Interchromosomal duplication of major histocompatibility complex class I regions in rainbow trout (Oncorhynchus mykiss), a species with a presumably recent tetraploid ancestry

Salmonid fishes are among the few animal taxa with a probable recent tetraploid ancestor. The present study is the first to compare large (>100 kb) duplicated genomic sequence fragments in such species. Two contiguous stretches with major histocompatibility complex (MHC) class I genes were detected in a rainbow trout BAC library, mapped and sequenced. The MHC class I duplicated regions, mapped by fluorescence in situ hybridization (FISH), were shown to be located on different metaphase chromosomes, Chr 14 and 18. Gene organization in both duplications is similar to that in other fishes, in that the class I loci are tightly linked with the PSMB8, PSMB9, PSMB10 and ABCB3 genes. Whereas one region, Onmy-IA, has a classical MHC class I locus (UBA), Onmy-IB encodes only non-classical class Ib proteins. The nucleotide diversity between the Onmy-IA and Onmy-IB noncoding regions is about 14%. This suggests that the MHC class I duplication event has occurred about 60 mya close to the time of an hypothesized ancestral tetraploid event. The present article is the first convincing report on the co-existence of two closely related MHC class I core regions on two different chromosomes. The interchromosomal duplication and the homology levels are supportive of the tetraploid model.Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank database under the accession numbers AB162342, AB162343 and from AY525774 to AY525776.     

FREQUENCY‐DEPENDENT SOCIAL DOMINANCE IN A COLOR POLYMORPHIC CICHLID FISH

A mechanism commonly suggested to explain the persistence of color polymorphisms in animals is negative frequency‐dependent selection. It could result from a social dominance advantage to rare morphs. We tested for this in males of red and blue color morphs of the Lake Victoria cichlid, Pundamilia. Earlier work has shown that males preferentially attack the males of their own morph, while red males are more likely to win dyadic contests with blue males. In order to study the potential contribution of both factors to the morph co‐existence, we manipulated the proportion of red and blue males in experimental assemblages and studied its effect on social dominance. We then tried to disentangle the effects of the own‐morph attack bias and social dominance of red using simulations. In the experiment, we found that red males were indeed socially dominant to the blue ones, but only when rare. However, blue males were not socially dominant when rare. The simulation results suggest that an own‐morph attack bias reduces the social dominance of red males when they are more abundant. Thus, there is no evidence of symmetric negative frequency‐dependent selection acting on social dominance, suggesting that additional fitness costs to the red morph must explain their co‐existence.     

The X-ray structure of the haloalcohol dehalogenase HheA from Arthrobacter sp. strain AD2: insight into enantioselectivity and halide binding in the haloalcohol dehalogenase family

Haloalcohol dehalogenases are bacterial enzymes that cleave the carbon-halogen bond in short aliphatic vicinal haloalcohols, like 1-chloro-2,3-propanediol, some of which are recalcitrant environmental pollutants. They use a conserved Ser-Tyr-Arg catalytic triad to deprotonate the haloalcohol oxygen, which attacks the halogen-bearing carbon atom, producing an epoxide and a halide ion. Here, we present the X-ray structure of the haloalcohol dehalogenase HheA(AD2) from Arthrobacter sp. strain AD2 at 2.0-A resolution. Comparison with the previously reported structure of the 34% identical enantioselective haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 shows that HheA(AD2) has a similar quaternary and tertiary structure but a much more open substrate-binding pocket. Docking experiments reveal that HheA(AD2) can bind both enantiomers of the haloalcohol substrate 1-p-nitrophenyl-2-chloroethanol in a productive way, which explains the low enantiopreference of HheA(AD2). Other differences are found in the halide-binding site, where the side chain amino group of Asn182 is in a position to stabilize the halogen atom or halide ion in HheA(AD2), in contrast to HheC, where a water molecule has taken over this role. These results broaden the insight into the structural determinants that govern reactivity and selectivity in the haloalcohol dehalogenase family.     

Effects of multiple global change treatments on soil N2O fluxes

Global environmental changes are expected to alter ecosystem carbon and nitrogen cycling, but the interactive effects of multiple simultaneous environmental changes are poorly understood. Effects of these changes on the production of nitrous oxide (N₂O), an important greenhouse gas, could accelerate climate change. We assessed the responses of soil N₂O fluxes to elevated CO₂, heat, altered precipitation, and enhanced nitrogen deposition, as well as their interactions, in an annual grassland at the Jasper Ridge Global Change Experiment (CA, USA). Measurements were conducted after 6, 7 and 8?years of treatments. Elevated precipitation increased N₂O efflux, especially in combination with added nitrogen and heat. Path analysis supported the idea that increased denitrification due to increased soil water content and higher labile carbon availability best explained increased N₂O efflux, with a smaller, indirect contribution from nitrification. In our data and across the literature, single-factor responses tended to overestimate interactive responses, except when global change was combined with disturbance by fire, in which case interactive effects were large. Thus, for chronic global environmental changes, higher order interactions dampened responses of N₂O efflux to multiple global environmental changes, but interactions were strongly positive when global change was combined with disturbance. Testing whether these responses are general should be a high priority for future research.     

