Thermodynamic basis of selectivity in guide-target-mismatched RNA interference

Silencing in RNAi is strongly affected by guide‐strand/target‐mRNA mismatches. Target nucleation is thought to occur at positions 2–8 of the guide (“seed region”); successful hybridization in this region is the primary determinant of target‐binding affinity and hence target cleavage. To define a molecular basis for the target sequence selectivity in RNAi, we studied all possible distinct single mismatches in seven positions of the seed region—a total of 21 substitutions. We report results from soft‐core thermodynamic integration simulations to determine changes in targeting binding‐free energies to Argonaute due to single mismatches in the guide strand, which arise during binding of an imperfectly matched target mRNA. In agreement with experiment, most mismatches impair target binding, consistent with a prominent role for binding affinity changes in RNAi sequence selectivity. Individual Argonaute residues located near the mismatched base pair are found to contribute significantly to binding affinity changes. We also use this methodology to analyze the mismatch‐dependent free energy changes for dissociation of a DNA?RNA hybrid from Argonaute, as a model for the escape of miRNAs from the silencing pathway. Several mismatched sequences of the miRNA have increased affinity to Argonaute, implying that some mismatches may reduce the probability for escape. Furthermore, calculations of base‐substitution‐dependent free energy changes for binding ssDNA reveal mild sequence sensitivity as expected for guide strand binding to Argonaute. Our findings give a thermodynamic basis for RNAi target sequence selectivity and suggest that miRNA mismatches may increase silencing effectiveness and thus could be evolutionarily advantageous. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Risk Perception and Energy Production

Mean risk magnitude judgments expressed by Belgian and French students on 107 items combining a particular energy domain (wood and biomass, coal, gas, oil, nuclear, water, wind, geothermal and solar) and a particular aspect of the energy production process (obtaining raw materials, storage of raw materials, transport of raw materials, energy production, waste products related to energy production, energy transport, waste products transport, waste products storage, utilization of energy) are reported, and analyzed. Questions were of the form: What is the level of risk (for health and the environment) associated with the item “Electrical energy production by thermodynamic conversion”? Concerning energy domains, nuclear energy received the highest ratings, almost regardless of the aspect of the energy production process considered (from the extraction of raw materials to the storage of production wastes). This was followed by oil, obtaining the next highest ratings after those for nuclear energy, then gas, considered more risky than biomass and coal. The brand image of these two latter energy sources would be almost as positive as that of water, solar, geothermal and wind energy if a solution could be found to the problem of atmospheric emission of carbon monoxide. Concerning production process aspects, waste products (as well as the transport and storage of waste) received the highest ratings. This is not unrelated to the fact that the vast majority of studies devoted to a particular area or particular aspect have concerned nuclear waste. In contrast, no very high degree of concern was found regarding the energy (electrical) transport aspect.     

Development of sexual dimorphism in two sympatric skinks with different growth rates

Sexual size dimorphism (SSD) is widespread in animals, especially in lizards (Reptilia: Squamata), and is driven by fecundity selection, male–male competition, or other adaptive hypotheses. However, these selective pressures may vary through different life history periods; thus, it is essential to assess the relationship between growth and SSD. In this study, we tracked SSD dynamics between a “fading‐tail color skink” (blue tail skink whose tail is only blue during its juvenile stage: Plestiodon elegans) and a “nonfade color” tail skink (retains a blue tail throughout life: Plestiodon quadrilineatus) under a controlled experimental environment. We fitted growth curves of morphological traits (body mass, SVL, and TL) using three growth models (Logistic, Gompertz, and von Bertalanffy). We found that both skinks have male‐biased SSD as adults. Body mass has a higher goodness of fit (as represented by very high R² values) using the von Bertalanffy model than the other two models. In contrast, SVL and TL for both skinks had higher goodness of fit when using the Gompertz model. Two lizards displayed divergent life history tactics: P. elegans grows faster, matures earlier (at 65 weeks), and presents an allometric growth rate, whereas P. quadrilineatus grows slower, matures later (at 106 weeks), and presents an isometric growth rate. Our findings imply that species‐ and sex‐specific trade‐offs in the allocation of energy to growth and reproduction may cause the growth patterns to diverge, ultimately resulting in the dissimilar patterns of SSD.     

