An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests an inchworm-type translocation mechanism

Tailed bacteriophages and large eukaryotic viruses employ powerful molecular motors to translocate dsDNA into a preassembled capsid shell. The phage T4 motor is composed of a dodecameric portal and small and large terminase subunits assembled at the special head-tail connector vertex of the prohead. The motor pumps DNA through the portal channel, utilizing ATP hydrolysis energy provided by an ATPase present in the large terminase subunit. We report that the ATPase motors of terminases, helicases, translocating restriction enzymes, and protein translocases possess a common coupling motif (C-motif). Mutations in the phage T4 terminase C-motif lead to loss of stimulated ATPase and DNA translocation activities. Surprisingly, the mutants can catalyze at least one ATP hydrolysis event but are unable to turn over and reset the motor. This is the first report of a catalytic block in translocating ATPase motor after ATP hydrolysis occurred. We suggest that the C-motif is an ATP hydrolysis sensor, linking product release to mechanical motion. A novel terminase-driven mechanism is proposed for translocation of dsDNA in viruses.     

古浪县北部荒漠植被主要植物种的生态位特征

利用Shannon-Wiener生态位宽度公式和Pianka生态位重叠公式,计测分析了甘肃省古浪县北部荒漠植被主要植物种在不同植被演替阶段的生态位宽度和生态位重叠。结果表明:在流动沙地上花棒的生态位宽度最大,其次是沙蒿;在半固定沙地上白刺的生态位宽度最大;在固定沙地上,不论是封育植被还是未封育植被中均是花棒的生态位最宽。同一植物种的生态位随着植被演替阶段的变化而发生变化,这种变化反映了不同演替阶段下的植被恢复效果。优势种的生态位重叠大,生态位宽的物种对重叠值也大,相同物种对在不同演替阶段的生态位重叠不一致。有些物种生态位宽度窄,但重叠值大,是由荒漠植被区物种分布存在生境斑块现象造成的。     

菜田蜘蛛群落组成及生态位分析

根据2006年5月至8月对蕃茄、茄子、豆角、青椒、尖椒及油菜共6种蔬菜田蜘蛛种类及数量的系统调查,经初步整理鉴定,隶属于9科19属27种。通过时空二维生态位分析,星豹蛛的二维宽度最大,草间钻头蛛和齿螯额角蛛的二维重叠值最大。应用模糊聚类法对群落的相似性进行分析,以λ=0.68为聚类阈值,可将9种菜田优势种蜘蛛划分为1个明显竞争群及3个分离种。以λ=0.9736为聚类阈值,可将菜田蜘蛛时间序列分为5月份,6、7月份和8月份3个状态集,即蜘蛛群落建立、发展和瓦解3个阶段。     

Environmental and neighbourhood effects on tree fern distributions in a neotropical lowland rain forest

Questions: To what extent are the distributions of tropical rain forest tree ferns (Cyatheaceae) related to environmental variation, and is habitat specialization likely to play a role in their local coexistence? Location: Lowland rain forest at La Selva Biological Station, Costa Rica. Methods: Generalized linear (GLM) and generalized additive (GAM) logistic regression were used to model the incidence of four tree fern species in relation to environmental and neighbourhood variables in 1154 inventory plots regularly distributed across 6 km² of old‐growth forest. Small and large size classes of the two most abundant species were modelled separately to see whether habitat associations change with ontogeny. Results: GLM and GAM model results were similar. All species had significant distributional biases with respect to micro‐habitat. Environmental variables describing soil variation were included in the models most often, followed by topographic and forest structural variables. The distributions of small individuals were more strongly related to environmental variation than those of larger individuals. Significant neighbourhood effects (spatial autocorrelation in intraspecific distributions and non‐random overlaps in the distributions of certain species pairs) were also identified. Overlaps between congeners did not differ from random, but there was a highly significant overlap in the distributions of the two most common species. Conclusions: Our results support the view that habitat specialization is an important determinant of where on the rain forest landscape tree ferns grow, especially for juvenile plants. However, other factors, such as dispersal limitation, may also contribute to their local coexistence.     

Paneth cells drive intestinal stem cell competition and clonality in aging and calorie restriction

Calorie restriction has been recently shown to increase intestinal stem cell competition and to reduce mutation fixation in young mice. However, the impact of aging on this process is unknown. By employing Confetti reporter mice, here we show that, unexpectedly, old mice have more intestinal stem cell (ISC) competition than young mice. Moreover, differently from what observed in young mice, calorie restriction, when applied at late-life, decreases this process. Importantly, we also observed a strong correlation between the ISC competition and Paneth cell number. In vivo analysis and in vitro organoid experiments indicated that Paneth cells play a major role in driving intestinal stem cell competition and crypt clonality. Taken together, our results provide evidence that increasing the number of Paneth cells can increase the number of competitive ISCs, representing a valuable therapeutic target to delay fixation of mutated intestinal stem cells.     

