the Lower Jurassic of the Grey Limestones of Veneto (Northern Italy). The cuticular diagnosis of the genus is emended and only Dichopteris visianica De Zigno is retained within the genus. In addition, transverse and longitudinal sections of cuticles examined using a transmission electron microscope (TEM) indicate close similarities between D. visianica and other pteridosperm cuticles, especially the occurrence of granules arranged in areas of different densities in the epidermal cells and stomatal apparatus. Moreover, the dichotomy and the impressive size of the frond of D. visianica imply a specific architecture with a typical arrangement of the pinnae and pinnules. They preclude an herbaceous habit for the plant. Finally, architectural, microstructural and ultrastructural observations are consistent with palaeoclimatic and palaeoenvironmental data, and most probably support an understorey habit for D. visianica .  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 149 , 313–332.     

Chromosome Rearrangement Breakpoint Clustering: The Role of Clonal Selection

Chromosome rearrangements may result in fusion genes that encode chimeric proteins. The break-points of many such rearrangements cluster in definite genomic regions. In addition, many breakpoint clusters contain specific genomic elements, such as topoisomerase II consensus sites, nuclear matrix attachment sites, and various nucleotide sequences capable of assuming noncanonical secondary structure. Studies on breakpoint location are reviewed in terms of the available data on chromatin structure. In addition, the relationship between the location of breakpoints and the domain organization of the respective proteins, which has not been dealt with in published studies, is analyzed. The possible mechanisms of chromosome rearrangements are discussed.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 355–363.Original Russian Text Copyright © 2005 by Umanskaya, Bystritskiy, Razin.     

树木高生长限制的几个假说

树木生长到一定年龄后高生长停滞,对这一现象的解释存在很多争议.成熟假说认为树木顶端分生组织分裂活性下降导致树木高生长减慢.营养限制假说认为土壤中营养元素(特别是氮素)在植物活体或枯落物中积累使土壤中可利用的养分含量降低,细根生物量增加和叶片光合能力下降导致了地上部分生长的减缓.呼吸假说认为边材呼吸消耗随个体发育的增加使投入到高生长的碳减少.水力限制假说认为水分运输阻力随高度增加而增加导致了叶片总光合碳同化下降,分配到高生长的生物量减少.树木发展假说认为植物用多种调节机制克服随个体发育增加的水力阻力,包括叶片结构和生理特征的变化,叶/边材面积比降低,边材渗透性和树干储水能力的增加等.水力限制假说得到了较多的关注,对不同高度树木的叶比导率、光合特征和树干生长量等测定结果支持这一假说.但对这一假说也存在很多的争议,主要表现在:水力阻力是否确实随高度的增加而增加,水力阻力的分布,补偿机制的作用和生物量分配转变等.本文综述了树木高生长限制的4个假说以及争论的焦点,并总结了目前研究的热点问题和今后的研究方向.     

Effects of species and soil‐nitrogen availability on root system architecture traits – study on a set of weed and crop species

Better managing crop : weed competition in cropping systems while reducing both nitrogen and herbicide inputs is a real challenge that requires a better understanding of crop and weed root architecture in relation to soil‐nitrogen availability. An original approach was used which considered the parameters of a simulation model of root architecture as traits to analyse (a) the interspecific diversity of root system architecture, and (b) its response to soil‐nitrogen availability. Two greenhouse experiments were conducted using three crop and nine weed species grown at two contrasted concentrations of soil‐nitrogen availability. Plant traits were measured to characterise both overall plant growth and root architecture, with a focus on primary root emergence, root elongation and branching. The studied root traits varied among species (from a twofold to a fourfold factor, depending on the trait), validating their use as indicators to analyse the interspecific variability of root architecture. The largest interspecies differences were for two traits: ‘maximal apical root diameter’ and ‘interbranch distance’ (distance between two successive laterals on the same root). Conversely, most of the studied root traits varied little with soil‐nitrogen availability (from no variation to a 1.1‐fold factor, depending on the trait) even though soil‐nitrogen availability varied with a 17‐fold factor and impacted the overall shoot and root biomass. So, the root traits used in this article are stable whatever soil‐nitrogen availability. As they reflect processes underlying root system architecture, this low effect of nitrogen suggests that the rules governing root architecture are little affected by plant nitrogen status and soil‐nitrogen availability. We propose that the determinants of differences in root system architecture between soils with contrasted nitrogen availability mainly originate from differences in the amount of carbon allocated to and within the root system. Characterising each plant species by a combination of root traits gave insights regarding the potential species competitive ability for soil resources in agroecosystems.     

