Correlated trait responses to multiple selection pressures in larval amphibians reveal conflict avoidance strategies

1. Larval amphibians frequently experience simultaneous, conflicting selection pressures from ultraviolet‐B (UV‐B) radiation and predation risk, two stressors that can select for opposing defence strategies. When both UV‐B and predators are present, individuals can reconcile potential conflicts by correlating particular trait responses (e.g. combining dark or light body colouration with increased or decreased activity rates to create an appropriate multiple stressor strategy). Optimal combinations of body colour and activity rate are predicted to change across an elevation gradient with increasing UV‐B exposure. 2. In this study, we tested how larval amphibians combine changes in body colouration and activity rates to create a correlated response to potentially conflicting selection pressures. We quantified activity and colour response in two amphibian species, the pacific treefrog (Hyla regilla) and the long‐toed salamander (Ambystoma macrodactylum), from both high and low elevation populations, and exposed individuals to both a common predator and naturally relevant levels of UV‐B. 3. Hyla regilla and A. macrodactylum individuals from low elevation populations responded with correlated response strategies while high elevation populations did not. Low elevation H. regilla coupled decreased activity rates to reduce predator detection with dark body colouration to screen out UV‐B. Low elevation A. macrodactylum adopted cryptic colouration when predators were present and decreased activity in response to UV‐B. Individuals from high elevation H. regilla and A. macrodactylum populations responded only with changes in activity and not colour change. 4. The observed population differences may reflect variation in selection strengths across an elevation gradient. High elevation habitats may require individuals to focus defence efforts on the greatest potential risk. Additionally, pigmentation changes may not be an adequate defence in these UV‐B intense habitats.     

Compromise strategies for action selection

Among the many properties suggested for action-selection mechanisms, a prominent one is the ability to select compromise actions, i.e. actions that are not the best to satisfy any active goal in isolation, but rather compromise between multiple goals. This paper briefly reviews the history of compromise behaviour and presents experimental analyses of it in an attempt to determine how much compromise behaviour aids an agent. It concludes that optimal compromise behaviour has a surprisingly small benefit over non-compromise behaviour in the experiments performed, and presents some reasons why this may be true and hypothesizes cases where compromise behaviour is truly useful. In particular, it hypothesizes that a crucial factor is the level at which an action is taken (low-level actions are specific, such as 'move left leg'; high-level actions are vague, such as 'forage for food'). This paper hypothesizes that compromise behaviour is more beneficial for high- than low-level actions.     

Cross-correlations of center of mass and center of pressure displacements reveal multiple balance strategies in response to sinusoidal platform perturbations

Compared to static balance, dynamic balance requires a more complex strategy that goes beyond keeping the center of mass (COM) within the base of support, as established by the range of foot center of pressure (COP) displacement. Instead, neuromechanics must accommodate changing support conditions and inertial effects. Therefore, because they represent body's position and changes in applied moments, relative COM and COP displacements may also reveal dynamic postural strategies. To investigate this concept, kinetics and kinematics were recorded during three 12 cm, 1.25 Hz, sagittal perturbations. Forty-one individual trials were classified according to averaged cross-correlation lag between COM and COP displacement (lag(COM:COP)) and relative head-to-ankle displacement (Δ(head)/Δ(ankle)) using a k-means analysis. This process revealed two dominant patterns, one for which the lag(COM:COP) was positive (Group 1 (n=6)) and another for which it was negative (Group 2 (n=5)) . Group 1 (G1) absorbed power from the platform over most of the cycle, except during transitions in platform direction. Conversely, Group 2 (G2) participants applied power to the platform to maintain a larger margin between COM and COP position and also had larger knee flexion and ankle dorsiflexion, resulting in a lower stance. By the third repetition, the only kinematic differences were a slightly larger G2 linear knee displacement (p=0.008) and an antiphasic relationship of pelvis (linear) and trunk (angular) displacements. Therefore, it is likely that the strategy differences were detected by including COP in the initial screening method, because it reflects the pattern of force application that is not detectable by tracking body movements.     

