Unnecessary roughness? Testing the hypothesis that predators destined for molecular gut‐content analysis must be hand‐collected to avoid cross‐contamination

Molecular gut‐content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Mass‐collection methods, such as sweep‐netting, vacuum sampling and foliage beating, could lead to regurgitation or rupturing of predators along with uneaten prey, thereby contaminating specimens and compromising resultant gut‐content data. Proponents of this ‘cross‐contamination hypothesis’ advocate hand‐collection as the best way to avoid cross‐contamination. However, hand‐collection is inefficient when large samples are needed, as with most ecological research. We tested the cross‐contamination hypothesis by setting out onto potato plants immature Coleomegilla maculata and Podisus maculiventris that had been fed larvae of either Leptinotarsa decemlineata or Leptinotarsa juncta, or unfed individuals of these predator species along with L. decemlineata larvae. The animals were then immediately re‐collected, either by knocking them vigorously off the plants onto a beat cloth and capturing them en masse with an aspirator (‘rough’ treatment) or by hand‐searching and collection with a brush (‘best practice’). Collected predators were transferred in the field to individual vials of chilled ethanol and subsequently assayed by PCR for fragments of cytochrome oxidase I of L. decemlineata and L. juncta. Ten to 39 per cent of re‐collected fed predators tested positive by PCR for DNA of both Leptinotarsa species, and 14–38% of re‐collected unfed predators contained L. decemlineata DNA. Overall levels of cross‐contamination in the rough (31%) and best‐practice (11%) samples were statistically different and supported the cross‐contamination hypothesis. A pilot study on eliminating external DNA contamination with bleach prior to DNA extraction and amplification gave promising results.     

Crucial roles of sucrose and microRNA399 in systemic signaling of P deficiency: A tale of two team players?

MicroRNAs (miRNAs) have been recognized as important regulators in plant response to nutrient deficiencies. Of particular interest is the discovery that miR399 functions systemically in the maintenance of phosphate (Pi) homeostasis in response to external Pi fluctuation. Recent studies have further implicated both miR399 and sugars (mainly sucrose) as potential signal molecules in the shoot-to-root communication of phosphorus (P) status. Given that both miR399 and sucrose are transported via the phloem, their potential interaction (or cross-talk) along the signaling pathway is especially appealing for further exploration. In this mini-review, we highlight recent progress in unraveling crucial roles of both sucrose and miR399 in P-deficiency signaling. In particular, we further discuss recent findings that photosynthetic carbon (C) assimilation and subsequent partitioning, by overriding signaling of low external Pi, act as checkpoints upstream of miR399 for the onset of a systemic P-deficiency status.Key words: sucrose, microRNA399, systemic signaling, P deficiencyPhosphorus (P) is an essential macronutrient for plant growth and development. Phosphate (Pi) availability is a limiting factor for crop productivity in many parts of the world''s arable land.¹ Because P fertilizer is a non-renewable resource and its mining is becoming ever more expensive, P has been recently highlighted as “the disappearing nutrient” of strategic importance in a recent NEWS FEATURE in the Nature.²Plant acclimation to P deficiency is a highly coordinated process with an extensive re-programming of biochemical and metabolic pathways. Altered carbon allocation between shoots and roots is a hallmark of most P-deficient plants resulting in a higher root-to-shoot ratio. In this process, sucrose, the main form of carbon (C) source from shoots to roots, has also been implicated to act as a secondary messenger for shoot-to-root signaling of P status to regulate gene expression and Pi uptake in roots.³ Sucrose has been found to be either required for or to enhance P deficiency-regulated gene expression in several plant species.^4–6 In recent years, microRNAs (miRNAs) have been recognized as crucial regulators in plant response to P deficiency. The mode of miRNA action is strictly based on the degree of sequence complementarity with target gene(s). It has been demonstrated that miR399 serves as a systemic signaling molecule in regulating systemic Pi homeostasis.^7–9 Both sucrose and miR399 are phloemmobile.^10–14 Several excellent reviews have been published recently to elucidate the roles of sucrose, miR399 and other aspects of P signaling.^3,14–18 However, a paradox arises between the seemingly ubiquitous role of sucrose in signaling various nutrient deficiencies, including those of nitrogen (N) and P, and the stringent specificity of plant responses to a particular nutrient deficiency. Here, we summarize recent advances in understanding the roles of both sucrose and miR399, as modulated by light regime and phloem transport, and discuss how plants may adopt C as a “common currency”, primarily in the form of sucrose, to initiate specific responses to P deficiency by regulating miRNA399 expression.     

