A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31

Although both the alpha-amylase super-family, i.e. the glycoside hydrolase (GH) clan GH-H (the GH families 13, 70 and 77), and family GH31 share some characteristics, their different catalytic machinery prevents classification of GH31 in clan GH-H. A significant but remote evolutionary relatedness is, however, proposed for clan GH-H with GH31. A sequence alignment, based on the idea that residues equivalent in the primordial catalytic GH-H/GH31 (beta/alpha)(8)-barrel may not be found in the present-day GH-H and GH31 structures at strictly equivalent positions, shows remote sequence homologies covering beta3, beta4, beta7 and beta8 of the GH-H and GH31 (beta/alpha)(8)-barrels. Structure comparison of GH13 alpha-amylase and GH31 alpha-xylosidase guided alignment of GH-H and GH31 members for construction of evolutionary trees. The closest sequence relationship displayed by GH31 is to GH77 of clan GH-H.     

Phosphorylation sites of Arabidopsis MAP kinase substrate 1 (MKS1)

The Arabidopsis MAP kinase 4 (MPK4) substrate MKS1 was expressed in Escherichia coli and purified, full-length, 6x histidine (His)-tagged MKS1 was phosphorylated in vitro by hemagglutinin (HA)-tagged MPK4 immuno-precipitated from plants. MKS1 phosphorylation was initially verified by electrophoresis and gel-staining with ProQ Diamond and the protein was digested by either trypsin or chymotrypsin for maximum sequence coverage to facilitate identification of phosphorylated positions. Prior to analysis by mass spectrometry, samples were either desalted, passed over TiO(2) or both for improved phosphopeptide detection. As MAP kinases generally phosphorylate serine or threonine followed by proline (Ser/Thr-Pro), theoretical masses of potentially phosphorylated peptides were calculated and mass spectrometric peaks matching these masses were fragmented and searched for a neutral-loss signal at approximately 98 Da indicative of phosphorylation. Additionally, mass spectrometric peaks present in the MPK4-treated MKS1, but not in the control peptide map of untreated MKS1, were fragmented. Fragmentation spectra were subjected to a MASCOT database search which identified three of the twelve Ser-Pro serine residues (Ser72, Ser108, Ser120) in the phosphorylated form.     

Models of ontogenetic allometry in cladoceran morphology studies

Ontogenetic variation of morphological traits in cladocerans is usually analysed by a simple allometry function. We found that common cyclomorphic and inducible traits in Bosmina and Daphnia sometimes deviate from simple allometry, however. Consequently, simple allometric analysis may at times be inadequate since important aspects of the ontogenetic development may not be revealed. We suggest that other allometric models should be used more extensively in ontogenetic studies of cladocerans morphology. Especially, complex allometric functions may help analyse the effects of size-selective predation on morphological defence traits when predators prefer prey of intermediate size. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

Thioredoxin-2 affects lifespan and oxidative stress in Drosophila

Thioredoxins are proteins that have thiol-reducing activity and a characteristic conserved active site (WCGPC). They have several documented functions, e.g. roles in defences against oxidative stress and as electron donors for ribonucleotide-reductase. In Drosophila melanogaster there are three "classical" thioredoxins with the conserved active site: deadhead, ThioredoxinT and Thioredoxin-2. Here, we report the creation of null-mutations in the Thioredoxin-2 (Trx-2) gene. Characterization of two Trx-2 mutants indicated that Trx-2 affects the lifespan of D. melanogaster, and is involved in the organism's oxidative stress protection system. We found that the mutants have a shorter lifespan than wild-type flies, and thioredoxin double mutant flies showed lower tolerance to oxidative stress than wild-type flies, while flies carrying multiple copies of a Trx-2 rescue construct showed higher tolerance. These findings suggest that Trx-2 has modest or redundant functions in Drosophila physiology under unstressed conditions, but could be important during times of environmental stress.     

Anaerobic digestion of alfalfa silage with recirculation of process liquid

Process liquid recirculation initially stimulated one-phase anaerobic digestion of alfalfa silage in two semi-continuously fed and stirred tank reactors. Thus, with increased pH, alkalinity and stability it was possible to increase the organic loading rate to 3 g VS L(-1) d(-1), as compared to 2.25 g VS L(-1) d(-1) in a control reactor without recirculation. However, the recirculation of liquid eventually caused an accumulation of organic and inorganic substances, leading to an inhibition of hydrolysis and methanogenesis. This inhibition of microbial activity was prevented in one of the processes by replacing 50% of the recirculated process liquid with water during the second half of the operation period. A multiple linear regression model of principal components using seven input variables explained the variance in output variables nearly as well as the original model using all 23 measured input variables. The results show that it is necessary to adjust the degree of liquid recirculation to reach an optimal process.     