Potential trade‐offs of employing perennial biomass crops for the bioeconomy in the EU by 2050: Impacts on agricultural markets in the EU and the world

Perennial biomass crops (PBC) are considered a crucial feedstock for sustainable biomass supply to the bioeconomy that compete less with food production compared to traditional crops. However, large‐scale development of PBC as a means to reach greenhouse gas (GHG) mitigation targets would require not only the production on land previously not used for agriculture, but also the use of land that is currently used for agricultural production. This study aims to evaluate agricultural market impacts with biomass demand for food, feed, and PBC in four bioeconomy scenarios (“Business as usual,” “Improved relevance of bioeconomy,” “Extensive transformation to a bioeconomy,” “Extensive transformation to a bioeconomy with diet change”) to achieve a 75% GHG reduction target in the emission trading sector of the EU until 2050. We simulated bioeconomy scenarios in the energy system model TIMES‐PanEU and the agricultural sector model ESIM and conducted a sensitivity analysis considering crop yields, PBC yields, and land use options of PBC. Our results show that all bioeconomy scenarios except the one with diet change lead to increasing food prices (the average food price index increases by about 11% in the EU and 2.5%–3.0% in world markets). A combination of the transformation to a bioeconomy combined with diet change toward less animal protein in the EU is the only scenario that results in only moderately increasing food prices within the EU (+3.0%) and even falling global food prices (–6.4%). In addition, crop yield improvement and cultivation of PBC on marginal land help to reduce increases in food prices, but higher land prices are inevitable because those measures have only small effects on sparing agricultural land for PBC. For a transition to a bioeconomy that acknowledges climate mitigation targets, counter‐measures for those substantial direct and indirect impacts on agricultural markets should be taken into account.     

Dominance of autochthonous autotrophic carbon in food webs of heterotrophic rivers

This paper addresses the river heterotrophy paradox, “How can animal biomass within riverine food webs be fueled primarily by autochthonous autotrophic production if the ecosystem as a whole is heterotrophic?”. Reviewed, stable isotope data from tropical, temperate, and arctic rivers provide evidence consistent with the revised riverine productivity model (RPM): “The primary, annual energy source supporting overall metazoan production and species diversity in mid‐ to higher‐trophic levels of most rivers (≥4th order) is autochthonous primary production entering food webs via algal‐grazer and decomposer pathways”. The revised RPM does not conflict with the heterotrophy paradox because: (a) the decomposer (microbial loop) food pathway processes most of the transported, allochthonous and autochthonous carbon and, with algal respiration in some cases, is primarily responsible for a river's heterotrophic state (P/R<1); but (b) biomass production of mid‐ to higher‐trophic levels is principally supported by an algal‐grazer (phytoplankton and benthic microalgae) pathway that is only weakly linked to the decomposer pathway. The reason the algal‐grazer pathway supports the majority of metazoan biomass is that allochthonous carbon is mostly recalcitrant, whereas carbon from autochthonous primary production, though much less plentiful, is commonly more labile (easier to assimilate), contains more energy per unit mass, and is typically preferred by metazoa.     

Fold homology detection using sequence fragment composition profiles of proteins

The effectiveness of sequence alignment in detecting structural homology among protein sequences decreases markedly when pairwise sequence identity is low (the so‐called “twilight zone” problem of sequence alignment). Alternative sequence comparison strategies able to detect structural kinship among highly divergent sequences are necessary to address this need. Among them are alignment‐free methods, which use global sequence properties (such as amino acid composition) to identify structural homology in a rapid and straightforward way. We explore the viability of using tetramer sequence fragment composition profiles in finding structural relationships that lie undetected by traditional alignment. We establish a strategy to recast any given protein sequence into a tetramer sequence fragment composition profile, using a series of amino acid clustering steps that have been optimized for mutual information. Our method has the effect of compressing the set of 160,000 unique tetramers (if using the 20‐letter amino acid alphabet) into a more tractable number of reduced tetramers (～15–30), so that a meaningful tetramer composition profile can be constructed. We test remote homology detection at the topology and fold superfamily levels using a comprehensive set of fold homologs, culled from the CATH database that share low pairwise sequence similarity. Using the receiver‐operating characteristic measure, we demonstrate potentially significant improvement in using information‐optimized reduced tetramer composition, over methods relying only on the raw amino acid composition or on traditional sequence alignment, in homology detection at or below the “twilight zone”. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

