Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases

Eukaryotes and archaea both possess multiple genes coding for family B DNA polymerases. In animals and fungi, three family B DNA polymerases, alpha, delta, and epsilon, are responsible for replication of nuclear DNA. We used a PCR-based approach to amplify and sequence phylogenetically conserved regions of these three DNA polymerases from Giardia intestinalis and Trichomonas vaginalis, representatives of early-diverging eukaryotic lineages. Phylogenetic analysis of eukaryotic and archaeal paralogs suggests that the gene duplications that gave rise to the three replicative paralogs occurred before the divergence of the earliest eukaryotic lineages, and that all eukaryotes are likely to possess these paralogs. One eukaryotic paralog, epsilon, consistently branches within archaeal sequences to the exclusion of other eukaryotic paralogs, suggesting that an epsilon-like family B DNA polymerase was ancestral to both archaea and eukaryotes. Because crenarchaeote and euryarchaeote paralogs do not form monophyletic groups in phylogenetic analysis, it is possible that archaeal family B paralogs themselves evolved by a series of gene duplications independent of the gene duplications that gave rise to eukaryotic paralogs.      

Widespread and ancient distribution of a noncanonical genetic code in diplomonads

Recently, a group of diplomonads has been found to use a genetic code in which TAA and TAG encode glutamine rather than termination. To survey the distribution of this characteristic in diplomonads, we sought to identify TAA and TAG codons at positions where glutamine is expected in genes for alpha-tubulin, elongation factor-1 alpha, and the gamma subunit of eukaryotic translation initiation factor-2. These sequences show that the variant genetic code is utilized by almost all diplomonads, with the genus Giardia alone using the universal genetic code. Comparative phylogenetic analysis reveals that the switch to this genetic code took place very early in the evolution of diplomonads and was likely a single event. Termination signals and downstream untranslated regions were also cloned from three Hexamita genes. In all three of these genes, the predicted TGA termination codon was found at the expected position. Interestingly, the untranslated regions of these genes are high in AT. This is incongruent with the coding regions, which are comparatively GC-rich.      

Feasibility of a liver transcriptomics approach to assess bovine treatment with the prohormone dehydroepiandrosterone (DHEA)

Background  

Within the European Union the use of growth promoting agents in animal production is prohibited. Illegal use of natural prohormones like dehydroepiandrosterone (DHEA) is hard to prove since prohormones are strongly metabolized in vivo. In the present study, we investigated the feasibility of a novel effect-based approach for monitoring abuse of DHEA. Changes in gene expression profiles were studied in livers of bull calves treated orally (PO) or intramuscularly (IM) with 1000 mg DHEA versus two control groups, using bovine 44K DNA microarrays. In contrast to controlled genomics studies, this work involved bovines purchased at the local market on three different occasions with ages ranging from 6 to 14 months, thereby reflecting the real life inter-animal variability due to differences in age, individual physiology, season and diet.     

Soil–atmosphere exchange of greenhouse gases in a Eucalyptus marginata woodland, a clover-grass pasture, and Pinus radiata and Eucalyptus globulus plantations

Soils provide the largest terrestrial carbon store, the largest atmospheric CO₂ source, the largest terrestrial N₂O source and the largest terrestrial CH₄ sink, as mediated through root and soil microbial processes. A change in land use or management can alter these soil processes such that net greenhouse gas exchange may increase or decrease. We measured soil–atmosphere exchange of CO₂, N₂O and CH₄ in four adjacent land‐use systems (native eucalypt woodland, clover‐grass pasture, Pinus radiata and Eucalyptus globulus plantation) for short, but continuous, periods between October 2005 and June 2006 using an automated trace gas measurement system near Albany in southwest Western Australia. Mean N₂O emission in the pasture was 26.6 μg N m⁻² h⁻¹, significantly greater than in the natural and managed forests (< 2.0 μg N m⁻² h⁻¹). N₂O emission from pasture soil increased after rainfall events (up to 100 μg N m⁻² h⁻¹) and as soil water content increased into winter, whereas no soil water response was detected in the forest systems. Gross nitrification through ¹⁵N isotope dilution in all land‐use systems was small at water holding capacity < 30%, and under optimum soil water conditions gross nitrification ranged between < 0.1 and 1.0 mg N kg⁻¹ h⁻¹, being least in the native woodland/eucalypt plantation < pine plantation < pasture. Forest soils were a constant CH₄ sink, up to −20 μg C m⁻² h⁻¹ in the native woodland. Pasture soil was an occasional CH₄ source, but weak CH₄ sink overall (−3 μg C m⁻² h⁻¹). There were no strong correlations (R < 0.4) between CH₄ flux and soil moisture or temperature. Soil CO₂ emissions (35–55 mg C m⁻² h⁻¹) correlated with soil water content (R < 0.5) in all but the E. globulus plantation. Soil N₂O emissions from improved pastures can be considerable and comparable with intensively managed, irrigated and fertilised dairy pastures. In all land uses, soil N₂O emissions exceeded soil CH₄ uptake on a carbon dioxide equivalent basis. Overall, afforestation of improved pastures (i) decreases soil N₂O emissions and (ii) increases soil CH₄ uptake.     

