Ontogenetic scaling patterns and functional anatomy of the pelvic limb musculature in emus (Dromaius novaehollandiae)
Emus (Dromaius novaehollandiae) are exclusively terrestrial, bipedal and cursorial ratites with some similar biomechanical characteristics to humans. Their growth rates are impressive, as their body mass increases eighty-fold from hatching to adulthood whilst maintaining the same mode of locomotion throughout life. These ontogenetic characteristics stimulate biomechanical questions about the strategies that allow emus to cope with their rapid growth and locomotion, which can be partly addressed via scaling (allometric) analysis of morphology. In this study we have collected pelvic limb anatomical data (muscle architecture, tendon length, tendon mass and bone lengths) and calculated muscle physiological cross sectional area (PCSA) and average tendon cross sectional area from emus across three ontogenetic stages (n = 17, body masses from 3.6 to 42 kg). The data were analysed by reduced major axis regression to determine how these biomechanically relevant aspects of morphology scaled with body mass. Muscle mass and PCSA showed a marked trend towards positive allometry (26 and 27 out of 34 muscles respectively) and fascicle length showed a more mixed scaling pattern. The long tendons of the main digital flexors scaled with positive allometry for all characteristics whilst other tendons demonstrated a less clear scaling pattern. Finally, the two longer bones of the limb (tibiotarsus and tarsometatarsus) also exhibited positive allometry for length, and two others (femur and first phalanx of digit III) had trends towards isometry. These results indicate that emus experience a relative increase in their muscle force-generating capacities, as well as potentially increasing the force-sustaining capacities of their tendons, as they grow. Furthermore, we have clarified anatomical descriptions and provided illustrations of the pelvic limb muscle–tendon units in emus.
Lamas et al. (2014) Ontogenetic scaling patterns and functional anatomy of the pelvic limb musculature in emus (Dromaius novaehollandiae). PeerJ 2:e716 https://doi.org/10.7717/peerj.716
Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs
Attempts to reconstruct the neutral neck posture of sauropod dinosaurs, or indeed any tetrapod, are doomed to failure when based only on the geometry of the bony cervical vertebrae. The thickness of the articular cartilage between the centra of adjacent vertebrae affects posture. It extends (raises) the neck by an amount roughly proportional to the thickness of the cartilage. It is possible to quantify the angle of extension at an intervertebral joint: it is roughly equal, in radians, to the cartilage thickness divided by the height of the zygapophyseal facets over the centre of rotation. Applying this formula to published measurements of well-known sauropod specimens suggests that if the thickness of cartilage were equal to 4.5%, 10% or 18% of centrum length, the neutral pose of the Apatosaurus louisae holotype CM 3018 would be extended by an average of 5.5, 11.8 or 21.2 degrees, respectively, at each intervertebral joint. For the Diplodocus carnegii holotype CM 84, the corresponding angles of additional extension are even greater: 8.4, 18.6 or 33.3 degrees. The cartilaginous neutral postures (CNPs) calculated for 10% cartilage—the most reasonable estimate—appear outlandish. But it must be remembered that these would not have been the habitual life postures, because tetrapods habitually extend the base of their neck and flex the anterior part, yielding the distinctive S-curve most easily seen in birds.
Taylor (2014) Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs. PeerJ 2:e712 https://doi.org/10.7717/peerj.712
Structure, ontogeny and evolution of the patellar tendon in emus (Dromaius novaehollandiae) and other palaeognath birds
The patella (kneecap) exhibits multiple evolutionary origins in birds, mammals, and lizards, and is thought to increase the mechanical advantage of the knee extensor muscles. Despite appreciable interest in the specialized anatomy and locomotion of palaeognathous birds (ratites and relatives), the structure, ontogeny and evolution of the patella in these species remains poorly characterized. Within Palaeognathae, the patella has been reported to be either present, absent, or fused with other bones, but it is unclear how much of this variation is real, erroneous or ontogenetic. Clarification of the patella’s form in palaeognaths would provide insight into the early evolution of the patella in birds, in addition to the specialized locomotion of these species. Findings would also provide new character data of use in resolving the controversial evolutionary relationships of palaeognaths. In this study, we examined the gross and histological anatomy of the emu patellar tendon across several age groups from five weeks to 18 months. We combined these results with our observations and those of others regarding the patella in palaeognaths and their outgroups (both extant and extinct), to reconstruct the evolution of the patella in birds. We found no evidence of an ossified patella in emus, but noted its tendon to have a highly unusual morphology comprising large volumes of adipose tissue contained within a collagenous meshwork. The emu patellar tendon also included increasing amounts of a cartilage-like tissue throughout ontogeny. We speculate that the unusual morphology of the patellar tendon in emus results from assimilation of a peri-articular fat pad, and metaplastic formation of cartilage, both potentially as adaptations to increasing tendon load. We corroborate previous observations of a ‘double patella’ in ostriches, but in contrast to some assertions, we find independent (i.e., unfused) ossified patellae in kiwis and tinamous. Our reconstructions suggest a single evolutionary origin of the patella in birds and that the ancestral patella is likely to have been a composite structure comprising a small ossified portion, lost by some species (e.g., emus, moa) but expanded in others (e.g., ostriches).
