Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

Since their initial discovery, transposons have been widely used as mutagens for forward and reverse genetic screens in a range of organisms. The problems of high copy number and sequence divergence among related transposons have often limited the efficiency at which tagged genes can be identified. A method was developed to identity the locations of Mutator (Mu) transposons in the Zea mays genome using a simple enrichment method combined with genome resequencing to identify transposon junction fragments. The sequencing library was prepared from genomic DNA by digesting with a restriction enzyme that cuts within a perfectly conserved motif of the Mu terminal inverted repeats (TIR). Paired-end reads containing Mu TIR sequences were computationally identified and chromosomal sequences flanking the transposon were mapped to the maize reference genome. This method has been used to identify Mu insertions in a number of alleles and to isolate the previously unidentified lazy plant1 (la1) gene. The la1 gene is required for the negatively gravitropic response of shoots and mutant plants lack the ability to sense gravity. Using bioinformatic and fluorescence microscopy approaches, we show that the la1 gene encodes a cell membrane and nuclear localized protein. Our Mu-Taq method is readily adaptable to identify the genomic locations of any insertion of a known sequence in any organism using any sequencing platform.     

Equal reproductive success of phenotypes in the Larus glaucescens–occidentalis complex

Glaucous‐winged gulls Larus glaucescens and western gulls L. occidentalis hybridize extensively where their ranges overlap along the coasts of Washington and Oregon, producing a continuum of phenotypic intergrades between the two parental species. This zone often is considered an example of geographically bounded hybrid superiority, but studies of relative success among parental types and hybrids have not provided consistent support for this model. We tested the predictions of the dynamic‐equilibrium and geographically bounded hybrid superiority hypotheses by studying mate choice and reproductive success among gulls on Protection Island, Washington, the largest breeding colony of glaucous‐winged/western gulls within the hybrid zone. The dynamic‐equilibrium hypothesis posits that hybridization due to dispersal balances selection against less fit hybrids and assortative mating is adaptive. Geographically bounded hybrid superiority posits that hybrids are better fit than parental types within an ecotone between the environments to which the parental species are adapted, and a preference for hybrid mates is adaptive. Additionally, we investigated whether hatching success and nest site choice are correlated for Protection Island gulls. We assigned a hybrid index to each sample bird by examining plumage melanism and bare part coloration in the field. Sheltered nests contained larger clutches and exhibited increased hatching success, but choice of nest habitat was not associated with hybrid index. Western gull‐like pairs produced smaller third eggs; however, hybrid index was not correlated with clutch size or hatching success. Protection Island gulls did exhibit assortative mating. In short, we did not find strong support for either geographically bounded hybrid superiority or the dynamic‐equilibrium hypothesis.     

The scale-dependence of population density–body mass allometry: Statistical artefact or biological mechanism?

The relation between population density and body mass has vexed ecologists for nearly 30 years as a consequence of high variability in the observed slope of the relation: No single generalisation of the relation has been accepted as universally representative. Here, we use a simple computational approach to examine how observational scale (the body mass range considered) determines variation in the density–mass pattern. Our model relies on two assumptions: (1) resources are partitioned in an unbiased manner among species with different masses; (2) the number of individuals that can be supported by a given quantity of resources is related to their metabolic rate (which is a function of their mass raised to the power of a scaling coefficient, b). We show that density (1) scales as a function of body mass raised to the power of ?b on average, but (2) the slope of the relation varies considerably at smaller scales of observation (over narrow ranges of body mass) as a consequence of details of species’ ecology associated with resource procurement. Historically, the effect of body mass range on the slope of the density–mass relation has been unfailingly attributed to a statistical effect. Here we show that the effect of body mass range on the slope of the density–mass relation may equally result from a biological mechanism, though we find it impossible to distinguish between the two. We observe that many of the explanations that have been offered to account for the variability in the slope of the relation invoke mechanisms associated with differences in body mass and we therefore suggest that body mass range itself might be the most important explanatory factor. Notably, our results imply that the energetic equivalence rule should not be expected to hold at smaller scales of observation, which suggests that it may not be possible to scale the mass- and temperature-dependence of organism metabolism to predict patterns at higher levels of biological organisation at smaller scales of observation.     

Modeling of Environmental Effects in Genome-Wide Association Studies Identifies SLC2A2 and HP as Novel Loci Influencing Serum Cholesterol Levels

Genome-wide association studies (GWAS) have identified 38 larger genetic regions affecting classical blood lipid levels without adjusting for important environmental influences. We modeled diet and physical activity in a GWAS in order to identify novel loci affecting total cholesterol, LDL cholesterol, HDL cholesterol, and triglyceride levels. The Swedish (SE) EUROSPAN cohort (N _SE = 656) was screened for candidate genes and the non-Swedish (NS) EUROSPAN cohorts (N _NS = 3,282) were used for replication. In total, 3 SNPs were associated in the Swedish sample and were replicated in the non-Swedish cohorts. While SNP rs1532624 was a replication of the previously published association between CETP and HDL cholesterol, the other two were novel findings. For the latter SNPs, the p-value for association was substantially improved by inclusion of environmental covariates: SNP rs5400 (p _{SE,unadjusted} = 3.6×10⁻⁵, p _SE,adjusted = 2.2×10⁻⁶, p _{NS,unadjusted} = 0.047) in the SLC2A2 (Glucose transporter type 2) and rs2000999 (p _{SE,unadjusted} = 1.1×10⁻³, p _SE,adjusted = 3.8×10⁻⁴, p _{NS,unadjusted} = 0.035) in the HP gene (Haptoglobin-related protein precursor). Both showed evidence of association with total cholesterol. These results demonstrate that inclusion of important environmental factors in the analysis model can reveal new genetic susceptibility loci.     