疏叶骆驼刺根系对土壤异质性和种间竞争的响应

近年来, 植物根系对土壤异质性的响应和植物根系之间的相互作用一直是研究的热点。过去的研究主要是针对一年生短命植物进行的, 而且多是在人工控制的温室条件下进行的。而对于多年生植物根系对养分异质性和竞争的综合作用研究很少。该文对塔里木盆地南缘多年生植物疏叶骆驼刺(Alhagi sparsifolia)根系生长对养分异质性和竞争条件的响应途径与适应策略进行了研究, 结果表明: (1)在无竞争的条件下, 疏叶骆驼刺根系优先向空间大的地方生长, 即使另一侧有养分斑块存在, 其根系也向着空间大的一侧生长; (2)在有竞争的条件下, 疏叶骆驼刺根系生长依然是优先占领空间大的一侧, 但是竞争者的存在抑制了疏叶骆驼刺的生长, 导致其枝叶生物量和根系生物量都明显减少(p < 0.01), 而养分斑块的存在促进了疏叶骆驼刺根系的生长; (3)疏叶骆驼刺根系的生长不仅需要养分, 也需要足够的空间, 空间比养分更重要; (4)有竞争者存在的时候, 两株植物的根系都先长向靠近竞争者一侧的空间, 即先占据“共有空间”。研究结果对理解植物根系觅食行为和植物对环境的适应策略有重要意义。     

Confusing Selective Feeding with Differential Digestion in Bacterivorous Nanoflagellates

Food selectivity and the mechanisms of food selection were analyzed by video microscopy for three species (Spumella, Ochromonas, Cafeteria) of interception-feeding heterotrophic nanoflagellates. The fate of individual prey particles, either live bacteria and/or inert particles, was recorded during the different stages of the particle-flagellate-interaction, which included capture, ingestion, digestion, and egestion. The experiments revealed species-specific differences and new insights into the underlying mechanisms of particle selection by bacterivorous flagellates. When beads and bacteria were offered simultaneously, both particles were ingested unselectively at similar rates. However, the chrysomonads Spumella and Ochromonas egested the inert beads after a vacuole passage time of only 2-3 min, which resulted in an increasing proportion of bacteria in the food vacuoles. Vacuole passage time for starved flagellates was significantly longer compared to that of exponential-phase flagellates for Spumella and Ochromonas. The bicosoecid Cafeteria stored all ingested particles, beads as well as bacteria, in food vacuoles for more then 30 min. Therefore "selective digestion" is one main mechanism responsible for differential processing of prey particles. This selection mechanism may explain some discrepancies of former experiments using inert particles as bacterial surrogates for measuring bacterivory.     

极端干旱条件下多年生植物水分关系参数变化特性

通过对生长在塔克拉玛干沙漠南缘极端干旱区野外生境条件下的4种多年生植物胡杨、柽柳、沙拐枣和骆驼刺的主要水分关系参数(P100为膨压最大时的渗透势;P0为膨压为零时的渗透势;emax为最大细胞弹性模量;RWCa为细胞在质壁分离点时的相对含水量)在植物生长周期内的变化特征进行了分析,结合对植物清晨水势和土壤含水率变化的系统进行测定。结果表明:4种植物在低水势下保持膨压能力大小的排序为柽柳>胡杨>骆驼刺>沙拐枣。4种植物应对水分胁迫的共同反应是在细胞出现质壁分离时,保持高的体内含水量;在耐旱机理上,沙拐枣和骆驼刺属于高水势延迟脱水类型,胡杨和柽柳属于低水势忍耐脱水类型;在植物生长期内,4种植物清晨水势的变化特征是,骆驼刺的清晨水势值最高,沙拐枣和胡杨的清晨水势值的季节变化较为稳定,柽柳的清晨水势值最低;植物清晨水势的变化趋势同其水分关系参数的变化特性基本一致;4种植物没有受到严重的水分胁迫,灌溉对植物水分关系参数变化的影响不显著;植物处并利用地下水来满足其生存和生长需求,维持地下水位的基本稳定,是保证多年生植物恢复重建的重要前提。