Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents
One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this ‘up-to-dateness’ came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains ‘up-to-dateness’ of the results. Availability: http://metres.udl.cat/index.php/downloads, Contact: metres.cmb@gmail.com.
Usie et al. (2014) Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents. PeerJ 2:e276 https://doi.org/10.7717/peerj.276
System wide analyses have underestimated protein abundances and the importance of transcription in mammals
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 9% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.14). Based on this, our second strategy suggests that mRNA levels explain ∼84% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed.
Li et al. (2014) System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2:e270 https://doi.org/10.7717/peerj.270
Landscape fragmentation and pollinator movement within agricultural environments: a modelling framework for exploring foraging and movement ecology
Pollinator decline has been linked to landscape change, through both habitat fragmentation and the loss of habitat suitable for the pollinators to live within. One method for exploring why landscape change should affect pollinator populations is to combine individual-level behavioural ecological techniques with larger-scale landscape ecology. A modelling framework is described that uses spatially-explicit individual-based models to explore the effects of individual behavioural rules within a landscape. The technique described gives a simple method for exploring the effects of the removal of wild corridors, and the creation of wild set-aside fields: interventions that are common to many national agricultural policies. The effects of these manipulations on central-place nesting pollinators are varied, and depend upon the behavioural rules that the pollinators are using to move through the environment. The value of this modelling framework is discussed, and future directions for exploration are identified.
Rands (2014) Landscape fragmentation and pollinator movement within agricultural environments: a modelling framework for exploring foraging and movement ecology. PeerJ 2:e269 https://doi.org/10.7717/peerj.269
Analyzing machupo virus-receptor binding by molecular dynamics simulations
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions.
Meyer et al. (2014) Analyzing machupo virus-receptor binding by molecular dynamics simulations. PeerJ 2:e266 https://doi.org/10.7717/peerj.266
A global meta-analytic contrast of cushion-plant effects on plants and on arthropods
Nurse plant facilitation is a commonly reported plant–plant interaction and is an important factor influencing community structure in stressful environments. Cushion plants are an example of alpine nurse plants that modify microclimatic conditions within their canopies to create favourable environments for other plants. In this meta-analysis, the facilitative effects of cushion plants was expanded from previous syntheses of the topic and the relative strength of facilitation for other plants and for arthropods were compared globally.The abundance, diversity, and species presence/absence effect size estimates were tested as plant responses to nurse plants and a composite measure was tested for arthropods. The strength of facilitation was on average three times greater for arthropods relative to all plant responses to cushions. Plant species presence, i.e., frequency of occurrence, was not enhanced by nurse-plants. Cushion plants nonetheless acted as nurse plants for both plants and arthropods in most alpine contexts globally, and although responses by other plant species currently dominate the facilitation literature, preliminary synthesis of the evidence suggests that the potential impacts of nurses may be even greater for other trophic levels.
Liczner et al. (2014) A global meta-analytic contrast of cushion-plant effects on plants and on arthropods. PeerJ 2:e265 https://doi.org/10.7717/peerj.265
Smoking close to others and butt littering at bus stops: pilot observational study
Background. Transportation settings such as bus stops and train station platforms are increasingly the target for new smokefree legislation. Relevant issues include secondhand smoke exposure, nuisance, litter, fire risks and the normalization of smoking. We therefore aimed to pilot study aspects of smoking behavior and butt disposal at bus stops. Methods. Systematic observation of smoking and butt disposal by smokers at bus stops. The selection of 11 sites was a mix of convenience and purposeful (bus stops on main routes) in two New Zealand cities. Results. During 27 h of observation, a total of 112 lit cigarettes were observed being smoked. Smoking occurred in the presence of: just adults (46%), both young people and adults (44%), just young people (6%) and alone (5%). An average of 6.3 adults and 3.8 young people were present at the bus stops while smoking occurred, at average minimum distances of 1.7 and 2.2 m respectively. In bus stops that included an enclosed shelter, 33% of the cigarettes were smoked inside the shelter with others present. Littering was the major form of cigarette disposal with 84% of cigarettes smoked being littered (95% CI; 77%–90%). Also, 4% of disposals were into vegetation, which may pose a fire risk. Conclusions. This pilot study is limited by its small size and various methodological aspects but it appears to be a first attempt to provide observational evidence around smoking at bus stops. The issues described could be considered by policy makers who are investigating national smokefree laws or by-laws covering transportation settings.