Regnault et al. (2014) Structure, ontogeny and evolution of the patellar tendon in emus (Dromaius novaehollandiae) and other palaeognath birds. PeerJ 2:e711 https://doi.org/10.7717/peerj.711
Confirmation bias leads to overestimation of losses of woody plant foliage to insect herbivores in tropical regions
Confirmation bias, i.e., the tendency of humans to seek out evidence in a manner that confirms their hypotheses, is almost overlooked in ecological studies. For decades, insect herbivory was commonly accepted to be highest in tropical regions. By comparing the data collected blindly (when the observer was not aware of the research hypothesis being tested) with the results of non-blind studies (when the observer knew what results could be expected), we tested the hypothesis that the records made in the tropics could have overestimated community-wide losses of plant foliage to insects due to the confirmation bias. The average loss of leaf area of woody plants to defoliating insects in Brazil, when measured by a blind method (1.11%), was significantly lower than the loss measured in non-blind studies, both original (5.14%) and published (6.37%). We attribute the overestimation of the community-wide losses of plant foliage to insects in non-blind studies to the unconsciously preconceived selection of study species with higher-than-average levels of herbivory. Based on our findings, we urge for caution in obtaining community-wide characteristics from the results of multiple single-species studies. Our data suggest that we may need to revise the paradigm of the highest level of background insect herbivory in the tropical regions. More generally, we argue that more attention should be paid by ecologists to the problem of biases occurring at the pre-publication phases of the scientific research and, consequently, to the development and the wide application of methods that avoid biases occurring due to unconscious psychological processes.
Kozlov et al. (2014) Confirmation bias leads to overestimation of losses of woody plant foliage to insect herbivores in tropical regions. PeerJ 2:e709 https://doi.org/10.7717/peerj.709
Three-dimensional anatomy of the ostrich (Struthio camelus) knee joint
The three-dimensional anatomy of the ostrich (Struthio camelus) knee (femorotibial, femorofibular, and femoropatellar) joint has scarcely been studied, and could elucidate certain mechanobiological properties of sesamoid bones. The adult ostrich is unique in that it has double patellae, while another similar ratite bird, the emu, has none. Understanding why these patellae form and what purpose they may serve is dually important for future studies on ratites as well as for understanding the mechanobiological characteristics of sesamoid bone development. For this purpose, we present a three-dimensional anatomical study of the ostrich knee joint, detailing osteology, ligaments and menisci, and myology. We have identified seven muscles which connect to the two patellae and compare our findings to past descriptions. These descriptions can be used to further study the biomechanical loading and implications of the double patella in the ostrich.
Chadwick et al. (2014) Three-dimensional anatomy of the ostrich (Struthio camelus) knee joint. PeerJ 2:e706 https://doi.org/10.7717/peerj.706
Mobile gene silencing in Arabidopsis is regulated by hydrogen peroxide
In plants and nematodes, RNAi can spread from cells from which it is initiated to other cells in the organism. The underlying mechanism controlling the mobility of RNAi signals is not known, especially in the case of plants. A genetic screen designed to recover plants impaired in the movement but not the production or effectiveness of the RNAi signal identified RCI3, which encodes a hydrogen peroxide (H2O2)-producing type III peroxidase, as a key regulator of silencing mobility in Arabidopsis thaliana. Silencing initiated in the roots of rci3 plants failed to spread into leaf tissue or floral tissue. Application of exogenous H2O2 reinstated the spread in rci3 plants and accelerated it in wild-type plants. The addition of catalase or MnO2, which breaks down H2O2, slowed the spread of silencing in wild-type plants. We propose that endogenous H2O2, under the control of peroxidases, regulates the spread of gene silencing by altering plasmodesmata permeability through remodelling of local cell wall structure, and may play a role in regulating systemic viral defence.