同域分布的黑麂和小麂的时空生态位分化

生态位分化是解释物种共存的重要理论。Schonenr认为空间维度对生态位差异形成的影响程度最高,营养维度次之,时间维度则最后被启动。为验证这一假说,我们于2018年12月至2019年11月,在浙江清凉峰国家级自然保护区龙塘山区域采用公里网格法布设52台红外相机,对同域分布且食性相似的黑麂和小麂种群进行监测,计算平均拍摄率,分析不同季节黑麂和小麂对不同植被类型、海拔、坡位、水源距离的选择差异,并运用核密度估计法分析二者日活动节律及重叠程度。结果显示,(1) 黑麂和小麂对空间生态位的选择出现分化：黑麂偏好针阔混交林,主要栖息于1 301 ~ 1 500 m的高海拔地区,回避下坡位和谷地,在距离水源较近的区域内活动频繁;小麂则偏好落叶阔叶林,主要栖息于901 ~ 1 100 m的中海拔地区,偏好中坡位,回避谷地,对水源距离没有明显的选择倾向。(2) 黑麂和小麂均为晨昏性活动的昼行性动物,二者全年日活动节律重叠程度较高 (Δ4 = 0.86),仅冬季较低 (Δ1 = 0.65)。上述结果支持Schonenr的假说：首先,空间维度对物种生态位分化的影响大于时间维度,龙塘山区域黑麂和小麂主要通过选择不同的栖息地来增加空间回避,降低二者的竞争;其次,这种模式存在季节差异,冬季由于可利用的资源减少,竞争加剧,二者通过调整日活动节律,增加时间生态位分化程度,从而实现同域共存。     

Variation in the thermal ecology of an endemic iguana from Mexico reduces its vulnerability to global warming

The persistence of reptile populations in a specific location is influenced by individuals’ capacity to regulate their body temperatures, among other factors. Anthropogenic climate change may pose a risk to the survival of ectothermic animals due to their dependence on external heat sources to thermoregulate. In this study, we calculated indices of thermal habitat quality, thermoregulatory precision, and thermoregulatory effectiveness for the endemic spiny-tailed iguana Ctenosaura oaxacana. We evaluated these indices and the thermoregulatory behavior of the iguanas in the four types of vegetation that provide the most favorable conditions for thermoregulation. We also performed our experiments during both the wet and dry seasons to capture the full range of thermal conditions available to C. oaxacana over the course of a year. Finally, we evaluated the potential niche for the iguana in the years 2020, 2050, and 2080. Thermoregulation depends on both seasonal and environmental factors in this species. We found that thermoregulation effectiveness in both wet and dry seasons depends not only on the thermal conditions of the immediate environment, but also on the cover vegetation and habitat structure available across the range of habitats the species uses. Thus, heterogeneous habitats with dispersed vegetation may be most suitable for this species’ thermoregulatory strategy. Likewise, niche modeling results suggested that suitable habitat for our study species may continue to be available for the next few decades, despite global warming tendencies, as long as cover vegetation remains unaltered. Our results suggest that thermoregulation is a complex process that cannot be generalized for all ectothermic species inhabiting a given region. We also found that temperature changes are not the only factor one must consider when estimating the risk of species loss. To understand the necessary thermal conditions and extinction risk for any ectothermic species, it is necessary to focus studies on the species’ general ecology.     

Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

Emergence of thousands of crystal structures of noncoding RNA molecules indicates its structural and functional diversity. RNA function is based upon a large variety of structural elements which are specifically assembled in the folded molecules. Along with the canonical Watson‐Crick base pairs, different orientations of the bases to form hydrogen‐bonded non‐canonical base pairs have also been observed in the available RNA structures. Frequencies of occurrences of different non‐canonical base pairs in RNA indicate their important role to maintain overall structure and functions of RNA. There are several reports on geometry and energetic stabilities of these non‐canonical base pairs. However, their stacking geometry and stacking stability with the neighboring base pairs are not well studied. Among the different non‐canonical base pairs, the G:U wobble base pair (G:U W:WC) is most frequently observed in the RNA double helices. Using quantum chemical method and available experimental data set we have studied the stacking geometry of G:U W:WC base pair containing dinucleotide sequences in roll‐slide parameters hyperspace for different values of twist. This study indicates that the G:U W:WC base pair can stack well with the canonical base pairs giving rise to large interaction energy. The overall preferred stacking geometry in terms of roll, twist and slide for the eleven possible dinucleotide sequences is seen to be quite dependent on their sequences. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 328–338, 2015.