PARP‐mediated proteasome activation: A co‐ordination of DNA repair and protein degradation?

During the evolution of aerobic life, antioxidant defence systems developed that either directly prevent oxidative modifications of the cellular constituents or remove the modified components. An example of the latter is the proteasome, which removes cytosolic oxidised proteins. Recently, a novel mechanism of activation of the nuclear 20S proteasome was discovered: automodified poly-(ADP-ribose) polymerase-1 (PARP-1) activates the proteasome to facilitate selective degradation of oxidatively damaged histones. Since activation of the PARP-1 itself is induced by DNA damage and is supposed to play a role in DNA repair, these new results suggest a joint role of PARP-1 in the removal of oxidised nucleoproteins and in DNA repair. We hypothesise that PARP-1 could provide a co-ordinative link between two nuclear antioxidant defence systems, whose concerted activation would produce a fast and efficient restoration of the native chromatin structure following oxidative stress.     

Always together: mate guarding or predator avoidance as determinants of group cohesion in white‐breasted mesites?

Being a member of a cohesive group can have fitness benefits such as decreased predation risk, increased feeding efficiency as well as enhanced access to social information and mates. However, competition and the risk of parasite transmission exert centrifugal forces on group‐living. Thus, the actual degree of cohesion is expected to vary as a function of the relative importance of several social and ecological factors. White‐breasted mesites Mesitornis variegata are medium‐sized ground‐dwelling birds endemic to the dry deciduous forests of western Madagascar. They live in stable breeding pairs or small family groups, mate monogamously and often form temporary heterospecific associations with canopy‐dwelling bird species that give alarm calls to which mesites respond with anti‐predator behaviours. We investigated the potential effects of predation risk and mate defence on mesite group cohesion by analysing inter‐individual distances of 20 groups as a function of mesite social organization, alarm call events, the size of associated heterospecific flocks, and the adults' reproductive state. Mesite social units were very cohesive, particularly in families, when associated with smaller heterospecific flocks, and after an alarm call event. Adult reproductive state did not influence breeding partners' cohesion. Therefore, the pronounced group cohesion in mesites seems to be mainly a response to the high predation risk typically associated with a terrestrial life‐style, and not to mate‐guarding. However, we suggest that high group cohesion due to predation risk could limit opportunities for solitary extra‐territorial forays to obtain extra‐pair copulations, thereby contributing to a strictly monogamous system in this species.     

Post‐dispersal granivory in a tall‐tussock grassland: A positive feedback mechanism of dominance?

Questions: Is post‐dispersal seed predation a factor contributing to a positive feedback mechanism for dominance of tall‐tussock grasslands? Do seeds dispersed into neighbouring microhabitats of contrasting dominance differ in their probabilities of being predated? Does predation rate vary among predator groups? Do seed eaters selectively forage among the available seeds? Location: The southern and flooding sub‐regions of the Argentinian Pampas. Methods: We examined seed predation by vertebrate and invertebrate predators within two microhabitats of grassland mosaics (highly dominated tall‐grass patches vs. scarcely dominated short‐grass matrix) for different seed species in semi‐natural grasslands. Proportion of seeds eaten by different predator groups was estimated through exclusion experiments and analysed using ANOVA for split‐split‐plot designs. Experiments were performed during the autumn of two consecutive years in both Pampa sub‐regions. Results: Removal of seeds after a five day trial was two to four times higher in the tall‐grass patches than in the short‐grass matrix. During the same period, vertebrate predation was six times higher than invertebrate predation in the tall‐grass phase of the Southern Pampa, but it did not differ in the short‐grass matrix. Relative predation among phases showed the same pattern in the Hooding Pampa, where preferences by seed species also varied according to phase. Conclusions: The highest predation intensity shown by vertebrates in the tall‐grass patches indicates that they are the main seed predators in these systems, possibly because this microhabitat grants them refuge against carnivorous predators. This could significantly reduce the available seeds for recruitment of subordinate species after different disturbance events (fires, trampling by large herbivores, burrowing), representing an active filter to the floristic composition of the patch and contributing with other mechanisms to the dominance of tall‐grass species.     