Liang et al. (2014) Mobile gene silencing in Arabidopsis is regulated by hydrogen peroxide. PeerJ 2:e701 https://doi.org/10.7717/peerj.701
Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish
The extravasation of cancer cells, a key step for distant metastasis, is thought to be initiated by disruption of the endothelial barrier by malignant cancer cells. An endothelial covering-type extravasation of cancer cells in addition to conventional cancer cell invasion-type extravasation was dynamically visualized in a zebrafish hematogenous metastasis model. The inhibition of VEGF-signaling impaired the invasion-type extravasation via inhibition of cancer cell polarization and motility. Paradoxically, the anti-angiogenic treatment showed the promotion, rather than the inhibition, of the endothelial covering-type extravasation of cancer cells, with structural changes in the endothelial walls. These findings may be a set of clues to the full understanding of the metastatic process as well as the metastatic acceleration by anti-angiogenic reagents observed in preclinical studies.
Kanada et al. (2014) Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish. PeerJ 2:e688 https://doi.org/10.7717/peerj.688
Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii
The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and were raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.
Avarre et al. (2014) Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii. PeerJ 2:e702 https://doi.org/10.7717/peerj.702
Response of reef corals on a fringing reef flat to elevated suspended-sediment concentrations: Molokaʻi, Hawaiʻi
A long-term (10 month exposure) experiment on effects of suspended sediment on the mortality, growth, and recruitment of the reef corals Montipora capitata and Porites compressa was conducted on the shallow reef flat off south Molokaʻi, Hawaiʻi. Corals were grown on wire platforms with attached coral recruitment tiles along a suspended solid concentration (SSC) gradient that ranged from 37 mg l−1 (inshore) to 3 mg l−1 (offshore). Natural coral reef development on the reef flat is limited to areas with SSCs less than 10 mg l−1 as previously suggested in the scientific literature. However, the experimental corals held at much higher levels of turbidity showed surprisingly good survivorship and growth. High SSCs encountered on the reef flat reduced coral recruitment by one to three orders of magnitude compared to other sites throughout Hawaiʻi. There was a significant correlation between the biomass of macroalgae attached to the wire growth platforms at the end of the experiment and percentage of the corals showing mortality. We conclude that lack of suitable hard substrate, macroalgal competition, and blockage of recruitment on available substratum are major factors accounting for the low natural coral coverage in areas of high turbidity. The direct impact of high turbidity on growth and mortality is of lesser importance.
Jokiel et al. (2014) Response of reef corals on a fringing reef flat to elevated suspended-sediment concentrations: Molokaʻi, Hawaiʻi. PeerJ 2:e699 https://doi.org/10.7717/peerj.699
A statistical assessment of population trends for data deficient Mexican amphibians
Background. Mexico has the world’s fifth largest population of amphibians and the second country with the highest quantity of threatened amphibian species. About 10% of Mexican amphibians lack enough data to be assigned to a risk category by the IUCN, so in this paper we want to test a statistical tool that, in the absence of specific demographic data, can assess a species’ risk of extinction, population trend, and to better understand which variables increase their vulnerability. Recent studies have demonstrated that the risk of species decline depends on extrinsic and intrinsic traits, thus including both of them for assessing extinction might render more accurate assessment of threats. Methods. We harvested data from the Encyclopedia of Life (EOL) and the published literature for Mexican amphibians, and used these data to assess the population trend of some of the Mexican species that have been assigned to the Data Deficient category of the IUCN using Random Forests, a Machine Learning method that gives a prediction of complex processes and identifies the most important variables that account for the predictions. Results. Our results show that most of the data deficient Mexican amphibians that we used have decreasing population trends. We found that Random Forests is a solid way to identify species with decreasing population trends when no demographic data is available. Moreover, we point to the most important variables that make species more vulnerable for extinction. This exercise is a very valuable first step in assigning conservation priorities for poorly known species.