Genetic perturbations of RNA reveal structure-based recognition in protein-RNA interaction

Protein-RNA recognition is an essential foundation of cellular processes, yet much remains unknown about these important interactions. The recognition between aminoacyl-tRNA synthetases and their cognate tRNA substrates is highly specific and essential for cell viability, due to the necessity for accurate translation of the genetic code into protein sequences. We selected an active tRNA that is highly mutated in the recognition nucleotides of the acceptor stem region in the alanine system. The functional properties of this mutant and its secondary derivatives demonstrate that recognition cannot be reduced to isolated structural elements, but rather the amino acid acceptor stem is being recognized as a unit.     

A general framework for marker-assisted selection

Early simulation studies have showed that the inclusion of epistatic components (especially the additive-by-additive effects) into marker-assisted selection (MAS) can improve selection efficiency for a short-term breeding program. In this study I extend Lande and Thompson's theory to incorporate both additive and non-additive effects into MAS with reference to the mass selection case. Four different indices are analytically examined in terms of the type of genetic components involved in the marker scores: phenotype-, general combining ability (GCA)-, and GCA and reciprocal effects-based marker scores. The phenotype-based marker index is applicable to any population of non-random mating, while the other three indices are applicable to the synthetic population derived from diallel crosses. All these indices may have higher selection efficiencies than the index with solely additive effects-associated markers as long as the detectable transient non-additive effects are present. The improvement in selection efficiency depends on the magnitude of non-additive variances and the proportion of them explained by markers. The index with the phenotype-based marker scores operates on the whole of the additive and non-additive effects, and has the largest selection efficiency. The indices with the GCA-based marker scores operate only on additive and additive-by-additive genetic variation and have relatively small selection efficiencies. Inclusion of the markers from organelle genomes can also increase selection efficiency, depending upon the proportion of the total genetic variation attributable to organelle genomes and the proportion of them explained by organelle genomic markers. Sharing of markers among different marker scores does not facilitate the improvement of selection efficiency.     

Distinct fast and slow processes contribute to the selection of preferred step frequency during human walking

Humans spontaneously select a step frequency that minimizes the energy expenditure of walking. This selection might be embedded within the neural circuits that generate gait so that the optimum is pre-programmed for a given walking speed. Or perhaps step frequency is directly optimized, based on sensed feedback of energy expenditure. Direct optimization is expected to be slow due to the compounded effect of delays and iteration, whereas a pre-programmed mechanism presumably allows for faster step frequency selection, albeit dependent on prior experience. To test for both pre-programmed selection and direct optimization, we applied perturbations to treadmill walking to elicit transient changes in step frequency. We found that human step frequency adjustments (n = 7) occurred with two components, the first dominating the response (66 ± 10% of total amplitude change; mean ± SD) and occurring quite quickly (1.44 ± 1.14 s to complete 95% of total change). The other component was of smaller amplitude (35 ± 10% of total change) and took tens of seconds (27.56 ± 16.18 s for 95% completion). The fast process appeared to be too fast for direct optimization and more indicative of a pre-programmed response. It also persisted even with unusual closed-loop perturbations that conflicted with prior experience and rendered the response energetically suboptimal. The slow process was more consistent with the timing expected for direct optimization. Our interpretation of these results is that humans may rely heavily on pre-programmed gaits to rapidly select their preferred step frequency and then gradually fine-tune that selection with direct optimization.     

Solvent selection strategies for extractive biocatalysis.

This report follows the development of systematic solvent screening strategies for the identification of superior pure solvents and introduces techniques for the identification of effective coextractants. Specifically, methods to predict the biocompatibility and extractant capability of solvents are discussed. Biocompatibility is predicted by using heuristic data or the correlations between bioactivity and the logarithm of the partition coefficient of the solvent or the concentration of solvent in the cell membrane. A computer program, known as the extractant screening program or ESP, has been developed to effectively predict the behavior of virtually any product in any solvent/aqueous system. It is demonstrated that a biocompatible yet poor solvent can be mixed with a toxic solvent that has better extractant properties to yield a mixture with improved solvent characteristics that is still biocompatible. The fact that solvents do not mix in an ideal manner is exploited by using ESP to identify solvent mixtures that are still biocompatible at relatively high concentrations of toxic solvent.     