Applications of microwave dielectric heating in environment-related heterogeneous gas-phase catalytic systems

The application of microwave dielectric heating in a range of environment-related heterogeneous catalytic reaction systems has been reviewed. The reactions investigated include the decomposition of hydrogen sulfide, the reduction of sulfur dioxide with methane, the reformation of methane by carbon dioxide, the hydrodesulfurization of thiophene, and the oxidative coupling of methane. The interaction of microwave irradiation with heterogeneous catalytic systems and its consequence for the microwave heating behaviour of catalysts have been examined. The effect/mechanism of microwave dielectric heating on heterogeneous catalytic reaction systems has also been discussed.     

Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

Background  

Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes) but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability.     

Temperature preferences of the mite, Alaskozetes antarcticus, and the collembolan, Cryptopygus antarcticus from the maritime Antarctic

Abstract. The thermal preferences of Alaskozetes antarcticus (Acari, Cryptostigmata) and Cryptopygus antarcticus (Collembola, Isotomidae) were investigated over 6 h within a temperature gradient (?3 to +13 °C), under 100% relative humidity (RH) conditions. After 10 days of acclimation at ?2 or +11 °C, individual supercooling points (SCP) and thermopreferences were assessed, and compared with animals maintained for 10 days under fluctuating field conditions (?6 to +7 °C). Acclimation at ?2 °C lowered the mean SCP of both A. antarcticus (?24.2 ± 9.1) and C. antarcticus (?14.7 ± 7.7) compared to field samples (?19.0 ± 9.0 and ?10.7 ± 5.2, respectively). Acclimation at +11 °C increased A. antarcticus mean SCP values (?13.0 ± 8.5) relative to field samples, whereas those of C. antarcticus again decreased (?16.7 ± 9.1). Mites acclimated under field conditions or at +11 °C selected temperatures between ?3 and +1 °C. After acclimation at ?2 °C, both species preferred +1 to +5 °C. Cryptopygus antarcticus maintained under field conditions preferred +5 to +9 °C, whereas individuals acclimated at +11 °C selected +9 to +13 °C. For A. antarcticus, thermopreference was not influenced by its cold hardened state. The distribution of field specimens was further assessed within two combined temperature and humidity gradient systems: (i) 0–3 °C/12% RH, 3–6 °C/33% RH, 6–9 °C/75% RH and 9–12 °C/100% RH and (ii) 0–3 °C/100% RH, 3–6 °C/75% RH, 6–9 °C/33% RH and 9–12 °C/12% RH. In gradient (i), C. antarcticus distributed homogeneously, but, in gradient (ii), C. antarcticus preferred 0–3 °C/100% RH. Alaskozetes antarcticus selected temperatures between 0 and +6 °C regardless of RH conditions. Cryptopygus antarcticus appears better able than A. antarcticus to opportunistically utilize developmentally favourable thermal microclimates, when moisture availability is not restricted. The distribution of A. antarcticus appears more influenced by temperature, especially during regular freeze‐thaw transitions, when this species may select low temperature microhabitats to maintain a cold‐hardened state.     

Effects of an Introduced Piscivore on Native Trout: Insights from a Demographic Model

Introductions of exotic species pose a significant threat to the persistence of many native populations, including many inland fishes. In 1994, piscivorous lake trout (Salvelinus namaycush) were discovered in Yellowstone Lake, Yellowstone National Park, Wyoming, USA, one of the last strongholds of the native Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri). Predation by lake trout is expected to lead to a substantial decline in the native cutthroat trout population, which may have significant negative consequences for terrestrial predators that depend on cutthroat trout for prey and for the recreational fishery of the Park. We developed a matrix demographic model for the cutthroat trout population in Yellowstone Lake to identify the life stages that are most critical for understanding population dynamics. Parameter estimates (vital rates) were manipulated to explore the possible consequences of lake trout invasion. Comparisons of our results with current estimates of population trend and age structure suggested that our model reflected current conditions of the system. Elasticity analysis of the model revealed that population growth was most sensitive to annual survival of young trout, the group that is expected to be most vulnerable to lake trout predation. Projection of our deterministic model suggested that, in addition to a decline in abundance of cutthroat trout, the effects of lake trout may be manifest as changes in age and breeding structure of the population. Simulations of a stochastic version of the model indicated that a 60% or greater decline in the cutthroat trout population could be expected within 100 years if the lake trout population were permitted to grow uncontrolled. However, an effective control strategy that prevented the establishment of a large population of lake trout substantially reduced population decline, although the reduction in the availability of adult trout to terrestrial predators and anglers may be still be substantial (20–40%). In addition to current control activities in place in the Park, we recommend a renewed emphasis on understanding and monitoring juvenile life stages of cutthroat trout. Our results demonstrate the value of existing data sets for developing models to estimate the potential impact of biological invasions on the management and conservation of native populations, especially when opportunities and resources for additional empirical studies are limited.