Wilson et al. (2014) Smoking close to others and butt littering at bus stops: pilot observational study. PeerJ 2:e272 https://doi.org/10.7717/peerj.272
Germination of Acacia harpophylla (Brigalow) seeds in relation to soil water potential: implications for rehabilitation of a threatened ecosystem
Initial soil water conditions play a critical role when seeding is the primary approach to revegetate post-mining areas. In some semi-arid climates, such as the Brigalow Belt Bioregion in eastern Australia, extensive areas are affected by open-cut mining. Together with erratic rainfall patterns and clayey soils, the Brigalow Belt denotes a unique biome which is representative of other water-limited ecosystems worldwide. Apart from other environmental stressors, germination is governed by the water potential of the surrounding soil material. While previous studies have confirmed the high tolerance of Brigalow (Acacia harpophylla) seeds to a broad range of temperature and salinity, the question of how soil water potential triggers seed germination remains. In this study, we used three replicates of 50 seeds of Brigalow to investigate germination in relation to water potential as an environmental stressor. Solutions of Polyethylene Glycol (PEG 6000) were applied to expose seeds to nine osmotic water potentials ranging from soil water saturation (0 MPa) and field capacity (−.01 to −.03 MPa) to the permanent wilting point (−1.5 MPa). We measured germinability (number of germinated seeds relative to total number of seeds per lot) and mean germination time (mean time required for maximum germination of a seed lot) to quantify germination. Based on the empirical data of the germination we estimated the parameters of the hydrotime model which simulates timing and success of seed emergence. Our findings indicate that Brigalow seeds are remarkably tolerant to water stress, with germination being observed at a water potential as low as −1.5 MPa. Likewise, the average base water potential of a seed population (hydrotime model) was very low and ranged between −1.533 and −1.451 MPa. In general, Brigalow seeds germinate opportunistically over a broad range of abiotic conditions related to temperature, salinity, and water availability. Direct seeding and germination of native plants on post-mining land may be an effective and economically viable solution in order to re-establish plant communities. However, due to their capacity to reproduce asexually, alternative rehabilitation approaches such as transplantation of whole soil-root compartments may become attractive for restoration ecologists to achieve safe, stable, and non-polluting ecosystems.
Arnold et al. (2014) Germination of Acacia harpophylla (Brigalow) seeds in relation to soil water potential: implications for rehabilitation of a threatened ecosystem. PeerJ 2:e268 https://doi.org/10.7717/peerj.268
Microbial metabolism: optimal control of uptake versus synthesis
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of resources through the multiple species that create a microbial community. This article analyzes a simple mathematical model of the tradeoff between uptake and synthesis. Key factors include the influx rate from external sources relative to the outflux rate, the rate of internal decay within cells, and the cost of synthesis. Aspects of demography also matter, such as cellular birth and death rates, the expected time course of a local resource flow, and the associated lifespan of the local population. Spatial patterns of genetic variability and differentiation between populations may also strongly influence the evolution of metabolic regulatory controls of individual species and thus the structuring of microbial communities. The widespread use of optimality approaches in recent work on microbial metabolism has ignored demography and genetic structure.
Frank (2014) Microbial metabolism: optimal control of uptake versus synthesis. PeerJ 2:e267 https://doi.org/10.7717/peerj.267
Strong Stackelberg reasoning in symmetric games: An experimental replication and extension
In common interest games in which players are motivated to coordinate their strategies to achieve a jointly optimal outcome, orthodox game theory provides no general reason or justification for choosing the required strategies. In the simplest cases, where the optimal strategies are intuitively obvious, human decision makers generally coordinate without difficulty, but how they achieve this is poorly understood. Most theories seeking to explain strategic coordination have limited applicability, or require changes to the game specification, or introduce implausible assumptions or radical departures from fundamental game-theoretic assumptions. The theory of strong Stackelberg reasoning, according to which players choose strategies that would maximize their own payoffs if their co-players could invariably anticipate any strategy and respond with a best reply to it, avoids these problems and explains strategic coordination in all dyadic common interest games. Previous experimental evidence has provided evidence for strong Stackelberg reasoning in asymmetric games. Here we report evidence from two experiments consistent with players being influenced by strong Stackelberg reasoning in a wide variety of symmetric 3 × 3 games but tending to revert to other choice criteria when strong Stackelberg reasoning generates small payoffs.
