The limits of protein sequence comparison?

Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized.     

What limits the Serengeti zebra population?

The populations of the ecologically dominant ungulates in the Serengeti ecosystem (zebra, wildebeest and buffalo) have shown markedly different trends since the 1960s: the two ruminants both irrupted after the elimination of rinderpest in 1960, while the zebras have remained stable. The ruminants are resource limited (though parts of the buffalo population have been limited by poaching since the 1980s). The zebras resource acquisition tactics should allow them to outcompete the ruminants, but their greater spatial dispersion makes them more available to predators, and it has been suggested that this population is limited by predation. To investigate the mechanisms involved in the population dynamics of Serengeti zebra, we compared population dynamics among the three species using demographic models based on age-class-specific survival and fecundity. The only major difference between zebra and the two ruminants occurred in the first-year survival. We show that wildebeest have a higher reproductive potential than zebra (younger age at first breeding and shorter generation time). Nevertheless, these differences in reproduction cannot account for the observed differences in the population trends between the zebra and the ruminants. On the other hand, among-species differences in first-year survival are great enough to account for the constancy of zebra population size. We conclude that the very low first-year survival of zebra limits this population. We provide new data on predation in the Serengeti and show that, as in other ecosystems, predation rates on zebras are high, so predation could hold the population in a predator pit. However, lion and hyena feed principally on adult zebras, and further work is required to discover the process involved in the high mortality of foals.     

What limits nitrate uptake from soil?

Abstract. An accepted view, that unless nitrate concentrations in the soil solution are very low (e.g. below 0.1–0.2 mol m^?3) the growth of high-yielding crops is not limited by the availability of nitrogen, is challenged. Conventional analyses of nutrient supply and demand, based on calculations of apparent inflow rates (uptake rates per unit total root length) are invalid. Apparent inflow rates are inversely proportional to root length. The convention of using total root length grossly overestimates the fraction of the root system active in nutrient uptake. Consequently, inflow rates based on total root lengths underestimate the true values, indicating unrealistically low nutrient concentration differentials between bulk soil and root surfaces required to drive uptake. An alternative method of analysis is suggested. This is based on total nutrient uptake rather than on inflow rate. Measurements of the former do not depend on estimates of active root length and can be made directly and reliably. The method was applied to data obtained from a pot experiment using spring wheat (Triticum aestivum L., cv. Wembley) grown in soil without nitrogen fertilizer (N₀) or with nitrogen fertilizer equivalent to 200kg N ha^?1 (N⁺). Soil nitrate concentrations calculated using the conventional method based on total root length, suggested that any increases in concentration above those measured in the N⁰ treatment should not have resulted in increased uptake and growth. However, the N⁺ plants were always bigger than those in the No treatment, refuting this suggestion. Theoretical uptakes of nitrogen (calculated initially on the basis of a fully active root system) were adjusted, by reducing the effective root length incrementally, until the theoretical uptake matched the measured net uptake of nitrogen. The mean fractions of the root systems likely to have been involved in nitrate uptake were 11% and 3.5% of the total lengths of root in the N⁰ and N⁺ treatments, respectively.     

What limits the evolutionary emergence of pathogens?

The ability of a pathogen to cause an epidemic when introduced in a new host population often relies on its ability to adapt to this new environment. Here, we give a brief overview of recent theoretical and empirical studies of such evolutionary emergence of pathogens. We discuss the effects of several ecological and genetic factors that may affect the likelihood of emergence: migration, life history of the infectious agent, host heterogeneity, and the rate and effects of mutations. We contrast different modelling approaches and indicate how details in the way we model each step of a life cycle can have important consequences on the predicted probability of evolutionary emergence. These different theoretical perspectives yield important insights into optimal surveillance and intervention strategies, which should aim for a reduction in the emergence (and re-emergence) of infectious diseases.     

Can natural enemies enforce geographical range limits?

We develop a simple mathematical model to investigate the question as to whether a specialised consumer can be responsible for creating a range limit in the population of its dynamic resource. The model is most attuned for parasitoid-host relationships, but the central results should apply to a broad range of systems. Specifically, at the beginning of each simulation host and parasitoid populations are distributed at random along a string of patches. In each discrete generation and for each patch, host and parasitoid populations grow and interact, and then a constant fraction of those remaining disperses one or more patch distances in either direction according to a geometric distribution. We iterate the model 200 generations, and in any generation for any patch, either host and/or parasitoid can go locally extinct if its population falls below a threshold density. We find that a specialised parasitoid can enforce a limit, and it is even more likely to fragment its host population. The two most important conditions for parasitoid-enforced range limits are: 1) the theoretical host equilibrium density in the presence of the parasitoid be very small at sites eliminated from the host's range, and 2) the parasitoid disperses at high rates. We close by discussing our findings for specialist and generalist natural enemies, and the relevance of our study to the wealth of investigations on the causes of geographical range limits.     