Quintero et al. (2014) A statistical assessment of population trends for data deficient Mexican amphibians. PeerJ 2:e703 https://doi.org/10.7717/peerj.703
Public stigma associated with mental illnesses in Pakistani university students: a cross sectional survey
Background. The objectives of the study were to explore the knowledge and attitudes of Pakistani university students toward mental illnesses. People with mental illnesses are challenged not only by their symptoms but also by the prejudices associated with their illness. Acknowledging the stigma of mental illness should be the first essential step toward devising an appropriate treatment plan. Methods. A cross-sectional survey was conducted at the University of Punjab, Lahore, CMH Lahore Medical and Dental College, Lahore, and University of Sargodha, Sub-campus Lahore, from February to May 2014. The self-administered questionnaire consisted of three sections: demographics, general knowledge of psychiatric illnesses, and Community Attitudes towards Mental Illnesses (CAMI) Scale. The questionnaire was distributed to 650 participants enrolled in different disciplines (Social Sciences, Medicine and Formal Sciences). Results. Response rate was 81% (527/650 respondents). Mean age was 20.98 years. Most of the students (331, 62.8%) had an urban background and studied Social Sciences (238, 45.2%). Four hundred and eighteen respondents (79.3%) considered religion very important and most respondents considered psychiatrists (334, 63.4%) and spiritual leaders (72, 13.7%) to be best able to treat mental illnesses. One hundred and sixty nine respondents (32.1%) considered black magic to be a cause of mental illness. Only 215 (41%) respondents had ever read an article on mental illnesses. Multiple regression analysis revealed study discipline, exposure, perceived causes of mental illnesses and superstitions to be significantly associated with attitudes towards mental illnesses (p < .05). Conclusion. Although low awareness and exposure were found in this sample of Pakistani university students, their attitude towards mental illnesses was generally positive. Most respondents gave supernatural explanations for mental illnesses but only a few believed that spiritual leaders can play a role in treatment.
Waqas et al. (2014) Public stigma associated with mental illnesses in Pakistani university students: a cross sectional survey. PeerJ 2:e698 https://doi.org/10.7717/peerj.698
Combining physical and virtual contexts through augmented reality: design and evaluation of a prototype using a drug box as a marker for antibiotic training
Introduction. Antimicrobial resistance is a global health issue. Studies have shown that improved antibiotic prescription education among healthcare professionals reduces mistakes during the antibiotic prescription process. The aim of this study was to investigate novel educational approaches that through the use of Augmented Reality technology could make use of the real physical context and thereby enrich the educational process of antibiotics prescription. The objective is to investigate which type of information related to antibiotics could be used in an augmented reality application for antibiotics education. Methods. This study followed the Design-Based Research Methodology composed of the following main steps: problem analysis, investigation of information that should be visualized for the training session, and finally the involvement of the end users the development and evaluation processes of the prototype. Results. Two of the most important aspects in the antibiotic prescription process, to represent in an augmented reality application, are the antibiotic guidelines and the side effects. Moreover, this study showed how this information could be visualized from a mobile device using an Augmented Reality scanner and antibiotic drug boxes as markers. Discussion. In this study we investigated the usage of objects from a real physical context such as drug boxes and how they could be used as educational resources. The logical next steps are to examine how this approach of combining physical and virtual contexts through Augmented Reality applications could contribute to the improvement of competencies among healthcare professionals and its impact on the decrease of antibiotics resistance.
Nifakos et al. (2014) Combining physical and virtual contexts through augmented reality: design and evaluation of a prototype using a drug box as a marker for antibiotic training. PeerJ 2:e697 https://doi.org/10.7717/peerj.697
Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence
Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes.
Avitia et al. (2014) Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence. PeerJ 2:e696 https://doi.org/10.7717/peerj.696
Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras
Hosting symbionts provides many eukaryotes with access to the products of microbial metabolism that are crucial for host performance. On tropical coral reefs, many (High Microbial Abundance [HMA]) but not all (Low Microbial Abundance [LMA]) marine sponges host abundant symbiont communities. Although recent research has revealed substantial variation in these sponge-microbe associations (termed holobionts), little is known about the ecological implications of this diversity. We investigated the expansion of diverse sponge species across isotopic niche space by calculating niche size (as standard ellipse area [SEAc]) and assessing the relative placement of common sponge species in bivariate (δ13C and δ15N) plots. Sponges for this study were collected from the relatively isolated reefs within the Miskito Cays of Honduras. These reefs support diverse communities of HMA and LMA species that together span a gradient of photosymbiont abundance, as revealed by chlorophyll a analysis. HMA sponges occupied unique niche space compared to LMA species, but the placement of some HMA sponges was driven by photosymbiont abundance. In addition, photosymbiont abundance explained a significant portion of the variation in isotope values, suggesting that access to autotrophic metabolism provided by photosymbionts is an important predictor in the location of species within isotopic space. Host identity accounted for over 70% of the variation in isotope values within the Miskito Cays and there was substantial variation in the placement of individual species within isotopic niche space, suggesting that holobiont metabolic diversity may allow taxonomically diverse sponge species to utilize unique sources of nutrients within a reef system. This study provides initial evidence that microbial symbionts allow sponges to expand into novel physiochemical niche space. This expansion may reduce competitive interactions within coral reefs and promote diversification of these communities.