A Dynamic Energy Budget model based on partitioning of net production

We formulate a Dynamic Energy Budget (DEB) model for the growth and reproduction of individual organisms based on partitioning of net production (i.e. energy acquisition rate minus maintenance rate) between growth and energy reserves. Reproduction uses energy from reserves. The model describes both feeding and non-feeding stages, and hence is applicable to embryos (which neither feed nor reproduce), juveniles (which feed but do not reproduce), and adults (which commonly both feed and reproduce). Embryonic growth can have two forms depending on the assumptions for acquisition of energy from yolk. By default, when the energy acquisition rate exceeds the maintenance rate, a fixed proportion of the resulting net production is spent on growth (increase in structural biomass), and the remaining portion is channelled to the reserves. Feeding organisms, however, modulate their allocation of net production energy in response to their total energy content (energy in the reserves plus energy bounded to structural biomass). In variable food environment an organism alternates between periods of growth, no-growth, and balanced-growth. In the latter case the organism adopts an allocation strategy that keeps its total energy constant. Under constant environmental conditions, the growth of a juvenile is always of von Bertalanffy type. Depending on the values of model parameters there are two long-time possibilities for adults: (a) von Bertalanffy growth accompanied by reproduction at a rate that approaches zero as the organism approaches asymptotic size, or (b) abrupt cessation of growth at some finite time, following which, the rate of reproduction is constant. We illustrate the model's applicability in life history theory by studying the optimum values of the energy allocation parameters for constant environment and for each of the dynamic regimes described above. Received: 11 May 1998 / Revised version: 18 February 2000 / Published online: 4 October 2000     

Identifying compartments in ecological networks based on energy channels

It has been confirmed in many food webs that the interactions between species are divided into “compartments,” that is, subgroups of highly interacting taxa with few weak interactions between the subgroups. Many of the current methods for detecting compartments in food webs are borrowed from network theory, which do little to improve our understanding of the mechanisms underpinning them. Therefore, a method based on ecological context is needed. Here, we develop a new method for detecting compartments in food webs based on the reliance of each node on energy derived from basal resources (i.e., producers or decomposers). Additional Monte Carlo simulations were conducted to test the significance of the compartmentalization. Further, we applied a food web dynamics model to test whether the effects of permutation would be retained within a single compartment. The proposed method identified significant compartments in 23 of the 28 empirical food webs that were investigated. We further demonstrated that the effects of node removal were significantly higher within compartments than between compartments. Our methods and results emphasize the importance of energy channels in forming food web structures, which sheds light on the mechanisms of self‐organization within food webs.     

Maternal feeding strategies, child eating behaviors, and child BMI in low-income African-American preschoolers

Objective: To test the hypothesis that low‐income African‐American preschool children would have a higher BMI if their mothers reported greater “restriction” and “control” in feeding and if mothers reported that children showed greater “food responsiveness” and “desire to drink.” In addition, to test whether higher maternal “pressure to eat” would be associated with lower child BMI. Research Methods and Procedures: A questionnaire was completed by 296 low‐income African‐American mothers of preschool children. It assessed three constructs on maternal feeding strategies (“restriction,” “pressure to eat,” and “control”) and two on child eating behaviors (“food responsiveness” and “desire to drink”). Children's BMI was measured, and mothers’ BMI was self‐reported. Results: The mean (standard deviation) BMI z‐score of the children was 0.34 (1.5), and 44% of the mothers were obese (BMI ≥30 kg/m²). Only maternal “pressure to eat” had a significant overall association with child BMI z‐score (r = ?0.16, p < 0.01). Both maternal “restriction” and “control” were positively associated with children's BMI z‐score in the case of obese mothers (r = 0.20, p = 0.03 and r = 0.24, p = 0.007, respectively), but this was not so in the case of non‐obese mothers (r = ?0.16, p = 0.05 and r = ?0.07, p = 0.39, respectively). Discussion: Among low‐income African Americans, the positive association between maternal restriction and control in feeding and their preschoolers’ BMI was limited to obese mothers. Relations between parent feeding strategies and child weight status in this population may differ on the basis of maternal weight status.     

Structural complexity and land‐surface energy exchange along a gradient from arctic tundra to boreal forest

Question: Current climate changes in the Alaskan Arctic, which are characterized by increases in temperature and length of growing season, could alter vegetation structure, especially through increases in shrub cover or the movement of treeline. These changes in vegetation structure have consequences for the climate system. What is the relationship between structural complexity and partitioning of surface energy along a gradient from tundra through shrub tundra to closed canopy forest? Location: Arctic tundra‐boreal forest transition in the Alaskan Arctic. Methods: Along this gradient of increasing canopy complexity, we measured key vegetation characteristics, including community composition, biomass, cover, height, leaf area index and stem area index. We relate these vegetation characteristics to albedo and the partitioning of net radiation into ground, latent, and sensible heating fluxes. Results: Canopy complexity increased along the sequence from tundra to forest due to the addition of new plant functional types. This led to non‐linear changes in biomass, cover, and height in the understory. The increased canopy complexity resulted in reduced ground heat fluxes, relatively conserved latent heat fluxes and increased sensible heat fluxes. The localized warming associated with increased sensible heating over more complex canopies may amplify regional warming, causing further vegetation change in the Alaskan Arctic.     

