Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea
Acoustic recording has been recognized as a valuable tool for non-intrusive monitoring of the marine environment, complementing traditional visual surveys. Acoustic surveys conducted on coral ecosystems have so far been restricted to barrier reefs and to shallow depths (10–30 m). Since they may provide refuge for coral reef organisms, the monitoring of outer reef slopes and describing of the soundscapes of deeper environment could provide insights into the characteristics of different biotopes of coral ecosystems. In this study, the acoustic features of four different habitats, with different topographies and substrates, located at different depths from 10 to 100 m, were recorded during day-time on the outer reef slope of the north Coast of Moorea Island (French Polynesia). Barrier reefs appeared to be the noisiest habitats whereas the average sound levels at other habitats decreased with their distance from the reef and with increasing depth. However, sound levels were higher than expected by propagation models, supporting that these habitats possess their own sound sources. While reef sounds are known to attract marine larvae, sounds from deeper habitats may then also have a non-negligible attractive potential, coming into play before the reef itself.
Bertucci et al. (2017) Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea. PeerJ 5:e4019 https://doi.org/10.7717/peerj.4019
Attribute amnesia is greatly reduced with novel stimuli
Attribute amnesia is the counterintuitive phenomenon where observers are unable to report a salient aspect of a stimulus (e.g., its colour or its identity) immediately after the stimulus was presented, despite both attending to and processing the stimulus. Almost all previous attribute amnesia studies used highly familiar stimuli. Our study investigated whether attribute amnesia would also occur for unfamiliar stimuli. We conducted four experiments using stimuli that were highly familiar (colours or repeated animal images) or that were unfamiliar to the observers (unique animal images). Our results revealed that attribute amnesia was present for both sets of familiar stimuli, colour (p < .001) and repeated animals (p = .001); but was greatly attenuated, and possibly eliminated, when the stimuli were unique animals (p = .02). Our data shows that attribute amnesia is greatly reduced for novel stimuli.
Chen et al. (2017) Attribute amnesia is greatly reduced with novel stimuli. PeerJ 5:e4016 https://doi.org/10.7717/peerj.4016
Bed site selection by a subordinate predator: an example with the cougar (Puma concolor) in the Greater Yellowstone Ecosystem
As technology has improved, our ability to study cryptic animal behavior has increased. Bed site selection is one such example. Among prey species, bed site selection provides thermoregulatory benefits and mitigates predation risk, and may directly influence survival. We conducted research to test whether a subordinate carnivore also selected beds with similar characteristics in an ecosystem supporting a multi-species guild of competing predators. We employed a model comparison approach in which we tested whether cougar (Puma concolor) bed site attributes supported the thermoregulatory versus the predator avoidance hypotheses, or exhibited characteristics supporting both hypotheses. Between 2012–2016, we investigated 599 cougar bed sites in the Greater Yellowstone Ecosystem and examined attributes at two scales: the landscape (second-order, n = 599) and the microsite (fourth order, n = 140). At the landscape scale, cougars selected bed sites in winter that supported both the thermoregulatory and predator avoidance hypotheses: bed sites were on steeper slopes but at lower elevations, closer to the forest edge, away from sagebrush and meadow habitat types, and on southern, eastern, and western-facing slopes. In the summer, bed attributes supported the predator avoidance hypothesis over the thermoregulation hypothesis: beds were closer to forest edges, away from sagebrush and meadow habitat classes, and on steeper slopes. At the microsite scale, cougar bed attributes in both the winter and summer supported both the predator avoidance and thermoregulatory hypotheses: they selected bed sites with high canopy cover, high vegetative concealment, and in a rugged habitat class characterized by cliff bands and talus fields. We found that just like prey species, a subordinate predator selected bed sites that facilitated both thermoregulatory and anti-predator functions. In conclusion, we believe that measuring bed site attributes may provide a novel means of measuring the use of refugia by subordinate predators, and ultimately provide new insights into the habitat requirements and energetics of subordinate carnivores.
Kusler et al. (2017) Bed site selection by a subordinate predator: an example with the cougar (Puma concolor) in the Greater Yellowstone Ecosystem. PeerJ 5:e4010 https://doi.org/10.7717/peerj.4010
Colour change of twig-mimicking peppered moth larvae is a continuous reaction norm that increases camouflage against avian predators
Camouflage, and in particular background-matching, is one of the most common anti-predator strategies observed in nature. Animals can improve their match to the colour/pattern of their surroundings through background selection, and/or by plastic colour change. Colour change can occur rapidly (a few seconds), or it may be slow, taking hours to days. Many studies have explored the cues and mechanisms behind rapid colour change, but there is a considerable lack of information about slow colour change in the context of predation: the cues that initiate it, and the range of phenotypes that are produced. Here we show that peppered moth (Biston betularia) larvae respond to colour and luminance of the twigs they rest on, and exhibit a continuous reaction norm of phenotypes. When presented with a heterogeneous environment of mixed twig colours, individual larvae specialise crypsis towards one colour rather than developing an intermediate colour. Flexible colour change in this species has likely evolved in association with wind dispersal and polyphagy, which result in caterpillars settling and feeding in a diverse range of visual environments. This is the first example of visually induced slow colour change in Lepidoptera that has been objectively quantified and measured from the visual perspective of natural predators.