Pulford et al. (2014) Strong Stackelberg reasoning in symmetric games: An experimental replication and extension. PeerJ 2:e263 https://doi.org/10.7717/peerj.263
Invasion success of a scarab beetle within its native range: host range expansion versus host-shift
Only recently has it been formally acknowledged that native species can occasionally reach the status of ‘pest’ or ‘invasive species’ within their own native range. The study of such species has potential to help unravel fundamental aspects of biological invasions. A good model for such a study is the New Zealand native scarab beetle, Costelytra zealandica (White), which even in the presence of its natural enemies has become invasive in exotic pastures throughout the country. Because C. zealandica still occurs widely within its native habitat, we hypothesised that this species has only undergone a host range expansion (ability to use equally both an ancestral and new host) onto exotic hosts rather than a host shift (loss of fitness on the ancestral host in comparison to the new host). Moreover, this host range expansion could be one of the main drivers of its invasion success. In this study, we investigated the fitness response of populations of C. zealandica from native and exotic flora, to several feeding treatments comprising its main exotic host plant as well as one of its ancestral hosts. Our results suggest that our initial hypothesis was incorrect and that C. zealandica populations occurring in exotic pastures have experienced a host-shift rather than simply a host-range expansion. This finding suggests that an exotic plant introduction can facilitate the evolution of a distinct native host-race, a phenomenon often used as evidence for speciation in phytophagous insects and which may have been instrumental to the invasion success of C. zealandica.
Lefort et al. (2014) Invasion success of a scarab beetle within its native range: host range expansion versus host-shift. PeerJ 2:e262 https://doi.org/10.7717/peerj.262
Reduced object related negativity response indicates impaired auditory scene analysis in adults with autistic spectrum disorder
Auditory Scene Analysis provides a useful framework for understanding atypical auditory perception in autism. Specifically, a failure to segregate the incoming acoustic energy into distinct auditory objects might explain the aversive reaction autistic individuals have to certain auditory stimuli or environments. Previous research with non-autistic participants has demonstrated the presence of an Object Related Negativity (ORN) in the auditory event related potential that indexes pre-attentive processes associated with auditory scene analysis. Also evident is a later P400 component that is attention dependent and thought to be related to decision-making about auditory objects. We sought to determine whether there are differences between individuals with and without autism in the levels of processing indexed by these components. Electroencephalography (EEG) was used to measure brain responses from a group of 16 autistic adults, and 16 age- and verbal-IQ-matched typically-developing adults. Auditory responses were elicited using lateralized dichotic pitch stimuli in which inter-aural timing differences create the illusory perception of a pitch that is spatially separated from a carrier noise stimulus. As in previous studies, control participants produced an ORN in response to the pitch stimuli. However, this component was significantly reduced in the participants with autism. In contrast, processing differences were not observed between the groups at the attention-dependent level (P400). These findings suggest that autistic individuals have difficulty segregating auditory stimuli into distinct auditory objects, and that this difficulty arises at an early pre-attentive level of processing.
Lodhia et al. (2014) Reduced object related negativity response indicates impaired auditory scene analysis in adults with autistic spectrum disorder. PeerJ 2:e261 https://doi.org/10.7717/peerj.261
Evidence for protection of targeted reef fish on the largest marine reserve in the Caribbean
Marine reserves can restore fish abundance and diversity in areas impacted by overfishing, but the effectiveness of reserves in developing countries where resources for enforcement are limited, have seldom been evaluated. Here we assess whether the establishment in 1996 of the largest marine reserve in the Caribbean, Gardens of the Queen in Cuba, has had a positive effect on the abundance of commercially valuable reef fish species in relation to neighboring unprotected areas. We surveyed 25 sites, including two reef habitats (reef crest and reef slope), inside and outside the marine reserve, on five different months, and over a one-and-a-half year period. Densities of the ten most frequent, highly targeted, and relatively large fish species showed a significant variability across the archipelago for both reef habitats that depended on the month of survey. These ten species showed a tendency towards higher abundance inside the reserve in both reef habitats for most months during the study. Average fish densities pooled by protection level, however, showed that five out of these ten species were at least two-fold significantly higher inside than outside the reserve at one or both reef habitats. Supporting evidence from previously published studies in the area indicates that habitat complexity and major benthic communities were similar inside and outside the reserve, while fishing pressure appeared to be homogeneous across the archipelago before reserve establishment. Although poaching may occur within the reserve, especially at the boundaries, effective protection from fishing was the most plausible explanation for the patterns observed.