Freeman et al. (2014) Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras. PeerJ 2:e695 https://doi.org/10.7717/peerj.695
Positive affect and age as predictors of exercise compliance
Physical exercise is linked to individuals whose affect profiles are invariably positive and it induces anti-apoptotic and anti-excitotoxic effects, buttressing blood–brain barrier intactness in both healthy individuals and those suffering from disorders accompanying overweight and obesity. In this regard, exercise offers a unique non-pharmacologic, non-invasive intervention that incorporates different regimes, whether dynamic or static, endurance, or resistance. In this brief report we present a self-reported study carried out on an adolescent and adult population (N = 280, 144 males and 136 females), which indicated that the propensity and compliance for exercise, measured as the “Archer ratio”, was predicted by a positive affect. This association is discussed from the perspective of health, well-being, affect dimensions, and age.
Garcia et al. (2014) Positive affect and age as predictors of exercise compliance. PeerJ 2:e694 https://doi.org/10.7717/peerj.694
Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities
A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonistic interactions. In this study, we examined the ECM fungal communities associated with the host genus Alnus, which live in soils high in both nitrate and acidity. The nature of ECM fungal species interactions (i.e., antagonistic, neutral, or positive) was assessed using taxon co-occurrence and DNA sequence abundance correlational analyses. ECM fungal communities were sampled from root tips or mesh in-growth bags in three monodominant A. rubra plots at a site in Oregon, USA and identified using Illumina-based amplification of the ITS1 gene region. We found a total of 175 ECM fungal taxa; 16 of which were closely related to known Alnus-associated ECM fungi. Contrary to previous studies of ECM fungal communities, taxon co-occurrence analyses on both the total and Alnus-associated ECM datasets indicated that the ECM fungal communities in this system were not structured by interspecific competition. Instead, the co-occurrence patterns were consistent with either random assembly or significant positive interactions. Pair-wise correlational analyses were also more consistent with neutral or positive interactions. Taken together, our results suggest that interspecific competition does not appear to determine the structure of all ECM fungal communities and that abiotic conditions may be important in determining the specific type of interaction occurring among ECM fungi.
Kennedy et al. (2014) Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities. PeerJ 2:e686 https://doi.org/10.7717/peerj.686
Comparative analysis of early ontogeny in Bursatella leachii and Aplysia californica
Opisthobranch molluscs exhibit fascinating body plans associated with the evolution of shell loss in multiple lineages. Sea hares in particular are interesting because Aplysia californica is a well-studied model organism that offers a large suite of genetic tools. Bursatella leachii is a related tropical sea hare that lacks a shell as an adult and therefore lends itself to comparative analysis with A. californica. We have established an enhanced culturing procedure for B. leachii in husbandry that enabled the study of shell formation and loss in this lineage with respect to A. californica life staging.
Vue et al. (2014) Comparative analysis of early ontogeny in Bursatella leachii and Aplysia californica. PeerJ 2:e700 https://doi.org/10.7717/peerj.700
Spatial variation in the littoral vertebrate community of a reservoir relative to physical and biological gradients
Reservoirs possess gradients in conditions and resources along their long (deep-shallow) axis, but the response of littoral vertebrates (fish and turtles) to these gradients is poorly understood. We have quantified the littoral vertebrate communities throughout a small reservoir in Southeastern Ohio during July and August using traps, and related community composition to environmental variables using NMDS ordination. Ordination revealed that fish and turtles were broadly separated in ordination space, and three distinctly different environmental gradients were significantly associated with the underlying observed species abundances. Observed turtle abundance was explained by measurements of bathymetry, turbidity, and benthic resources, but none of these environmental variables were a reliable predictor of observed fish abundance. Temperature was a poor predictor of observed abundance for both fish and turtles independently, but when fish and turtles were considered together, it became apparent that there were cold areas of the reservoir where observed fish and turtle abundances were different than in other areas of the reservoir. These results suggest that the predictor (environmental) variables we used were appropriate for investigating turtle ecology in reservoirs, but that observed fish abundance is mediated by factors that were not modeled. The efficacy of using traps, the ecological implications of considering fish and turtles together as sympatric and potentially competing species, and directions for future study are discussed.