What limits herb biomass in grasslands: competition or herbivory?

Competition and herbivory are two of the main forces shaping plant communities. Although several studies have investigated their impact on plant populations separately, few investigations have examined how they might interact. With the purpose of clarifying the combined roles of competition and herbivory on herb biomass in a grassland, we assessed the effects of different herbivores with reduced grass competition. We conducted a field experiment in 2000-2001 in a British acid grassland (Oak Mead), where we experimentally reduced grass biomass and excluded rabbits, insects and molluscs in a factorial design. Removing the grasses from Oak Mead dramatically increased herb biomass and total above-ground biomass. Herbivore exclusions (i.e. rabbits, insects and molluscs) did not affect total above-ground biomass, but they altered relative abundance of several species. Grass removal and rabbit exclusion had positive interactions on biomass of several herb species, and there were some subtle interactions between different herbivore groups: monocots benefitted when both rabbits and molluscs were excluded, and some herb species had greater biomass when insects and rabbits were absent. We then compared the results with a 10-year experiment that manipulated similar variables in neighbouring grassland (Nashs Field). The comparison between Oak Mead and Nashs Field showed that cessation of herbicide application returns the system to its previous state of grass dominance after 3 years. Therefore, even when herbs were more abundant, they could not prevent reinvasion of the grasses once external factors were removed.     

What limits the velocity of fast-skeletal muscle contraction in mammals?

In rat skeletal muscle the unloaded shortening velocity (Vo) is defined by the myosin isoform expressed in the muscle fibre. In 2001 we suggested that ADP release from actomyosin in solution (controlled by k(-AD)) was of the right size to limit Vo. However, to compare mechanical and solution kinetic data required a series of corrections to compensate for the differences in experimental conditions (0.5 M KCl, 22 degrees C for kinetic assays of myosin, 200 mM ionic strength, 12 degrees C to measure Vo). Here, a method was developed to prepare heavy meromyosin (HMM) from pure myosin isoforms isolated from single muscle fibres and to study k(-AD) (determined from the affinity of the acto-myosin complex for ADP, KAD) and the rate of ATP-induced acto-HMM dissociation (controlled by K1k+2) under the same experimental condition used to measure Vo). In fast-muscle myosin isolated from a wide range of mammalian muscles, k(-AD) was found to be too fast to limit Vo, whereas K1k+2 was of the right magnitude for ATP-induced dissociation of the cross-bridge to limit shortening velocity. The result was unexpected and prompted further experiments using the stopped-flow approach on myosin subfragment-1 (S1) and HMM obtained from bulk preparations of rabbit and rat muscle. These confirmed that the rate of cross-bridge dissociation by ATP limits the velocity of contraction for fast myosin II isoforms at 12 degrees C, while k(-AD) limits the velocity of slow myosin II isoforms. Extrapolating our data to 37 degrees C suggests that at physiological temperature the rate of ADP dissociation may limit Vo for both isoforms.     

Wide limits and “equitable”; distribution of seabed resources

Abstract

This article discusses some drawbacks of a universally applicable 200‐mile limit for seabed resources in terms of the artificial nature of this limit, the jeopardy to the proposed international regime to govern deep seabed resources, and the views of land‐locked and shelf‐locked countries. Given the uncertain political acceptability of a 200‐mile limit, a systems approach is suggested as a means of devising a compromise solution that would maximize the objectives of: respect of existing internationally agreed conventions; promotion of the rational development of deep seabed resources; provision of equitable distribution of seabed resources and provision of acceptable benefits to all major groups of countries. One possible solution would be to have the limit of coastal jurisdiction over seabed resources defined in terms of the continental margin coupled with a system for sharing the “take”; in the area between 12 miles and the limit of the margin. The share payable to the international seabed authority would increase progressively with the distance of exploitation from the coast but would be moderated by the relative income level of the coastal State.     

Why are not all chilies hot? A trade-off limits pungency

Evolutionary biologists increasingly recognize that evolution can be constrained by trade-offs, yet our understanding of how and when such constraints are manifested and whether they restrict adaptive divergence in populations remains limited. Here, we show that spatial heterogeneity in moisture maintains a polymorphism for pungency (heat) among natural populations of wild chilies (Capsicum chacoense) because traits influencing water-use efficiency are functionally integrated with traits controlling pungency (the production of capsaicinoids). Pungent and non-pungent chilies occur along a cline in moisture that spans their native range in Bolivia, and the proportion of pungent plants in populations increases with greater moisture availability. In high moisture environments, pungency is beneficial because capsaicinoids protect the fruit from pathogenic fungi, and is not costly because pungent and non-pungent chilies grown in well-watered conditions produce equal numbers of seeds. In low moisture environments, pungency is less beneficial as the risk of fungal infection is lower, and carries a significant cost because, under drought stress, seed production in pungent chilies is reduced by 50 per cent relative to non-pungent plants grown in identical conditions. This large difference in seed production under water-stressed (WS) conditions explains the existence of populations dominated by non-pungent plants, and appears to result from a genetic correlation between pungency and stomatal density: non-pungent plants, segregating from intra-population crosses, exhibit significantly lower stomatal density (p = 0.003), thereby reducing gas exchange under WS conditions. These results demonstrate the importance of trait integration in constraining adaptive divergence among populations.     