The importance of shore height and host identity for amphipod assemblages

The spatial distribution of organisms associated with marine intertidal macroalgae may be a direct result of their tolerance to air exposure or an indirect consequence of the distribution of their host. We compared amphipod assemblages from five intertidal macroalgae to investigate their relationship with algal identity. To test the effect of height regardless of algal characteristics, we transplanted coralline algal turfs to three different levels within the intertidal zone and compared amphipod assemblages after 1 and 14 days. Interstitial volume was positively correlated to the abundance of amphipods, suggesting that this attribute may correspond better to the potential space for their occupation when compared to algal biomass, thallus volume or the ratio between thallus and interstitial volume. Algal level determined the structure of the amphipod assemblages. Upper-level (Acanthophora spicifera and Caulerpa racemosa) and intermediate-level (coralline) algae host similar amphipod assemblages dominated by Apohyale media, but different from lower-level algae (Padina gymnospora and Sargassum cymosum), which were dominated by Hyale niger. Ten of the 15 amphipod species reported from natural communities were found in the transplanted plots. Distinct pools of amphipod species colonized coralline transplants at upper and lower levels after 1 day. However, regardless of the position on the shore, transplanted coralline turfs supported similar assemblages after 14 days, indicating that algal identity is also important for species assemblages. Our results suggest that both height on the shore and host identity combine to determine the vertical structure of amphipod assemblages in the rocky intertidal.     

山西毛榛植物构型特征分析

以山西省中条山大河林场、太岳山绵山林场、兴唐寺林场和七里峪林场、五台山金岗库林场、恒山王庄堡林场的毛榛（Corylus mandshurica Maxim.）为研究对象,采用样方调查方法,系统研究了毛榛在不同生境中的构型和分形维数特征。结果显示,大河林场毛榛的总体分枝率和枝径比（RBD_2：1、RBD_3：2）均大于其它地区,逐步分枝率（SBR_1：2、SBR_2：3）与总体分枝率呈现出相反的趋势,五台山金岗库林场毛榛的逐步分枝率最大;山西省各研究地毛榛的分枝角度差异显著,北部地区从1级到3级有减小的趋势,金岗库林场的毛榛1级分枝角度最大;分枝长度也呈现出从1级到3级逐渐减小的趋势,其各级分枝长度排序为：金岗库林场 > 王庄堡林场 > 七里峪林场 > 兴唐寺林场 > 绵山林场 > 大河林场;从分形维数来看,金岗库林场毛榛的树冠分维数和分枝分维数均为最大;各研究地毛榛的叶面积和地上生物量从北到南均表现为逐渐减小;金岗库林场毛榛叶面积的平均值、叶生物量和枝生物量均最大。研究结果表明6个研究区中金岗库林场的毛榛长势最好,该地的气候条件最适宜毛榛生长。     

硫化氢对淹水平邑甜茶根系形态构型、叶片活性氧和光合特性的影响

以盆栽平邑甜茶为试材,分别将盆浸没于5种浓度硫化氢(H₂S)释放剂硫氢化钠(NaHS;0、0.02、0.05、0.1、0.2 mmol·L^-1)水溶液,以及添加有次牛磺酸(HT;H₂S清除剂)的NaHS水溶液中,10 d后调查根系形态构型、叶片活性氧生成和光合气体交换参数以及植株生长的变化.结果表明: 在淹水处理液中加入0.02～0.1 mmol·L^-1 NaHS,能增加土壤淹水时根系总长度、表面积、体积、直径、根尖数、分形维数、一级侧根数量和根系活力,降低叶片超氧阴离子(O₂^-·)生成速率和过氧化氢(H₂O₂)含量,提高叶片光合速率(P_n)、蒸腾速率(T_r)、气孔导度(g_s)、水分利用效率(WUE)和表观CO₂利用效率(CUE),还提高幼苗株高和植株生物量,其中NaHS在浓度0.1 mmol·L^-1 时作用效果最显著;当NaHS施用浓度达到0.2 mmol·L^-1或在0.1 mmol·L^-1 NaHS中加施次牛磺酸时,上述指标均降回到单纯淹水时的水平.这说明添加适量H₂S能够有效缓解土壤淹水对平邑甜茶根系生长的抑制,可以通过减少活性氧产生以及提高CUE,从而减轻淹水胁迫对叶片光合性能和植株生长的不利影响.