Ruhl et al. (2014) Spatial variation in the littoral vertebrate community of a reservoir relative to physical and biological gradients. PeerJ 2:e693 https://doi.org/10.7717/peerj.693
Franz Josef Land: extreme northern outpost for Arctic fishes
The remote Franz Josef Land (FJL) Archipelago is the most northerly land in Eurasia and its fish fauna, particularly in nearshore habitats, has been poorly studied. An interdisciplinary expedition to FJL in summer 2013 used scuba, seines, and plankton nets to comprehensively study the nearshore fish fauna of the archipelago. We present some of the first underwater images for many of these species in their natural habitats. In addition, deep water drop cameras were deployed between 32 and 392 m to document the fish fauna and their associated habitats at deeper depths. Due to its high latitude (79°–82°N), extensive ice cover, and low water temperatures (<0 °C much of the year), the fish diversity at FJL is low compared to other areas of the Barents Sea. Sixteen species of fishes from seven families were documented on the expedition, including two species previously unknown to the region. One Greenland shark, Somniosus microcephalus (Somniosidae), ca. 2 m in length, was recorded by drop camera near Hayes Island at 211 m, and Esipov’s pout, Gymnelus esipovi (Zoarcidae), was collected at Wilton Island at 15 m in a kelp forest. Including the tape-body pout, Gymnelus taeniatus, described earlier from the sub-littoral zone of Kuhn Island, 17 fish species are now known from FJL’s nearshore waters. Species endemic to the Arctic accounted for 75% of the nearshore species observed, followed by species with wider ranges. A total of 43 species from 15 families are known from FJL with the majority of the records from offshore trawl surveys between 110 and 620 m. Resident species have mainly high Arctic distributions, while transient species visit the archipelago to feed (e.g., Greenland shark), and others are brought by currents as larvae and later migrate to spawn grounds in the south (e.g., Atlantic cod Gadus morhua, Capelin Mallotus villosus, Beaked redfish Sebastes mentella). Another species group includes warmer-water fishes that are rare waifs (e.g., Glacier lanternfish Benthosema glaciale, White barracudina Arctozenus rissoi). The rapid warming of the Arctic will likely result in significant changes to the entire ecosystem and this study therefore serves as an important baseline for the nearshore fish assemblages in this unique and fragile region.
Chernova et al. (2014) Franz Josef Land: extreme northern outpost for Arctic fishes. PeerJ 2:e692 https://doi.org/10.7717/peerj.692
Optimization in the utility maximization framework for conservation planning: a comparison of solution procedures in a study of multifunctional agriculture
Quantitative methods of spatial conservation prioritization have traditionally been applied to issues in conservation biology and reserve design, though their use in other types of natural resource management is growing. The utility maximization problem is one form of a covering problem where multiple criteria can represent the expected social benefits of conservation action. This approach allows flexibility with a problem formulation that is more general than typical reserve design problems, though the solution methods are very similar. However, few studies have addressed optimization in utility maximization problems for conservation planning, and the effect of solution procedure is largely unquantified. Therefore, this study mapped five criteria describing elements of multifunctional agriculture to determine a hypothetical conservation resource allocation plan for agricultural land conservation in the Central Valley of CA, USA. We compared solution procedures within the utility maximization framework to determine the difference between an open source integer programming approach and a greedy heuristic, and find gains from optimization of up to 12%. We also model land availability for conservation action as a stochastic process and determine the decline in total utility compared to the globally optimal set using both solution algorithms. Our results are comparable to other studies illustrating the benefits of optimization for different conservation planning problems, and highlight the importance of maximizing the effectiveness of limited funding for conservation and natural resource management.