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post‐Darwinian biology?

The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric 'epigenetic landscape', which actually represents the quasi-potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re-wiring of regulatory interactions - offering a link between genetic mutation and sudden, broad evolutionary changes.     

Can indirect selection and genetic context contribute to trait diversification? A transition‐probability study of blossom‐colour evolution in two genera

Darwin recognized that biological diversity has accumulated as a result of both adaptive and nonadaptive processes. Very few studies, however, have addressed explicitly the contribution of nonadaptive processes to evolutionary diversification, and no general procedures have been established for distinguishing between adaptive and nonadaptive processes as sources of trait diversity. I use the diversification of flower colour as a model system for attempting to identify adaptive and nonadaptive causes of trait diversification. It is widely accepted that variation in flower colour reflects direct, adaptive response to divergent selective pressures generated by different pollinators. However, diversification of flower colour may also result from the effects of nonadaptive, pleiotropic relationships with vegetative traits. Floral pigments that have pleiotropic relationships to vegetative pigments may evolve and diversify in at least two nonadaptive ways. (1) Indirect response to selection on the pleiotropically related nonfloral traits may occur (indirect selection). (2) Divergent evolution in response to parallel selective pressures (e.g. selection by pollinators for visually obvious flowers) may occur because populations are at different genetic starting points, and each population follows its own genetic `line of least resistance.' A survey of literature suggests that pleiotropic relationships between flower colour and vegetative traits are common. Phylogenetically informed analyses of comparative data from Dalechampia (Euphorbiaceae) and Acer (Aceraceae), based on trait‐transition probabilities and maximum likelihood, indicated that floral and vegetative pigments are probably pleiotropically related in these genera, and this relationship better explains the diversification of floral colour than does direct selection by pollinators. In Dalechampia pink/purple floral bract colour may have originated by indirect response to selection on stem and leaf pigments. In Acer selection by pollinators for visually obvious flowers may to have led to the evolution of red or purple flowers in lineages synthesizing and deploying red anthocyanins in leaves, and pale‐green or yellow flowers in species not deploying red anthocyanins in vegetative structures. This study illustrates the broader potential of indirect selection and parallel selection on different genetic starting points to contribute to biological diversity, and the value of testing directly for the operation of these nonadaptive diversifying processes.     

At what spatial scales does resource selection vary? A case study of koalas in a semi‐arid region

The conservation of any species requires understanding and predicting the distribution of its habitat and resource use, including the effects of scale‐dependent variation in habitat and resource quality. Consequently, testing for resource selection at the appropriate scales is critical. We investigated how the resource selection process varies across scales, using koalas in a semi‐arid landscape of eastern Australia as a case study. We asked: at what scales does tree selection by koalas vary across regions? We tested the importance of the variation of our ecological predictors at the following scales: (i) the site‐scale (a stand of trees representing an individual koala's perception of local habitat); (ii) the landscape‐scale (10 × 10 km area representing a space within which a population of koalas exists); and (iii) a combination of these scales. We used a mixed‐modelling approach to quantify variation in selection of individual trees by koalas among sites and landscapes within a 1600 km² study area. We found that tree species, and tree height, were the most important factors influencing tree selection, and that their effect did not vary across scales. In contrast, preferences for trees of different condition, which is the state of tree canopy health, did vary across landscapes, indicating spatial variation in the selection of trees with respect to tree condition at the landscape‐scale, but not at the site‐scale. We conclude that resource selection processes can depend on the quality of those resources at different scales and their heterogeneous nature across landscapes, highlighting the consequence of scale‐dependent ecological processes. Designing studies that capture the heterogeneity in habitat and resources used by species that have an extensive distribution is an important prerequisite for effective conservation planning and management.     

Non‐consumptive effects of predation: does perceived risk strengthen the genetic integration of behaviour and morphology in stickleback?

Predators can shape genetic correlations in prey by altering prey perception of risk. We manipulated perceived risk to test whether such non‐consumptive effects tightened behavioural trait correlations in wild‐caught stickleback from high‐ compared to low‐risk environments due to genetic variation in plasticity. We expected tighter genetic correlations within perceived risk treatments than across them, and tighter genetic correlations in high‐risk than in low‐risk treatments. We identified genetic variation in plasticity, with genetic correlations between boldness, sociality, and antipredator morphology, as expected, being tighter within treatments than across them, for both of two populations. By contrast, genetic correlations did not tighten with exposure to risk. Tighter phenotypic correlations in wild stickleback may thus arise because predators induce correlational selection on environmental components of these traits, or because predators tighten residual correlations by causing environmental heterogeneity that is controlled in the laboratory. Our study places phenotypic integration firmly into an ecological context.     