全基因组关联研究的深度分析策略

2005年至今,全基因组关联研究(Genome-wide association study,GWAS)发现了大量复杂疾病/性状相关变异。近来,科学家们关注的焦点又集中在了如何利用GWAS数据进行深入分析,期待发现更多复杂疾病/性状的易感基因。一些新的策略和方法已经被尝试应用到复杂疾病/性状GWAS的后续研究中,例如深入分析GWAS数据;鉴定新的复杂疾病/性状易感基因/位点;国际合作和Meta分析;易感区域精细定位及测序;多种疾病共同易感基因研究;以及基因型填补,基于通路的关联分析,基因-基因、基因-环境交互作用和上位研究等。这些策略和方法的应用弥补了经典GWAS的一些不足之处,进一步推动了人类对复杂疾病/性状遗传机制的认识。文章对上述研究的策略、方法以及所面临的问题和挑战进行了综述,为读者描绘了GWAS后期工作的一个简要框架。     

Microarray probe selection strategies.

During recent years, DNA microarrays have become the method of choice to monitor the expression level of a large number of genes. Depending on the focus of the study and the method of microarray fabrication, a number of different strategies for probe selection may be most appropriate. One consideration concerns the length of the probe, ranging from some 25 residues used for oligonucleotide arrays to complete cDNAs. Unless resources are truly unlimited, an important decision to be made is the amount of effort to be put into the selection of genes and gene fragments. While high-throughput cDNA arraying projects usually will select from a collection of existing cDNA clones, smaller projects focusing on a number of selected genes can afford to selectively amplify fragments optimised for that purpose. This paper discusses the full scope of probe selection strategies, highlighting the problems that may be encountered in the various systems.     

Microsatellite markers reveal the potential for kin selection on black grouse leks

The evolution of social behaviour has puzzled biologists since Darwin. Since Hamilton''s theoretical work in the 1960s it has been realized that social behaviour may evolve through the effects of kinship. By helping relatives, an individual may pass on its genes despite negative effects on its own reproduction. Leks are groups of males that females visit primarily to mate. The selective advantage for males to join such social groups has been given much recent attention, but no clear picture has yet emerged. Here we show, using microsatellite analysis, that males but not females of a lekking bird (the black grouse, Tetrao tetrix) are genetically structured at the lek level. We interpret this structuring to be the effects of strong natal philopatry in males. This has the consequence that males on any specific lek should be more related than expected by chance as indicated by our genetic data. Our results thus suggest that kin selection is a factor that needs to be considered in the evolution and maintenance of the lek mating system in black grouse and sheds new light on models of lek evolution.     

Outlook for cellulase improvement: screening and selection strategies

Cellulose is the most abundant renewable natural biological resource, and the production of biobased products and bioenergy from less costly renewable lignocellulosic materials is important for the sustainable development of human beings. A reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitution of cellulase components. Here, we review quantitative cellulase activity assays using soluble and insoluble substrates, and focus on their advantages and limitations. Because there are no clear relationships between cellulase activities on soluble substrates and those on insoluble substrates, soluble substrates should not be used to screen or select improved cellulases for processing relevant solid substrates, such as plant cell walls. Cellulase improvement strategies based on directed evolution using screening on soluble substrates have been only moderately successful, and have primarily targeted improvement in thermal tolerance. Heterogeneity of insoluble cellulose, unclear dynamic interactions between insoluble substrate and cellulase components, and the complex competitive and/or synergic relationship among cellulase components limit rational design and/or strategies, depending on activity screening approaches. Herein, we hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface.     