Kreitler et al. (2014) Optimization in the utility maximization framework for conservation planning: a comparison of solution procedures in a study of multifunctional agriculture. PeerJ 2:e690 https://doi.org/10.7717/peerj.690
Arterial spin labeling versus BOLD in direct challenge and drug-task interaction pharmacological fMRI
A carefully controlled study allowed us to compare the sensitivity of ASL (arterial spin labeling) and BOLD (blood oxygen level dependent) fMRI for detecting the effects of the adenosine A2a antagonist tozadenant in Parkinson disease. The study compared the effect of drug directly or the interaction of the drug with a cognitive task. Only ASL detected the direct effect of tozadenant. BOLD was more sensitive to the cognitive task, which (unlike most drugs) allows on–off comparisons over short periods of time. Neither ASL nor BOLD could detect a cognitive-pharmacological interaction. These results are consistent with the known relative advantages of each fMRI method, and suggest that for drug development, directly imaging pharmacodynamic effects with ASL may have advantages over cognitive-pharmacological interaction BOLD, which has hitherto been the more common approach to pharmacological fMRI.
Stewart et al. (2014) Arterial spin labeling versus BOLD in direct challenge and drug-task interaction pharmacological fMRI. PeerJ 2:e687 https://doi.org/10.7717/peerj.687
The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility
Wolbachia pipientis is a worldwide bacterial parasite of arthropods that infects germline cells and manipulates host reproduction to increase the ratio of infected females, the transmitting sex of the bacteria. The most common reproductive manipulation, cytoplasmic incompatibility (CI), is expressed as embryonic death in crosses between infected males and uninfected females. Specifically, Wolbachia modify developing sperm in the testes by unknown means to cause a post-fertilization disruption of the sperm chromatin that incapacitates the first mitosis of the embryo. As these Wolbachia-induced changes are stable, reversible, and affect the host cell cycle machinery including DNA replication and chromosome segregation, we hypothesized that the host methylation pathway is targeted for modulation during cytoplasmic incompatibility because it accounts for all of these traits. Here we show that infection of the testes is associated with a 55% increase of host DNA methylation in Drosophila melanogaster, but methylation of the paternal genome does not correlate with penetrance of CI. Overexpression and knock out of the Drosophila DNA methyltransferase Dnmt2 neither induces nor increases CI. Instead, overexpression decreases Wolbachia titers in host testes by approximately 17%, leading to a similar reduction in CI levels. Finally, strength of CI induced by several different strains of Wolbachia does not correlate with levels of DNA methylation in the host testes. We conclude that DNA methylation mediated by Drosophila’s only known methyltransferase is not required for the transgenerational sperm modification that causes CI.
LePage et al. (2014) The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility. PeerJ 2:e678 https://doi.org/10.7717/peerj.678
The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types
Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements—i.e., ingested with food—are important contributors to the composition, inter-individual variation, and function of our gut microbiota.
Lang et al. (2014) The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. PeerJ 2:e659 https://doi.org/10.7717/peerj.659
A localized PCR inhibitor in a porcelain crab suggests a protective role
A number of polymerase chain reaction (PCR) inhibitors have been identified from biological and environmental samples. By and large, such substances are treated as random nuisances and contaminants with alternate functions; their inhibitory effects on DNA replication being a coincidental property of their molecular structure. Here, we demonstrate the presence of a localized PCR inhibitor in the foregut of the porcelain crab Petrolisthes rufescens (Anomura: Porcellanidae) from the Red Sea. The inhibitor precluded amplification of 28s, 16s and 18s gene sequences effectively but lost activity at 10−2 dilutions from initial concentration. Heat treatment was ineffective in arresting inhibition and spectrophotometric techniques suggested that the inhibitor was not a melanin-type compound. The compound was not detected from midgut, hindgut, or gills of the crab. Activity of the inhibitor was precluded when samples were treated with suspensions from the midgut, suggesting that enzymatic degradation of the inhibitor likely happens at that part of the gut. As many microbial pathogens invade their hosts via ingestion, we suggest the presence of the localized inhibitor could carry a defensive or immunological role for P. rufescens. The identity of the inhibitory molecule remains unknown.