Eacock et al. (2017) Colour change of twig-mimicking peppered moth larvae is a continuous reaction norm that increases camouflage against avian predators. PeerJ 5:e3999 https://doi.org/10.7717/peerj.3999
Grassland habitat restoration: lessons learnt from long term monitoring of Swanworth Quarry, UK, 1997–2014
Habitat restoration projects are often conducted when prior use or extraction of natural resources results in land degradation. The success of restoration programmes, however, is variable, and studies that provide evidence of long term outcomes are valuable for evaluation purposes. This study focused on the restoration of vegetation within a limestone quarry in Dorset, UK between 1997 and 2014. Using a randomised block design, the effect of seed mix and seed rate on the development of community assemblage was investigated in comparison to a nearby target calcareous grassland site. We hypothesised that seed mix composition and sowing rate would influence both the trajectory of the grassland assemblage and final community composition. We found that species composition (in relation to both richness and community assemblage) was strongly influenced by time and to some extent by seed rate and seed mix. However, no treatments achieved strong resemblance to the calcareous grassland target vegetation; rather they resembled mesotrophic communities. We conclude that (as with previous studies) there is no “quick fix” for the establishment of a grassland community; long-term monitoring provides useful information on the trajectory of community development; sowing gets you something (in our case mesotrophic grassland), but, it may not be the target vegetation (e.g., calcicolous grassland) you want that is difficult to establish and regenerate; it is important to sow a diverse mix as subsequent recruitment opportunities are probably limited; post-establishment management should be explored further and carefully considered as part of a restoration project.
Smith et al. (2017) Grassland habitat restoration: lessons learnt from long term monitoring of Swanworth Quarry, UK, 1997–2014. PeerJ 5:e3942 https://doi.org/10.7717/peerj.3942
Supradapedon revisited: geological explorations in the Triassic of southern Tanzania
The upper Triassic deposits of the Selous Basin in south Tanzania have not been prospected for fossil tetrapods since the middle of last century, when Gordon M. Stockley collected two rhynchosaur bone fragments from the so called “Tunduru beds”. Here we present the results of a field trip conducted in July 2015 to the vicinities of Tunduru and Msamara, Ruvuma Region, Tanzania, in search for similar remains. Even if unsuccessful in terms of fossil discoveries, the geological mapping conducted during the trip improved our knowledge of the deposition systems of the southern margin of the Selous Basin during the Triassic, allowing tentative correlations to its central part and to neighbouring basins. Moreover, we reviewed the fossil material previously collected by Gordon M. Stockley, confirming that the remains correspond to a valid species, Supradapedon stockleyi, which was incorporated into a comprehensive phylogeny of rhynchosaurs and found to represent an Hyperodapedontinae with a set of mostly plesiomorphic traits for the group. Data gathered form the revision and phylogenetic placement of Su. stockleyi helps understanding the acquisition of the typical dental traits of Late Triassic rhynchosaurs, corroborating the potential of hyperodapedontines as index fossils of the Carnian-earliest Norian.
Langer et al. (2017) Supradapedon revisited: geological explorations in the Triassic of southern Tanzania. PeerJ 5:e4038 https://doi.org/10.7717/peerj.4038
Generation and characterization of cross neutralizing human monoclonal antibody against 4 serotypes of dengue virus without enhancing activity
Background Dengue disease is a leading cause of illness and death in the tropics and subtropics. Most severe cases occur among patients secondarily infected with a different dengue virus (DENV) serotype compared with that from the first infection, resulting in antibody-dependent enhancement activity (ADE). Our previous study generated the neutralizing human monoclonal antibody, D23-1B3B9 (B3B9), targeting the first domain II of E protein, which showed strong neutralizing activity (NT) against all four DENV serotypes. However, at sub-neutralizing concentrations, it showed ADE activity in vitro. Methods In this study, we constructed a new expression plasmid using the existing IgG heavy chain plasmid as a template for Fc modification at position N297Q by site-directed mutagenesis. The resulting plasmid was then co-transfected with a light chain plasmid to produce full recombinant IgG (rIgG) in mammalian cells (N297Q-B3B9). This rIgG was characterized for neutralizing and enhancing activity by using different FcγR bearing cells. To produce sufficient quantities of B3B9 rIgG for further characterization, CHO-K1 cells stably secreting N297Q-B3B9 rIgG were then established. Results The generated N297Q-B3B9 rIgG which targets the conserved N-terminal fusion loop of DENV envelope protein showed the same cross-neutralizing activity to all four DENV serotypes as those of wild type rIgG. In both FcγRI- and RII-bearing THP-1 cells and FcγRII-bearing K562 cells, N297Q-B3B9 rIgG lacked ADE activity against all DENV serotypes at sub-neutralizing concentrations. Fortunately, the N297Q-B3B9 rIgG secreted from stable cells showed the same patterns of NT and ADE activities as those of the N297Q-B3B9 rIgG obtained from transient expression against DENV2. Thus, the CHO-K1 stably expressing N297Q-B3B9 HuMAb can be developed as high producer stable cells and used to produce sufficient amounts of antibody for further characterization as a promising dengue therapeutic candidate. Discussion Human monoclonal antibody, targeted to fusion loop of envelope domainII (EDII), was generated and showed cross-neutralizing activity to 4 serotypes of DENV, but did not cause any viral enhancement activity in vitro. This HuMAb could be further developed as therapeutic candidates.