In situ warming strengthens trophic cascades in a coastal food web

Global warming may affect most organisms and their interactions. Theory and simple mesocosm experiments suggest that consumer top–down control over primary producer biomass should strengthen with warming, since consumer respiration increases faster with warming than plant photosynthesis. However, these predictions have so far not been tested on natural communities that have experienced warming over many generations. Natural systems display a higher diversity, heterogeneity and complexity than mesocosms, which could alter predicted effects of warming. Here we used an artificially heated part of the northern Baltic Sea (the Forsmark Biotest basin) to test how warming influences trophic interactions in a shallow coastal food web with four trophic levels: omnivorous fish, invertivorous fish, herbivorous invertebrates, and filamentous macroalgae. Monitoring of fish assemblages over six years showed that small invertivorous fish (gobiids, sticklebacks and minnows) were much less abundant in the heated basin than in unheated references areas. Stomach content analyses of the dominating omnivorous fish – Eurasian perch Perca fluviatilis – revealed a strikingly different diet within and outside the Biotest basin; gammarid crustaceans were the dominating prey at heated sites, whereas invertivorous fish (e.g. gobiids) dominated at unheated sites. A 45‐day cage experiment showed that fish exclusion did not affect the biomass of algal herbivores (gastropods and gammarids), but reduced algal biomass in heated sites (but not unheated). This suggests that warming induced a trophic cascade from fish to algae, and that this effect was mediated by predator‐induced changes in herbivore behavior, rather than number. Overall, our study suggests that warming has effectively compressed the food chain from four to three trophic levels (algae, gammarids and perch), which have benefitted the primary producers by reducing grazing pressure. Consequently, warming appears to have restructured this coastal food web through a combination of direct (physiological) and indirect (species interactions) effects.     

Body size evolution in an old insect order: No evidence for Cope's Rule in spite of fitness benefits of large size

We integrate field data and phylogenetic comparative analyses to investigate causes of body size evolution and stasis in an old insect order: odonates (“dragonflies and damselflies”). Fossil evidence for “Cope's Rule” in odonates is weak or nonexistent since the last major extinction event 65 million years ago, yet selection studies show consistent positive selection for increased body size among adults. In particular, we find that large males in natural populations of the banded demoiselle (Calopteryx splendens) over several generations have consistent fitness benefits both in terms of survival and mating success. Additionally, there was no evidence for stabilizing or conflicting selection between fitness components within the adult life‐stage. This lack of stabilizing selection during the adult life‐stage was independently supported by a literature survey on different male and female fitness components from several odonate species. We did detect several significant body size shifts among extant taxa using comparative methods and a large new molecular phylogeny for odonates. We suggest that the lack of Cope's rule in odonates results from conflicting selection between fitness advantages of large adult size and costs of long larval development. We also discuss competing explanations for body size stasis in this insect group.     

Technological Response of Wild Macaques (<Emphasis Type="Italic">Macaca fascicularis</Emphasis>) to Anthropogenic Change

Anthropogenic disturbances have a detrimental impact on the natural world; the vast expansion of palm oil monocultures is one of the most significant agricultural influences. Primates worldwide consequently have been affected by the loss of their natural ecosystems. Long-tailed macaques (Macaca fascilularis) in Southern Thailand have, however, learned to exploit oil palm nuts using stone tools. Using camera traps, we captured the stone tool behavior of one macaque group in Ao Phang-Nga National Park. Line transects placed throughout an abandoned oil palm plantation confirmed a high abundance of nut cracking sites. Long-tailed macaques previously have been observed using stone tools to harvest shellfish along the coasts of Thailand and Myanmar. The novel nut processing behavior indicates the successful transfer of existing lithic technology to a new food source. Such behavioral plasticity has been suggested to underlie cultural behavior in animals, suggesting that long-tailed macaques have potential to exhibit cultural tendencies. The use of tools to process oil palm nuts across multiple primate species allows direct comparisons between stone tool using nonhuman primates living in anthropogenic environments.