GPS tracking devices reveal foraging strategies of Black-legged Kittiwakes

The Black-legged Kittiwake Rissa tridactyla is the most abundant gull species in the world, but some populations have declined in recent years, apparently due to food shortage. Kittiwakes are surface feeders and thus can compensate for low food availability only by increasing their foraging range and/or devoting more time to foraging. The species is widely studied in many respects, but long-distance foraging and the limitations of conventional radio telemetry have kept its foraging behavior largely out of view. The development of Global Positioning System (GPS) loggers is advancing rapidly. With devices as small as 8 g now available, it is possible to use this technology for tracking relatively small species of oceanic birds like kittiwakes. Here we present the first results of GPS telemetry applied to Black-legged Kittiwakes in 2007 in the North Pacific. All but one individual foraged in the neritic zone north of the island. Three birds performed foraging trips only close to the colony (within 13 km), while six birds had foraging ranges averaging about 40 km. The maximum foraging range was 59 km, and the maximum distance traveled was 165 km. Maximum trip duration was 17 h (mean 8 h). An apparently bimodal distribution of foraging ranges affords new insight on the variable foraging behaviour of Black-legged Kittiwakes. Our successful deployment of GPS loggers on kittiwakes holds much promise for telemetry studies on many other bird species of similar size and provides an incentive for applying this new approach in future studies.     

Proteomic strategies to reveal tumor heterogeneity among urothelial papillomas

Proteomics and immunohistochemistry were used to reveal tumor heterogeneity among urothelial papillomas (UPs) with the long term goal of predicting their biological potential in terms of outcome. First, we identified proteins that were deregulated in invasive fresh lesions as compared with normal urothelium, and thereafter we immunostained UPs with a panel of antibodies against some of the markers. Twenty-two major proteins showing variations of 2-fold or more in at least one-third of the invasive lesions were selected. Specific antibodies against several of the proteins were obtained, but only a few reacted positively in immunostaining. A panel consisting of antibodies against keratinocytes (CKs) 5, 13, 18, and 20 and markers of squamous metaplasia (CKs 7, 8, and 14) was used to probe normal urothelium and 30 UPs collected during a period of five years. Four UPs showed a normal phenotype, whereas the rest could be grouped in five major types that shared aberrant staining with the CK20 antibody. Type 1 heterogeneity (n = 4) showed preferred staining of the umbrella cells with the CK8 antibody. Type 2 (n = 11) was typified by the staining of the basal and intermediate layers with the CK20 antibody. Type 3 (n = 7) was characterized by the predominant staining of the basal cell layer with the CK5 antibody. Type 4 (n = 1) showed areas of CK7 negative cells, whereas type 5 (n = 3) showed loss of staining of the basal cells with the CK20. 29% of the patients experienced recurrences, but none progressed to invasive disease. Patients harboring phenotypic alterations in the basal cell compartment (types 3 and 5) showed the highest number of recurrences (4/7 and 2/3, respectively), and all type 3 lesions progressed to a higher degree of dedifferentiation. Even though a long term prospective study involving a larger sample size is required to assess the biological potential of these lesions, we believe that this approach will prove instrumental for revealing early phenotypic changes in different types of cancer.     

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H₂, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.     

Human SNPs reveal no evidence of frequent positive selection

We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Using mouse as a second species for computing sequence divergences, we found no evidence of positive selection: for both housekeeping and tissue-specific genes, the ratio of nonsynonymous to synonymous common SNPs per site showed no significant difference from that of divergence. Similarly, we observed no evidence of positive selection for the 289 and 149 genes that have orthologs available for divergence calculation between humans and chimpanzees and between humans and Old World monkeys, respectively. A comparison with previous SNP studies suggests that approximately 20% of the nonsynonymous SNPs in the human population are nearly neutral and that positive selection in the human genome might not be as frequent as previously thought.     

Natural selection of memory-one strategies for the iterated prisoner's dilemma

In the iterated Prisoner's Dilemma, mutually cooperative behavior can become established through Darwinian natural selection. In simulated interactions of stochastic memory-one strategies for the Iterated Prisoner's Dilemma, Nowak and Sigmund discovered that cooperative agents using a Pavlov (Win-Stay Lose-Switch) type strategy eventually dominate a random population. This emergence follows more directly from a deterministic dynamical system based on differential reproductive success or natural selection. When restricted to an environment of memory-one agents interacting in iterated Prisoner's Dilemma games with a 1% noise level, the Pavlov agent is the only cooperative strategy and one of very few others that cannot be invaded by a similar strategy. Pavlov agents are trusting but no suckers. They will exploit weakness but repent if punished for cheating.