Biomass production in plantations: Land constraints increase dependency on irrigation water

Integrated assessment model scenarios project rising deployment of biomass‐using energy systems in climate change mitigation scenarios. But there is concern that bioenergy deployment will increase competition for land and water resources and obstruct objectives such as nature protection, the preservation of carbon‐rich ecosystems, and food security. To study the relative importance of water and land availability as biophysical constraints to bioenergy deployment at a global scale, we use a process‐detailed, spatially explicit biosphere model to simulate rain‐fed and irrigated biomass plantation supply along with the corresponding water consumption for different scenarios concerning availability of land and water resources. We find that global plantation supplies are mainly limited by land availability and only secondarily by freshwater availability. As a theoretical upper limit, if all suitable lands on Earth, besides land currently used in agriculture, were available for bioenergy plantations (“Food first” scenario), total plantation supply would be in the range 2,010–2,300 EJ/year depending on water availability and use. Excluding all currently protected areas reduces the supply by 60%. Excluding also areas where conversion to biomass plantations causes carbon emissions that might be considered unacceptably high will reduce the total plantation supply further. For example, excluding all areas where soil and vegetation carbon stocks exceed 150 tC/ha (“Carbon threshold savanna” scenario) reduces the supply to 170–290 EJ/year. With decreasing land availability, the amount of water available for irrigation becomes vitally important. In the least restrictive land availability scenario (“Food first”), up to 77% of global plantation biomass supply is obtained without additional irrigation. This share is reduced to 31% for the most restrictive “Carbon threshold savanna” scenario. The results highlight the critical—and geographically varying—importance of co‐managing land and water resources if substantial contributions of bioenergy are to be reached in mitigation portfolios.     

Mechanical energy oscillations of two brachiation gaits: measurement and simulation

How do arm‐swinging apes locomote effectively over a variety of speeds? One way to reduce the metabolic energy cost of locomotion is to transfer energy between reversible mechanical modes. In terrestrial animals, at least two transfer mechanisms have been identified: 1) a pendulum‐like mechanism for walking, with exchange between gravitational potential energy and translational kinetic energy, and 2) a spring‐like mechanism for running, where the elastic strain energy of stretched muscle and tendon is largely returned to reaccelerate the animal. At slower speeds, a brachiator will always have at least one limb in contact with the support, similar to the overlap of foot contact in bipedal walking. At faster speeds, brachiators exhibit an aerial phase, similar to that seen in bipedal running. Are there two distinct brachiation gaits even though the animal appears to simply swing beneath its overhead support? If so, are different exchange mechanisms employed? Our kinetic analysis of brachiation in a white‐handed gibbon (Hylobates lar) indicates that brachiation is indeed comprised of two mechanically distinct gaits. At slower speeds in “continuous contact” brachiation, the gibbon utilizes a simple pendulum‐like transfer of mechanical energy within each stride. At faster speeds in “ricochetal” brachiation, translational and rotational kinetic energy are exchanged in a novel “whip‐like” transfer. We propose that brachiators utilize the transfer between translational and rotational kinetic energy to control the dynamics of their swing. This maneuver may allow muscle action at the shoulder to control the transfer and adjust the ballistic portion of the step to meet the requirements for the next hand contact. Am J Phys Anthropol 115:319–326, 2001. © 2001 Wiley‐Liss, Inc.     

The structure of food webs along river networks

Do changes in the species composition of riverine fish assemblages along river networks lead to predictable changes in food‐web structure? We assembled empirical “fish‐centered” river food webs for three rivers located along a latitudinal gradient in the South Saskatchewan River Basin (SSRB) that differ in land‐use impacts and geomorphology but flow through similar mountain, foothill, and prairie physiographic regions. We then calculated 17 food‐web properties to determine whether the nine river food webs differed according to physiographic region or river sub‐basin. There were no statistically significant differences in the 17 food‐web properties calculated among the rivers. In contrast, fish species richness, connectance, the proportion of herbivores, and the proportion of cannibals changed longitudinally along the river network. Our results suggest that regional changes in river geomorphology and physicochemistry play an important role in determining longitudinal variation in food‐web properties such as fish species richness and connectance. In contrast, the overall structure of river food webs may be relatively similar and insensitive to regional influences such as zoogeography. Further explorations of river and other food webs would greatly illuminate this suggestion.     

