The energetic equivalence rule rejected because of a potentially common sampling error: evidence from carabid beetles

Abundance data from pitfall traps are widely used to estimate the relationship between beetle body size and abundance. Such data probably overestimate densities of large bodied species and may overestimate slopes of size‐abundance relationships. Here, we test this idea by comparing size‐abundance patterns found using data from pitfall trapping with those found with data from a quantitative method of estimating abundance, quadrat sampling. We use data from a total of 47 communities. As expected, slopes of size‐abundance relationships are significantly more positive when estimated using data from pitfall traps compared to when using quadrat sampling data. This was seen when looking across different communities, within communities sampled by both methods and when focusing on the set of species found by both methods within a community. These results were also generally found regardless of method of analysis, which were done using regression with species values as independent data points and using the independent contrast method, and with slopes estimated using ordinary least square regression or the structural relation. Most important, slopes of size‐abundance relationships based on data from pitfall traps were on average significantly more positive than ?0.75 on log–log scales, and thus inconsistent with the energetic equivalence rule. Slopes based on quadrat sampling, on the other hand, were on average not significantly different from ?0.75. The rejection of the energetic equivalence rule based on data from pitfall traps here is therefore a sampling artefact. Similar problems may apply to abundance data from virtually all insect trapping methods, and should make us consider re‐examining many of the size‐abundance patterns documented so far. As a large proportion of all animal species are insects, and traps are widely used to estimate abundance, this is a potentially important problem for our general understanding of the relationship between species body size and abundance.     

Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.     

Overexpression, physicochemical characterization, and modeling of a hyperthermophilic pyrococcus furiosus type 2 IPP isomerase

In the first step of this study, type 2 isopentenyl diphosphate isomerase (IDI2) from Pyrococcus furiosus (pf-IDI2), a hyperthermophilic microorganism, was cloned and overexpressed in E. coli. After purification, hyperthermophilic behavior of this protein was approached by means of enzymatic assays and thermal denaturation studies. Compared with the mesophilic Streptococcus pneumoniae IDI2, which unfolds and looses activity above 50 degrees C, pf-IDI2 is still folded and active at 80 degrees C. Molecular modeling was applied, in a parallel step, to understand the molecular basis of thermal stability. Comparison of IDI2 from S. pneumoniae, T. thermophilus, and P. furiosus suggested that additional charged residues present in the hyperthermophilic enzyme might contribute to its higher thermal stability. This could increase the number of salt bridges between monomers of IDI2 in P. furiosus enzyme and, hence, decrease flexibility of loops or N-terminal segment, thereby enhancing its thermal stability.     

Cognitive control and individual differences in economic ultimatum decision-making

Much publicity has been given to the fact that people's economic decisions often deviate from the rational predictions of standard economic models. In the classic ultimatum game, for example, most people turn down financial gains by rejecting unequal monetary splits. The present study points to neglected individual differences in this debate. After participants played the ultimatum game we tested for individual differences in cognitive control capacity of the most and least economic responders. The key finding was that people who were higher in cognitive control, as measured by behavioral (Go/No-Go performance) and neural (No-Go N2 amplitude) markers, did tend to behave more in line with the standard models and showed increased acceptance of unequal splits. Hence, the cognitively highest scoring decision-makers were more likely to maximize their monetary payoffs and adhere to the standard economic predictions. Findings question popular claims with respect to the rejection of standard economic models and the irrationality of human economic decision-making.     

Reviewing the low efficiency of protein utilization in heavy preruminant calves--a reductionist approach

The efficiency of protein utilization for growth in preruminant calves is decreasing with increasing body weight. In contrast to calves weighing less than 100 kg of body weight, heavy preruminant calves do not respond in protein retention to an increased intake of indispensable amino acids in dose-response studies. The marginal efficiency of protein utilization is low compared with pigs and milk-fed lambs at a similar stage of maturity. A reductionist approach was taken to perceive the potential mechanisms for the low protein utilization in preruminant calves. Neither an imbalance in the dietary protein to energy ratio nor a single limiting indispensable amino acid was responsible for the low efficiency. Also, amino acids were not specifically used to detoxify ammonia. Alternative hypotheses to explain the low efficiency are discussed and result in (i) a reduced post-absorptive supply of amino acids: e.g. by fermentation of milk in the (premature) rumen or preferential amino acid utilization by specific tissues; or (ii) a reduced post-absorptive amino acid utilization: e.g. by decreased insulin sensitivity, utilization of amino acids for gluconeogenesis or an asynchronous nutrient supply. In conclusion, several mechanisms for the low efficiency of protein utilization in heavy preruminant calves were excluded. Other physiological processes which are potentially involved remain to be studied, because the large potential for improving protein utilization in heavy preruminant calves asks for further exploration of their amino acid metabolism.     

Intraspecific queen parasitism in a highly eusocial bee

Insect societies are well-known for their advanced cooperation, but their colonies are also vulnerable to reproductive parasitism. Here, we present a novel example of an intraspecific social parasitism in a highly eusocial bee, the stingless bee Melipona scutellaris. In particular, we provide genetic evidence which shows that, upon loss of the mother queen, many colonies are invaded by unrelated queens that fly in from unrelated hives nearby. The reasons for the occurrence of this surprising form of social parasitism may be linked to the fact that unlike honeybees, Melipona bees produce new queens in great excess of colony needs, and that this exerts much greater selection on queens to seek alternative reproductive options, such as by taking over other nests. Overall, our results are the first to demonstrate that queens in highly eusocial bees can found colonies not only via supersedure or swarming, but also by infiltrating and taking over other unrelated nests.     

2‐photon excitation fluorescence microscopy enables deeper high‐resolution imaging of voltage and Ca2+ in intact mice,rat, and rabbit hearts

We describe a novel two‐photon (2P) laser scanning microscopy (2PLSM) protocol that provides ratiometric transmural measurements of membrane voltage (V_m) via Di‐4‐ANEPPS in intact mouse, rat and rabbit hearts with subcellular resolution. The same cells were then imaged with Fura‐2/AM for intracellular Ca²⁺ recordings. Action potentials (APs) were accurately characterized by 2PLSM vs. microelectrodes, albeit fast events (<1 ms) were sub‐optimally acquired by 2PLSM due to limited sampling frequencies (2.6 kHz). The slower Ca²⁺ transient (CaT) time course (>1ms) could be accurately described by 2PLSM. In conclusion, V_m ‐ and Ca²⁺‐sensitive dyes can be 2P excited within the cardiac muscle wall to provide AP and Ca²⁺ signals to ～400 µm. (© 2013 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

ProbeMaker: an extensible framework for design of sets of oligonucleotide probes

Background  

Procedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material. Such procedures require the design of large sets of probes using application-specific design constraints.     

The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser

The structure of photosystem II and the catalytic intermediate states of the Mn₄CaO₅ cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.