Age‐related increases in human lymphocyte DNA damage: is there a role of aerobic fitness?

Oxidative stress has been advanced as one of the major causes of damage to DNA and other macromolecules. Although physical exercise may also increase oxidative stress, an important role has been recognized for regular exercise in improving the overall functionality of the body, as indicated by an increase in maximal aerobic uptake (O_2max), and in resistance to cell damage. The aims of this study were 1) to evaluate the association between DNA damage in human lymphocytes and age and 2) to evaluate the association between DNA damage in human lymphocytes and O_2max. The sample was composed of 36 healthy and nonsmoking males, aged from 20 to 84 years. O_2max was evaluated through the Bruce protocol with direct measurement of oxygen consumption. The comet assay was used to evaluate the DNA damage, strand breaks and formamidopyrimidine DNA glycosylase (FPG)‐sensitive sites. We found a positive correlation of age with DNA strand breaks but not with FPG‐sensitive sites. O_2max was significantly inversely related with DNA strand breaks, but this relation disappeared when adjusted for age. A significantly positive relation between O_2max and FPG‐sensitive sites was verified. In conclusion, our results showed that younger subjects have lower DNA strand breaks and higher O_2max compared with older subjects and FPG‐sensitive sites are positively related with O_2max, probably as transient damage due to the acute effects of daily physical activity. Copyright © 2013 John Wiley & Sons, Ltd.     

Clinical and pathologic manifestation of oesophagostomosis in African great apes: does self‐medication in wild apes influence disease progression?

Nodular worms (Oesophagostomum spp.) are common intestinal parasites found in cattle, pig, and primates including humans. In human, they are responsible for serious clinical disease called oesophagostomosis resulting from the formation of granulomas, caseous lesions or abscesses in intestinal walls. In wild great apes, the fecal prevalence of this parasite is high, but little information is available concerning the clinical signs and lesions associated. In the present study, we describe six cases of multinodular oesophagostomosis in free-ranging and ex-captive chimpanzees and captive gorillas caused by Oesophagostomum stephanostomum. While severe clinical signs associated with this infection were observed in great apes raised in sanctuaries, nodules found in wild chimpanzees do not seem to affect their health status. One hypothesis to explain this difference would be that in wild chimpanzees, access to natural environment and behavior such as rough leaves swallowing combined with ingestion of plants having pharmacological properties would prevent severe infection and decrease potential symptoms.     

A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre‐columbian contact?

Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century. In an attempt to shed further light on the entry date of the C1 lineage into the Icelandic mtDNA pool and its geographical origin, we used the deCODE Genetics genealogical database to identify additional matrilineal ancestors that carry the C1 lineage and then sequenced the complete mtDNA genome of 11 contemporary C1 carriers from four different matrilines. Our results indicate a latest possible arrival date in Iceland of just prior to 1700 and a likely arrival date centuries earlier. Most surprisingly, we demonstrate that the Icelandic C1 lineage does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. Rather, it is presently the only known member of a new subclade, C1e. While a Native American origin seems most likely for C1e, an Asian or European origin cannot be ruled out.     

MM/PBSA analysis of molecular dynamics simulations of bovine β‐lactoglobulin: Free energy gradients in conformational transitions?

The pH-driven opening and closure of beta-lactoglobulin EF loop, acting as a lid and closing the internal cavity of the protein, has been studied by molecular dynamics (MD) simulations and free energy calculations based on molecular mechanics/Poisson-Boltzmann (PB) solvent-accessible surface area (MM/PBSA) methodology. The forms above and below the transition pH differ presumably only in the protonation state of residue Glu89. MM/PBSA calculations are able to reproduce qualitatively the thermodynamics of the transition. The analysis of MD simulations using a combination of MM/PBSA methodology and the colony energy approach is able to highlight the driving forces implied in the transition. The analysis suggests that global rearrangements take place before the equilibrium local conformation is reached. This conclusion may bear general relevance to conformational transitions in all lipocalins and proteins in general.