Big‐sized trees overrule remaining trees' attributes and species richness as determinants of aboveground biomass in tropical forests

Large‐diameter, tall‐stature, and big‐crown trees are the main stand structures of forests, generally contributing a large fraction of aboveground biomass, and hence play an important role in climate change mitigation strategies. Here, we hypothesized that the effects of large‐diameter, tall‐stature, and big‐crown trees overrule the effects of species richness and remaining trees attributes on aboveground biomass in tropical forests (i.e., we term the “big‐sized trees hypothesis”). Specifically, we assessed the importance of: (a) the “top 1% big‐sized trees effect” relative to species richness; (b) the “99% remaining trees effect” relative to species richness; and (c) the “top 1% big‐sized trees effect” relative to the “99% remaining trees effect” and species richness on aboveground biomass. Using environmental factor and forest inventory datasets from 712 tropical forest plots in Hainan Island of southern China, we tested several structural equation models for disentangling the relative effects of big‐sized trees, remaining trees attributes, and species richness on aboveground biomass, while considering for the full (indirect effects only) and partial (direct and indirect effects) mediation effects of climatic and soil conditions, as well as interactions between species richness and trees attributes. We found that top 1% big‐sized trees attributes strongly increased aboveground biomass (i.e., explained 55%–70% of the accounted variation) compared to species richness (2%–18%) and 99% remaining trees attributes (6%–10%). In addition, species richness increased aboveground biomass indirectly via increasing big‐sized trees but via decreasing remaining trees. Hence, we show that the “big‐sized trees effect” overrides the effects of remaining trees attributes and species richness on aboveground biomass in tropical forests. This study also indicates that big‐sized trees may be more susceptible to atmospheric drought. We argue that the effects of big‐sized trees on species richness and aboveground biomass should be tested for better understanding of the ecological mechanisms underlying forest functioning.     

Experimental nutrient enrichment of forest streams increases energy flow to predators along greener food‐web pathways

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不同种类无机盐对灰毡毛忍冬“渝蕾1号”悬浮培养体系中细胞生长和绿原酸含量的影响

为提高灰毡毛忍冬"渝蕾1号"悬浮培养体系中绿原酸的含量,该研究探讨了B_5培养基中不同浓度的无机盐对灰毡毛忍冬"渝蕾1号"悬浮培养细胞生物量及绿原酸含量的影响,通过在悬浮培养体系中添加不同浓度的无机盐,采用重量法测定灰毡毛忍冬"渝蕾1号"悬浮培养细胞的生物量及采用高效液相色谱法测定绿原酸的含量。结果表明:当硝态氮和铵态氮配比与B_5培养基中硝态氮和铵态氮配比一致时,即NO_3~-/NH_4~+摩尔比值为13∶1时,培养体系有利于细胞的生长和绿原酸的积累。当KNO_3浓度为3.5 g·L~(-1)时,细胞生物量达到最大,为19.26 g·L~(-1);当KNO_3在较低浓度(0.5 g·L~(-1)和1.5 g·L~(-1))时,积累较多的绿原酸。NO_3~-的两项研究结果均与对照浓度(2.5g·L~(-1))有一定的差异。另外,对(NH_4)_2SO_4来说,在高于对照浓度0.134 g·L~(-1),即浓度为0.268 g·L~(-1)时,生物量和绿原酸含量都达到了最大。P、Ca、Mg三种矿质元素的研究结果表明,当Na H_2PO_4·2H_2O浓度为0.10 g·L~(-1)、Ca Cl_2的浓度为0.20 g·L~(-1)时,细胞的生长和绿原酸的积累均可达到最大值;而对Mg~(2+)来说,低浓度促进细胞的生长,高浓度促进绿原酸的积累。兼顾细胞生物量和绿原酸含量两个指标,需选择适中的浓度。这些结果均与对照浓度有一定的差异。这说明灰毡毛忍冬"渝蕾1号"悬浮细胞所需无机盐的浓度与B_5培养基无机盐的浓度有一定的差异,选择适宜的浓度可促进其悬浮细胞的生长及次生代谢产物绿原酸的积累。该研究结果为绿原酸的工业化生产打下了基础。     