Pina-Amargós et al. (2014) Evidence for protection of targeted reef fish on the largest marine reserve in the Caribbean. PeerJ 2:e274 https://doi.org/10.7717/peerj.274
Asian elephants (Elephas maximus) reassure others in distress
Contact directed by uninvolved bystanders toward others in distress, often termed consolation, is uncommon in the animal kingdom, thus far only demonstrated in the great apes, canines, and corvids. Whereas the typical agonistic context of such contact is relatively rare within natural elephant families, other causes of distress may trigger similar, other-regarding responses. In a study carried out at an elephant camp in Thailand, we found that elephants affiliated significantly more with other individuals through directed, physical contact and vocal communication following a distress event than in control periods. In addition, bystanders affiliated with each other, and matched the behavior and emotional state of the first distressed individual, suggesting emotional contagion. The initial distress responses were overwhelmingly directed toward ambiguous stimuli, thus making it difficult to determine if bystanders reacted to the distressed individual or showed a delayed response to the same stimulus. Nonetheless, the directionality of the contacts and their nature strongly suggest attention toward the emotional states of conspecifics. The elephants’ behavior is therefore best classified with similar consolation responses by apes, possibly based on convergent evolution of empathic capacities.
Plotnik et al. (2014) Asian elephants (Elephas maximus) reassure others in distress. PeerJ 2:e278 https://doi.org/10.7717/peerj.278
Detecting deception via eyeblink frequency modulation
To assess the efficacy of using eyeblink frequency modulation to detect deception about a third party, 32 participants were sent on a mission to deliver a package to an interviewer. 17 of the participants lied to the interviewer about the details of their mock mission and 15 responded truthfully. During the interview, eyeblink frequency data were collected via electromyography and recorded video. Liars displayed eyeblink frequency suppression while lying, while truth tellers exhibited an increase in eyeblink frequency during the mission relevant questioning period. The compensatory flurry of eyeblinks following deception observed in previous studies was absent in the present study. A discriminant function using eyeblink suppression to predict lying correctly classified 81.3% of cases, with a sensitivity of 88.2% and a specificity of 73.3%. This technique, yielding a reasonable sensitivity, shows promise for future testing as, unlike polygraph, it is compatible with distance technology.
Perelman (2014) Detecting deception via eyeblink frequency modulation. PeerJ 2:e260 https://doi.org/10.7717/peerj.260
The affective profiles, psychological well-being, and harmony: environmental mastery and self-acceptance predict the sense of a harmonious life
Background. An important outcome from the debate on whether wellness equals happiness, is the need of research focusing on how psychological well-being might influence humans’ ability to adapt to the changing environment and live in harmony. To get a detailed picture of the influence of positive and negative affect, the current study employed the affective profiles model in which individuals are categorised into groups based on either high positive and low negative affect (self-fulfilling); high positive and high negative affect (high affective); low positive and low negative affect (low affective); and high negative and low positive affect (self-destructive). The aims were to (1) investigate differences between affective profiles in psychological well-being and harmony and (2) how psychological well-being and its dimensions relate to harmony within the four affective profiles. Method. 500 participants (mean age = 34.14 years, SD. = ±12.75 years; 187 males and 313 females) were recruited online and required to answer three self-report measures: The Positive Affect and Negative Affect Schedule; The Scales of Psychological Well-Being (short version) and The Harmony in Life Scale. We conducted a Multivariate Analysis of Variance where the affective profiles and gender were the independent factors and psychological well-being composite score, its six dimensions as well as the harmony in life score were the dependent factors. In addition, we conducted four multi-group (i.e., the four affective profiles) moderation analyses with the psychological well-being dimensions as predictors and harmony in life as the dependent variables. Results. Individuals categorised as self-fulfilling, as compared to the other profiles, tended to score higher on the psychological well-being dimensions: positive relations, environmental mastery, self-acceptance, autonomy, personal growth, and purpose in life. In addition, 47% to 66% of the variance of the harmony in life was explained by the dimensions of psychological well-being within the four affective profiles. Specifically, harmony in life was significantly predicted by environmental mastery and self-acceptance across all affective profiles. However, for the low affective group high purpose in life predicted low levels of harmony in life. Conclusions. The results demonstrated that affective profiles systematically relate to psychological well-being and harmony in life. Notably, individuals categorised as self-fulfilling tended to report higher levels of both psychological well-being and harmony in life when compared with the other profiles. Meanwhile individuals in the self-destructive group reported the lowest levels of psychological well-being and harmony when compared with the three other profiles. It is proposed that self-acceptance and environmental acceptance might enable individuals to go from self-destructive to a self-fulfilling state that also involves harmony in life.