The evolution of growth trajectories: what limits growth rate?

According to life‐history theory, growth rates are subject to strong directional selection due to reproductive and survival advantages associated with large adult body size. Yet, growth is commonly observed to occur at rates lower than the maximum that is physiologically possible and intrinsic growth rates often vary among populations. This implies that slower growth is favoured under certain conditions. Realized growth rate is thus the result of a compromise between the costs and advantages of growing rapidly, and the optimal rate of growth is not equivalent to the fundamental maximum rate. The ecological and evolutionary factors influencing growth rate are reviewed, with particular emphasis on how growth might be constrained by direct fitness costs. Costs of accelerating growth might contribute to the variance in fitness that is not attributable to age or size at maturity, as well as to the variation in life‐history strategies observed within and among species. Two main approaches have been taken to study the fitness trade‐offs relating to growth rate. First, environmental manipulations can be used to produce treatment groups with different rates of growth. Second, common garden experiments can be used to compare fitness correlates among populations with different intrinsic growth rates. Data from these studies reveal a number of potential costs for growth over both the short and long term. In order to acquire the energy needed for faster growth, animals must increase food intake. Accordingly, in many taxa, the major constraint on growth rate appears to arise from the trade‐off between predation risk and foraging effort. However, growth rates are also frequently observed to be submaximal in the absence of predation, suggesting that growth trajectories also impact fitness via other channels, such as the reallocation of finite resources between growth and other traits and functions. Despite the prevalence of submaximal growth, even when predators are absent, there is surprisingly little evidence to date demonstrating predator‐independent costs of growth acceleration. Evidence that does exist indicates that such costs may be most apparent under stressful conditions. Future studies should examine more closely the link between patterns of resource allocation to traits in the adult organism and lifetime fitness. Changes in body composition at maturation, for example, may determine the outcome of trade‐offs between reproduction and survival or between early and late reproduction. A number of design issues for studies investigating costs of growth that are imposed over the long term are discussed, along with suggestions for alternative approaches. Despite these issues, identifying costs of growth acceleration may fill a gap in our understanding of life‐history evolution: the relationships between growth rate, the environment, and fitness may contribute substantially to the diversification of life histories in nature.     

Phenotypic selection in natural populations: what limits directional selection?

Studies of phenotypic selection document directional selection in many natural populations. What factors reduce total directional selection and the cumulative evolutionary responses to selection? We combine two data sets for phenotypic selection, representing more than 4,600 distinct estimates of selection from 143 studies, to evaluate the potential roles of fitness trade-offs, indirect (correlated) selection, temporally varying selection, and stabilizing selection for reducing net directional selection and cumulative responses to selection. We detected little evidence that trade-offs among different fitness components reduced total directional selection in most study systems. Comparisons of selection gradients and selection differentials suggest that correlated selection frequently reduced total selection on size but not on other types of traits. The direction of selection on a trait often changes over time in many temporally replicated studies, but these fluctuations have limited impact in reducing cumulative directional selection in most study systems. Analyses of quadratic selection gradients indicated stabilizing selection on body size in at least some studies but provided little evidence that stabilizing selection is more common than disruptive selection for most traits or study systems. Our analyses provide little evidence that fitness trade-offs, correlated selection, or stabilizing selection strongly constrains the directional selection reported for most quantitative traits.     

What limits production of unusual monoenoic fatty acids in transgenic plants?