A mathematical model of phytoremediation for petroleum contaminated soil: sensitivity analysis

Phytoremediation is an attractive treatment technology for many contaminated sites due to its cost effectiveness and public acceptance. We present a sensitivity analysis of important parameters from a screening level model for phytoremediation by grass species of weathered petroleum-contaminated sites. The conceptual framework is that root movement through contaminated soil will enhance contaminant biodegradation by providing a local environment more favorable for petroleum degrading microorganisms—the so-called rhizosphere effect. Common questions in phytoremediation are, “What species should be planted?” and “What management practices should be followed?” These choices may affect degradation kinetics, root biomass (and therefore rhizosphere volume), and the root turnover. Important model parameters are the rate constants, rhizosphere volume, and the rate of root turnover. We present a sensitivity analysis with the aim of identifying the most important factors for improving phytoremediation effectiveness. For simulations of the phytoremediation of weathered diesel range organics, our results indicate that annual species, with higher root turnover, are preferred over perennial species with the caveat of equal degradation rate constants, that is, no species-dependent effects. In addition, the results suggest that the management of nonrhizosphere soil could play an important role in the overall effectiveness of phytoremediation. Finally, the effect of increasing root biomass or increasing the rhizosphere thickness is approximately equivalent with respect to the ultimate removal of the contaminants.     

Analysis of sequence-reactivity space for protein-protein interactions

Sequence–reactivity space is defined by the relationships between amino acid type choices at some residue positions in a protein and the reactivities of the resulting variants. We are studying Kazal superfamily serine proteinase inhibitors, under substitution of any combination of residue types at 10 binding‐region positions. Reactivities are defined by the standard free energy of association for an inhibitor against an enzyme, and we are interested in both the strength (the free energy value) and specificity (relative free energy values for one inhibitor against different enzymes). Characterizing the structure of such a space poses several interesting questions: (1) How many sequences achieve particular strength and specificity characteristics? (2) What is the best such sequence? (3) What are some nearly‐as‐good alternatives? (4) What are their common residue type characteristics (e.g., conservation and correlation)? Although these problems are all highly combinatorial in nature, this article develops an efficient, integrated mechanism to address them under a data‐driven model that predicts reactivity for given sequences. We employ sampling and a novel deterministic distribution propagation algorithm, in order to determine both the reactivity distribution and sequence composition statistics; integer programming and a novel branch‐and‐bound search algorithm, in order to optimize sequences and enumerate near‐optimal sequences; and correlation‐based sequence decomposition, in order to identify sequence motifs. We demonstrate the value of our mechanism in analyzing the Kazal superfamily sequence–reactivity space, providing insights into the underlying biochemistry and suggesting hypotheses for further experimental consideration. In general, our mechanism offers a valuable tool for investigating the available degrees of freedom in protein design within a combined computational–experimental framework. Proteins 2005. © 2004 Wiley‐Liss, Inc.     

Variation in plant performance in a grassland: Species‐specific and neighbouring root mass effects

Question: What characteristics of local biotic neighbourhood is the best proxy of competitive effects experienced by plants in a herbaceous community: (1) total above‐ground biomass, (2) root mass or (3) relative above‐ground abundance of selected species? Location: Grassland at ca. 1100 m a.s.l. in the Krkono?e Mts., northern Czech Republic. Methods: We implanted two phytometer species, Antho‐xanthum alpinum and Festuca rubra, into a mountain grassland, and examined their response to local variation in (1) total above‐ground biomass, (2) root mass at three soil depths, and (3) relative abundance of individual species above‐ground. Results : Performance of both phytometer species was determined much more consistently by the mass of neighbouring roots and by species composition of neighbours than by the total above‐ground biomass. The two phytometer species showed different responses to these parameters. The most important relationships were (1) negative relationship between performance of Anthoxanthum and mass of neighbouring roots at 0–3 cm, (2) positive relationship between performance of Festuca and mass of neighbouring roots at 3–6 cm, and (3) negative relationship between performance of Festuca and relative abundance of Festuca in the neighbourhood. Conclusions: Neighbouring root mass and above‐ground species composition are better determinants of biotic interactions than total above‐ground biomass of neighbours in the studied mountain grassland. However, the relationships found are not necessarily due to variation in competitive intensity but can be due to other hidden factors as well, e.g. local availability of resources.