A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

BackgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.ResultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.ConclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.

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Studying <Emphasis Type="Italic">Daphnia</Emphasis> feeding behavior as a black box: a novel electrochemical approach

We present a novel approach for examining the complex feeding behavior of a filter feeder at a previously unexploited scale. A Daphnia lives in a viscous environment and thus creates a feeding current with a distinct laminar inflow and a repetitive pulsed outflow. We propose that by treating the feeding apparatus as a black box, and using the pulsed outflow current as a surrogate to the inside working of the apparatus, we can calculate feeding rate in near real time. The structure of the outflow is interpreted as a direct representation of the organism’s response to its environment. Therefore, we examine how the work performed by an organism’s feeding apparatus is altered according to environmental factors and metabolic demands. Our approach is an integration of optical (Schlieren system) and electrochemical (chronoamperometry) techniques that allow for real time visualization and temporal analysis of flow systems, respectively. As electrochemistry requires a tracer chemical, we employed low dopamine concentrations (≤ 1mM), and tested the effect of dopamine on the heart rate and swimming of Daphnia. It appears that dopamine free in solution at concentrations below 10 mM has no adverse effects on the organism, and all observed differences in Daphnia feeding behavior were due to environmental or metabolic factors. The feeding nature of daphnids in the presence or absence of food, and differences between the sexes is reported. Our results indicate that in the absence of food a Daphnia has a strict and repetitive feeding behavior with short delays between pumping actions. However, in the presence of food this behavior becomes complex, with increased delays between pumps, perhaps designed to maximize feeding efficiency. Our observations demonstrate that males have a higher appendage beat frequency than females under identical conditions. We hypothesize that the difference may be dictated by metabolic demand, as a male spends more time actively seeking a mate. The application of electrochemistry to the study of Daphnia feeding behavior is an improvement over current methods for its near real time quantification of behavioral response, its versatile application under varying environmental conditions and its extreme sensitivity to changes in the organism’s feeding behavior. This technique is a valuable addition to the current tools available for studying Daphnia feeding behavior and will allow us to learn more about the interactions of an organism with its environment. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

Optimal foraging by zooplankton within patches: the case of Daphnia

The motions of many physical particles as well as living creatures are mediated by random influences or 'noise'. One might expect that over evolutionary time scales internal random processes found in living systems display characteristics that maximize fitness. Here we focus on animal random search strategies [G.M. Viswanathan, S.V. Buldyrev, S. Havlin, M.G.E. Da Luz, E.P. Raposo, H.E. Stanley, Optimizing the success of random searches, Nature 401 (1999) 911-914; F. Bartumeus, J. Catalan, U.L. Fulco, M.L. Lyra, G.M. Viswanathan, Optimizing the encounter rate in biological interactions: Lévy versus Brownian stratagies, Phys. Rev. Lett. 88 (2002) 097901 and 89 (2002) 109902], and we describe experiments with the following Daphnia species: D. magna, D. galeata, D. lumholtzi, D. pulicaria, and D. pulex. We observe that the animals, while foraging for food, choose turning angles from distributions that can be described by exponential functions with a range of widths. This observation leads us to speculate and test the notion that this characteristic distribution of turning angles evolved in order to enhance survival. In the case of theoretical agents, some form of randomness is often introduced into search algorithms, especially when information regarding the sought object(s) is incomplete or even misleading. In the case of living animals, many studies have focused on search strategies that involve randomness [H.C. Berg, Random Walks in Biology, Princeton University, Princeton, New Jersey, 1993; A. Okubo, S.A. Levin (Eds.), Diffusion and Ecological Problems: Modern Perspectives, second ed., Springer, New York, 2001]. A simple theory based on stochastic differential equations of the motion backed up by a simulation shows that the collection of material (information, energy, food, supplies, etc.) by an agent executing Brownian-type hopping motions is optimized while foraging for a finite time in a supply patch of limited spatial size if the agent chooses turning angles taken from an exponential distribution with a specific stochastic intensity or 'noise width'. Search strategies that lead to optimization is a topic of high current interest across many disciplines [D. Wolpert, W. MacReady, No free lunch theorems for optimization, IEEE Transactions on Evolutionary Computation 1 (1997) 67].     