Unusual monounsaturated fatty acids are major constituents (greater than 80%) in seeds of Coriandrum sativum L. (coriander) and Thunbergia alata Bojer, as well as in glandular trichomes (greater than 80% derived products) of Pelargonium x hortorum (geranium). These diverged fatty acid structures are produced via distinct plastidial acyl-acyl carrier protein (ACP) desaturases. When expressed in Arabidopsis thaliana (L.) Heynh. under strong seed-specific promoters the unusual acyl-ACP desaturases resulted in accumulation of unusual monoene fatty acids at 1-15% of seed fatty acid mass. In this study, we have examined several factors that potentially limit higher production of unusual monoenes in transgenic oilseeds. (i) Immunoblots indicated that the introduced desaturases were expressed at levels equivalent to or higher than the endogenous delta9 18:0-ACP desaturase. However, the level of unusual fatty acid produced in transgenic plants was not correlated with the level of desaturase expression. (ii) The unusual desaturases were expressed in several backgrounds, including antisense 18:0-ACP desaturase plants, in fab1 mutants, and co-expressed with specialized ACP or ferredoxin isoforms. None of these experiments led to high production of expected products. (iii) No evidence was found for degradation of the unusual fatty acids during seed development. (iv) Petroselinic acid added to developing seeds was incorporated into triacylglycerol as readily as oleic acid, suggesting no major barriers to its metabolism by enzymes of glycerolipid assembly. (v) In vitro and in situ assay of acyl-ACP desaturases revealed a large discrepancy of activity when comparing unusual acyl-ACP desaturases with the endogenous delta9 18:0-ACP desaturase. The combined results, coupled with the sensitivity of acyl-ACP desaturase activity to centrifugation and low salt or detergent suggests low production of unusual monoenes in transgenic plants may be due to the lack of, or incorrect assemble of, a necessary multi-component enzyme association.     

What limits the efficiency of double-strand break-dependent stress-induced mutation in Escherichia coli?

Stress-induced mutation is a collection of molecular mechanisms in bacterial, yeast and human cells that promote mutagenesis specifically when cells are maladapted to their environment, i.e. when they are stressed. Here, we review one molecular mechanism: double-strand break (DSB)-dependent stress-induced mutagenesis described in starving Escherichia coli. In it, the otherwise high-fidelity process of DSB repair by homologous recombination is switched to an error-prone mode under the control of the RpoS general stress response, which licenses the use of error-prone DNA polymerase, DinB, in DSB repair. This mechanism requires DSB repair proteins, RpoS, the SOS response and DinB. This pathway underlies half of spontaneous chromosomal frameshift and base substitution mutations in starving E. coli [Proc Natl Acad Sci USA 2011;108:13659-13664], yet appeared less efficient in chromosomal than F' plasmid-borne genes. Here, we demonstrate and quantify DSB-dependent stress-induced reversion of a chromosomal lac allele with DSBs supplied by I-SceI double-strand endonuclease. I-SceI-induced reversion of this allele was previously studied in an F'. We compare the efficiencies of mutagenesis in the two locations. When we account for contributions of an F'-borne extra dinB gene, strain background differences, and bypass considerations of rates of spontaneous DNA breakage by providing I-SceI cuts, the chromosome is still ～100 times less active than F. We suggest that availability of a homologous partner molecule for recombinational break repair may be limiting. That partner could be a duplicated chromosomal segment or sister chromosome.     

Hydraulic limits preceding mortality in a piñon-juniper woodland under experimental drought

Drought‐related tree mortality occurs globally and may increase in the future, but we lack sufficient mechanistic understanding to accurately predict it. Here we present the first field assessment of the physiological mechanisms leading to mortality in an ecosystem‐scale rainfall manipulation of a piñon–juniper (Pinus edulis–Juniperus monosperma) woodland. We measured transpiration (E) and modelled the transpiration rate initiating hydraulic failure (E_crit). We predicted that isohydric piñon would experience mortality after prolonged periods of severely limited gas exchange as required to avoid hydraulic failure; anisohydric juniper would also avoid hydraulic failure, but sustain gas exchange due to its greater cavitation resistance. After 1 year of treatment, 67% of droughted mature piñon died with concomitant infestation by bark beetles (Ips confusus) and bluestain fungus (Ophiostoma spp.); no mortality occurred in juniper or in control piñon. As predicted, both species avoided hydraulic failure, but safety margins from E_crit were much smaller in piñon, especially droughted piñon, which also experienced chronically low hydraulic conductance. The defining characteristic of trees that died was a 7 month period of near‐zero gas exchange, versus 2 months for surviving piñon. Hydraulic limits to gas exchange, not hydraulic failure per se, promoted drought‐related mortality in piñon pine.     

Protein function space: viewing the limits or limited by our view?

Given that the number of protein functions on earth is finite, the rapid expansion of biological knowledge and the concomitant exponential increase in the number of protein sequences should, at some point, enable the estimation of the limits of protein function space. The functional coverage of protein sequences can be investigated using computational methods, especially given the massive amount of data being generated by large-scale environmental sequencing (metagenomics). In completely sequenced genomes, the fraction of proteins to which at least some functional features can be assigned has recently risen to as much as approximately 85%. Although this fraction is more uncertain in metagenomics surveys, because of environmental complexities and differences in analysis protocols, our global knowledge of protein functions still appears to be considerable. However, when we consider protein families, continued sequencing seems to yield an ever-increasing number of novel families. Until we reconcile these two views, the limits of protein space will remain obscured.