Injampa et al. (2017) Generation and characterization of cross neutralizing human monoclonal antibody against 4 serotypes of dengue virus without enhancing activity. PeerJ 5:e4021 https://doi.org/10.7717/peerj.4021
Assessing Mongolian gerbil emotional behavior: effects of two shock intensities and response-independent shocks during an extended inhibitory-avoidance task
Despite step-down inhibitory avoidance procedures that have been widely implemented in rats and mice to study learning and emotion phenomena, performance of other species in these tasks has received less attention. The case of the Mongolian gerbil is of relevance considering the discrepancies in the parameters of the step-down protocols implemented, especially the wide range of foot-shock intensities (i.e., 0.4–4.0 mA), and the lack of information on long-term performance, extinction effects, and behavioral patterning during these tasks. Experiment 1 aimed to (a) characterize gerbils’ acquisition, extinction, and steady-state performance during a multisession (i.e., extended) step-down protocol adapted for implementation in a commercially-available behavioral package (Video Fear Conditioning System—MED Associates Fairfax, VT, USA), and (b) compare gerbils’ performance in this task with two shock intensities – 0.5 vs. 1.0 mA—considered in the low-to-mid range. Results indicated that the 1.0 mA protocol produced more reliable and clear evidence of avoidance learning, extinction, and reacquisition in terms of increments in freezing and on-platform time as well as suppression of platform descent. Experiment 2 aimed to (a) assess whether an alternate protocol consisting of a random delivery of foot shocks could replicate the effects of Experiment 1 and (b) characterize gerbils’ exploratory behavior during the step-down task (jumping, digging, rearing, and probing). Random shocks did not reproduce the effects observed with the first protocol. The data also indicated that a change from random to response-dependent shocks affects (a) the length of each visit to the platform, but not the frequency of platform descends or freezing time, and (b) the patterns of exploratory behavior, namely, suppression of digging and rearing, as well as increments in probing and jumping. Overall, the study demonstrated the feasibility of the extended step-down protocol for studying steady performance, extinction, and reacquisition of avoidance behavior in gerbils, which could be easily implemented in a commercially available system. The observation that 1.0 mA shocks produced a clear and consistent avoidance behavior suggests that implementation of higher intensities is unnecessary for reproducing aversive-conditioning effects in this species. The observed patterning of freezing, platform descents, and exploratory responses produced by the change from random to periodic shocks may relate to the active defensive system of the gerbil. Of special interest is the probing behavior, which could be interpreted as risk assessment and has not been reported in other rodent species exposed to step-down and similar tasks.
Hurtado-Parrado et al. (2017) Assessing Mongolian gerbil emotional behavior: effects of two shock intensities and response-independent shocks during an extended inhibitory-avoidance task. PeerJ 5:e4009 https://doi.org/10.7717/peerj.4009
Microbial agents in macroscopically healthy mammary gland tissues of small ruminants
Background Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. Methods This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria. Results Twenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%), followed by environmental opportunists (34.76%), others (10.14%) and pathogens (8.68%). Most mammary glands showed coinfections (75%). Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89) and acute suppurative mastitis (4/89). Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06–0.71]) of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69–37.77]) of being infected with lentiviruses. Discussion The results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock.
Spuria et al. (2017) Microbial agents in macroscopically healthy mammary gland tissues of small ruminants. PeerJ 5:e3994 https://doi.org/10.7717/peerj.3994
Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants
In tropics, ants can represent an important part of animal biomass and are known to be involved in ecosystem services, such as pest regulation. Understanding the mechanisms underlying the structuring of local ant communities is therefore important in agroecology. In the humid tropics of Africa, plantains are cropped in association with many other annual and perennial crops. Such agrosystems differ greatly in vegetation diversity and structure and are well-suited for studying how habitat-related factors affect the ant community. We analysed abundance data for the six numerically dominant ant taxa in 500 subplots located in 20 diversified, plantain-based fields. We found that the density of crops with foliage at intermediate and high canopy strata determined the numerical dominance of species. We found no relationship between the numerical dominance of each ant taxon with the crop diversity. Our results indicate that the manipulation of the densities of crops with leaves in the intermediate and high strata may help maintain the coexistence of ant species by providing different habitat patches. Further research in such agrosystems should be performed to assess if the effect of vegetation structure on ant abundance could result in efficient pest regulation.
Dassou et al. (2017) Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants. PeerJ 5:e3917 https://doi.org/10.7717/peerj.3917