Hang on or run? Copepod mating versus predation risk in contrasting environments

Mating durations of copepods were found to differ significantly between fishless high-altitude waters and lowland lakes containing fish. In lowland species the whole mating process was completed within a few minutes, but it averaged over an hour in high-altitude species. Alpine copepods showed a prolonged post-copulatory association between mates, during which the male clasped the female for an extended period after spermatophore transfer, while in lowland species males abandoned their partner immediately after copulation. Prolonged associations also occurred after transfer of spermatophores to heterospecific females with shorter conspecific mating duration, suggesting that male interests largely dictate the time spent in tandem. The differences observed may be adaptations to environments with different predation pressure, as pairs in tandem are more conspicuous and less reactive than single animals. We argue that differences in mating behavior and mating duration evolved under sexual versus natural selection, reflecting trade-offs between enhancement of fertilization success and reduction of vulnerability to visual predation. In fishless mountain lakes with high intrasexual competition, guarding males can reduce the risk of spermatophore displacement or the risk that the female will accept sperm from rival males without increased risk of being eaten, thereby maximizing paternity. Populations from fishless alpine lakes further differed from lowland species by exhibiting higher female/male size dimorphism and more intense pigmentation. While these traits vary between populations according to predation pressure, mating duration appears to be more species-specific.     

Creating Highly Active Atomic Layer Deposited NiO Electrocatalysts for the Oxygen Evolution Reaction

Atomic layer deposition (ALD) provides a promising route for depositing uniform thin coatings of electrocatalysts useful in many technologies, including the splitting of water. For materials such as NiO _x that readily form hydrous oxides, however, the smooth, compact films deposited by ALD may result in higher overpotentials due to low catalyst surface area compared to other deposition methods. Here, the use of ALD–NiO thin films as oxygen evolution reaction (OER) electrocatalysts is explored. Thin films of crystalline ALD­–NiO are deposited and OER activity is tested using cyclic voltammetry (CV). Fe incorporated from the electrolyte can increase the activity of NiO, and it is shown that the turnover frequency (TOF) increases tenfold by going from an Fe‐poor to Fe‐rich KOH electrolyte. Applying a potential exfoliates the NiO, increasing the number of electrochemically accessible Ni sites. Interestingly, by X‐ray photoelectron spectroscopy (XPS) and CV, it is found that an Fe‐rich electrolyte reduces the amount of restructuring and oxidation is found. It is shown that a high surface area, high TOF catalyst may be created by using a two‐step process in which the sample is sequentially conditioned in Fe‐poor then Fe‐rich KOH. This work highlights the importance of pretreatment on catalytic activity for compact NiO films deposited by ALD.     

The three-dimensional structure of the ZAP-70 kinase domain in complex with staurosporine: implications for the design of selective inhibitors

The ZAP-70 tyrosine kinase plays a critical role in T cell activation and the immune response and therefore is a logical target for immunomodulatory therapies. Although the crystal structure of the tandem Src homology-2 domains of human ZAP-70 in complex with a peptide derived from the zeta subunit of the T cell receptor has been reported (Hatada, M. H., Lu, X., Laird, E. R., Green, J., Morgenstern, J. P., Lou, M., Marr, C. S., Phillips, T. B., Ram, M. K., Theriault, K., Zoller, M. J., and Karas, J. L. (1995) Nature 377, 32-38), the structure of the kinase domain has been elusive to date. We crystallized and determined the three-dimensional structure of the catalytic subunit of ZAP-70 as a complex with staurosporine to 2.3 A resolution, utilizing an active kinase domain containing residues 327-606 identified by systematic N- and C-terminal truncations. The crystal structure shows that this ZAP-70 kinase domain is in an active-like conformation despite the lack of tyrosine phosphorylation in the activation loop. The unique features of the ATP-binding site, identified by structural and sequence comparison with other kinases, will be useful in the design of ZAP-70-selective inhibitors.     

Mass density contrast in relation to the feeding currents in calanoid copepods

Theoretical analyses show that positively buoyant copepods areable to generate feeding currents by adopting upside-down bodypositions and pushing water upward. Thus, the excess buoyancyacting on the copepods will be balanced and cone-shaped feedingcurrents generated to transport water to the capture areas.The intensities of the feeding currents, which can be measuredin the present modeling study by calculating the volumetricflux going through the capture areas, are proportional to themass density contrasts between the copepods and the ambientseawater. The mass density contrasts may vary spatially andtemporally depending on copepod body contents and on the propertiesof the seawater immediately surrounding them. We focus on thecase where the mass density contrast between a wax ester-richcopepod and its ambient seawater can vary strongly with depthbecause wax esters are more compressible and 6–10 timesmore thermally expansible than seawater. These theoretical analysesshow that the intensities of the feeding currents generatedby wax ester-rich copepods vary strongly with depth. Our conclusionsfrom these theoretical analyses need to be tested by directobservations. This paper is one of six on the subject of the role of zooplanktonpredator–prey interactions in structuring plankton communities.