El-Maklizi et al. (2014) A localized PCR inhibitor in a porcelain crab suggests a protective role. PeerJ 2:e689 https://doi.org/10.7717/peerj.689
Leaf litter decomposition rates increase with rising mean annual temperature in Hawaiian tropical montane wet forests
Decomposing litter in forest ecosystems supplies nutrients to plants, carbon to heterotrophic soil microorganisms and is a large source of CO2 to the atmosphere. Despite its essential role in carbon and nutrient cycling, the temperature sensitivity of leaf litter decay in tropical forest ecosystems remains poorly resolved, especially in tropical montane wet forests where the warming trend may be amplified compared to tropical wet forests at lower elevations. We quantified leaf litter decomposition rates along a highly constrained 5.2 °C mean annual temperature (MAT) gradient in tropical montane wet forests on the Island of Hawaii. Dominant vegetation, substrate type and age, soil moisture, and disturbance history are all nearly constant across this gradient, allowing us to isolate the effect of rising MAT on leaf litter decomposition and nutrient release. Leaf litter decomposition rates were a positive linear function of MAT, causing the residence time of leaf litter on the forest floor to decline by ∼31 days for each 1 °C increase in MAT. Our estimate of the Q10 temperature coefficient for leaf litter decomposition was 2.17, within the commonly reported range for heterotrophic organic matter decomposition (1.5–2.5) across a broad range of ecosystems. The percentage of leaf litter nitrogen (N) remaining after six months declined linearly with increasing MAT from ∼88% of initial N at the coolest site to ∼74% at the warmest site. The lack of net N immobilization during all three litter collection periods at all MAT plots indicates that N was not limiting to leaf litter decomposition, regardless of temperature. These results suggest that leaf litter decay in tropical montane wet forests may be more sensitive to rising MAT than in tropical lowland wet forests, and that increased rates of N release from decomposing litter could delay or prevent progressive N limitation to net primary productivity with climate warming.
Bothwell et al. (2014) Leaf litter decomposition rates increase with rising mean annual temperature in Hawaiian tropical montane wet forests. PeerJ 2:e685 https://doi.org/10.7717/peerj.685
Weakest students benefit most from a customized educational experience for Generation Y students
Most current dental students were born in the 1980s and 1990s and are defined as Generation Y (Gen Y). The authors developed a customized educational experience that brought together some characteristics of Gen Y and the objective of this educational experience was to develop the critical thinking skills of Gen Y students. The objective of the current study is to evaluate outcomes from pre-session and post-session tests. Additionally, we wanted to integrate aspects of team-based learning, self-directed learning and peer-to-peer teaching as a means of reducing the need for intense faculty supervision but maintain positive educational outcomes. Single bitewing x-ray was displayed and informal class discussion was facilitated by a Senior Tutor. A list of questions and concepts that needed to be understood more clearly was made. Student groups self allocated research tasks to members. After conducting research, students presented to class and faculty facilitated discussions aiming to foster critical thinking and identify what information needed to be more thoroughly understood. Pre-session and post-session tests were conducted and compared. Students who scored below 85% in their pre-session test improved their score in the post-session test by a mean of 9.5 points (p = 0.02). Those who scored above 95% in their pre-session test scored less in the post-session test (mean reduction of 6.31 points, p = 0.001). Findings from this study demonstrate that the weakest students in the class (those who scored below 85% correct in the pre-session test) benefitted most from this unique educational experience.
Nalliah et al. (2014) Weakest students benefit most from a customized educational experience for Generation Y students. PeerJ 2:e682 https://doi.org/10.7717/peerj.682
Susceptibility to experimental infection of the invertebrate locusts (Schistocerca gregaria) with the apicomplexan parasite Neospora caninum
Neuropathogenesis is a feature of Neospora caninum infection. In order to explore this in the absence of acquired host immunity to the parasite, we have tested infection in locusts (Schistocerca gregaria). We show for the first time that locusts are permissive to intra-hemocoel infection with N. caninum tachyzoites. This was characterized by alteration in body weight, fecal output, hemoparasitemia, and sickness-related behavior. Infected locusts exhibited progressive signs of sickness leading to mortality. Also, N. caninum showed neuropathogenic affinity, induced histological changes in the brain and was able to replicate in the brain of infected locusts. Fatty acid (FA) profiling analysis of the brains by gas chromatography and multi-variate prediction models discriminated with high accuracy (98%) between the FA profiles of the infected and control locusts. DNA microarray gene expression profiling distinguished infected from control S. gregaria brain tissues on the basis of distinct differentially-expressed genes. These data indicate that locusts are permissible to infection with N. caninum and that the parasite retains its tropism for neural tissues in the invertebrate host. Locusts may facilitate preclinical testing of interventional strategies to inhibit the growth of N. caninum tachyzoites. Further studies on how N. caninum brings about changes in locust brain tissue are now warranted.
Alkurashi et al. (2014) Susceptibility to experimental infection of the invertebrate locusts (Schistocerca gregaria) with the apicomplexan parasite Neospora caninum. PeerJ 2:e674 https://doi.org/10.7717/peerj.674