Functional and structural characterization of α-(1->2) branching sucrase derived from DSR-E glucansucrase

ΔN₁₂₃-glucan-binding domain-catalytic domain 2 (ΔN₁₂₃-GBD-CD2) is a truncated form of the bifunctional glucansucrase DSR-E from Leuconostoc mesenteroides NRRL B-1299. It was constructed by rational truncation of GBD-CD2, which harbors the second catalytic domain of DSR-E. Like GBD-CD2, this variant displays α-(1→2) branching activity when incubated with sucrose as glucosyl donor and (oligo-)dextran as acceptor, transferring glucosyl residues to the acceptor via a ping-pong bi-bi mechanism. This allows the formation of prebiotic molecules containing controlled amounts of α-(1→2) linkages. The crystal structure of the apo α-(1→2) branching sucrase ΔN₁₂₃-GBD-CD2 was solved at 1.90 Å resolution. The protein adopts the unusual U-shape fold organized in five distinct domains, also found in GTF180-ΔN and GTF-SI glucansucrases of glycoside hydrolase family 70. Residues forming subsite −1, involved in binding the glucosyl residue of sucrose and catalysis, are strictly conserved in both GTF180-ΔN and ΔN₁₂₃-GBD-CD2. Subsite +1 analysis revealed three residues (Ala-2249, Gly-2250, and Phe-2214) that are specific to ΔN₁₂₃-GBD-CD2. Mutation of these residues to the corresponding residues found in GTF180-ΔN showed that Ala-2249 and Gly-2250 are not directly involved in substrate binding and regiospecificity. In contrast, mutant F2214N had lost its ability to branch dextran, although it was still active on sucrose alone. Furthermore, three loops belonging to domains A and B at the upper part of the catalytic gorge are also specific to ΔN₁₂₃-GBD-CD2. These distinguishing features are also proposed to be involved in the correct positioning of dextran acceptor molecules allowing the formation of α-(1→2) branches.     

Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3

Neuroligins act as heterophilic adhesion molecules at neuronal synapses. Their cytoplasmic domains interact with synaptic scaffolding proteins, and have been shown to be intrinsically disordered. Here we report the backbone and side chain ¹H, ¹³C and ¹⁵N resonance assignments for the cytoplasmic domain of human neuroligin 3.     

RETRACTED ARTICLE: CO<Subscript>2</Subscript> effects on plant nutrient concentration depend on plant functional group and available nitrogen: a meta-analysis

Elevated CO₂ is expected to lower plant nutrient concentrations via carbohydrate dilution and increased nutrient use efficiency. Elevated CO₂ consistently lowers plant foliar nitrogen, but there is no consensus on CO₂ effects across the range of plant nutrients. We used meta-analysis to quantify elevated CO₂ effects on leaf, stem, root, and seed concentrations of B, Ca, Cu, Fe, K, Mg, Mn, P, S, and Zn among four plant functional groups and two levels of N fertilization. CO₂ effects on plant nutrient concentration depended on the nutrient, plant group, tissue, and N status. CO₂ reduced B, Cu, Fe, and Mg, but increased Mn concentration in the leaves of N₂ fixers. Elevated CO₂ increased Cu, Fe, and Zn, but lowered Mn concentration in grass leaves. Tree leaf responses were strongly related to N status: CO₂ significantly decreased Cu, Fe, Mg, and S at high N, but only Fe at low N. Elevated CO₂ decreased Mg and Zn in crop leaves grown with high N, and Mn at low N. Nutrient concentrations in crop roots were not affected by CO₂ enrichment, but CO₂ decreased Ca, K, Mg and P in tree roots. Crop seeds had lower S under elevated CO₂. We also tested the validity of a “dilution model.” CO₂ reduced the concentration of plant nutrients 6.6% across nutrients and plant groups, but the reduction is less than expected (18.4%) from carbohydrate accumulation alone. We found that elevated CO₂ impacts plant nutrient status differently among the nutrient elements, plant functional groups, and among plant tissues. Our synthesis suggests that differences between plant groups and plant organs, N status, and differences in nutrient chemistry in soils preclude a universal hypothesis strictly related to carbohydrate dilution regarding plant nutrient response to elevated CO₂.     

Phylogeny, classification and taxonomy of European dragonflies and damselflies (Odonata): a review

Although Europe is the cradle of dragonfly systematics and despite great progress in the last 2 decades, many issues in naming its species and understanding their evolutionary history remain unresolved. Given the public interest, conservation importance and scientific relevance of Odonata, it is time that remaining questions on the species?? status, names and affinities are settled. We review the extensive but fragmentary literature on the phylogeny, classification and taxonomy of European Odonata, providing summary phylogenies for well-studied groups and an ecological, biogeographic and evolutionary context where possible. Priorities for further taxonomic, phylogenetic and biogeographic research are listed and discussed. We predict that within a decade the phylogeny of all European species will be known.     

Fluorescently labeled branched polymers and thermal responsive nanoparticles for live cell imaging

Branched poly(methoxy-PEG acrylate) and thermally responsive poly(methoxy-PEG acrylate)-block-poly(N-isopropylacrylamide) are synthesized by RAFT polymerization. After reduction, these polymers are fluorescently labeled by reacting the free thiol groups with N-(5-fluoresceinyl)maleimide. As shown by DLS, the labeled copolymer poly(methoxy-PEG acrylate)-block-poly(N-isopropylacrylamide) forms nanoparticles at body temperature (37 °C) due to the presence of the thermosensitive poly(N-isopropylacrylamide). These materials were used as bioprobes for imaging HUVECs in vitro and chick embryo CAM in vivo. Both labeled polymer and nanoparticles are biocompatible and can be used as efficient fluorescent bioprobes.