Garcia et al. (2014) The affective profiles, psychological well-being, and harmony: environmental mastery and self-acceptance predict the sense of a harmonious life. PeerJ 2:e259 https://doi.org/10.7717/peerj.259
Hawksbill × loggerhead sea turtle hybrids at Bahia, Brazil: where do their offspring go?
Hybridization between hawksbill (Eretmochelys imbricata) and loggerhead (Caretta caretta) breeding groups is unusually common in Bahia state, Brazil. Such hybridization is possible because hawksbill and loggerhead nesting activities overlap temporally and spatially along the coast of this state. Nevertheless, the destinations of their offspring are not yet known. This study is the first to identify immature hawksbill × loggerhead hybrids (n = 4) from this rookery by analyzing the mitochondrial DNA (mtDNA) of 157 immature turtles morphologically identified as hawksbills. We also compare for the first time modeled dispersal patterns of hawksbill, loggerhead, and hybrid offspring considering hatching season and oceanic phase duration of turtles. Particle movements varied according to season, with a higher proportion of particles dispersing southwards throughout loggerhead and hybrid hatching seasons, and northwards during hawksbill season. Hybrids from Bahia were not present in important hawksbill feeding grounds of Brazil, being detected only at areas more common for loggerheads. The genetic and oceanographic findings of this work indicate that these immature hybrids, which are morphologically similar to hawksbills, could be adopting behavioral traits typical of loggerheads, such as feeding in temperate waters of the western South Atlantic. Understanding the distribution, ecology, and migrations of these hybrids is essential for the development of adequate conservation and management plans.
Proietti et al. (2014) Hawksbill × loggerhead sea turtle hybrids at Bahia, Brazil: where do their offspring go?. PeerJ 2:e255 https://doi.org/10.7717/peerj.255
Craniofacial ontogeny in Centrosaurus apertus
Centrosaurus apertus, a large bodied ceratopsid from the Late Cretaceous of North America, is one of the most common fossils recovered from the Belly River Group. This fossil record shows a wide diversity in morphology and size, with specimens ranging from putative juveniles to fully-grown individuals. The goal of this study was to reconstruct the ontogenetic changes that occur in the craniofacial skeleton of C. apertus through a quantitative cladistic analysis. Forty-seven cranial specimens were independently coded in separate data matrices for 80 hypothetical multistate growth characters and 130 hypothetical binary growth characters. Both analyses yielded the max-limit of 100,000 most parsimonious saved trees and the strict consensus collapsed into large polytomies. In order to reduce conflict resulting from missing data, fragmentary individuals were removed and the analyses were rerun. Among both the complete and the reduced data sets the multistate analyses recovered a shorter tree with a higher consistency index (CI) than the additive binary data sets. The arrangement within the trees shows a progression of specimens with a recurved nasal horn in the least mature individuals, followed by specimens with straight nasal horns in relatively more mature individuals, and finally specimens with procurved nasal horns in the most mature individuals. The most mature individuals are further characterized by the reduction of the cranial horn ornamentations in late growth stages, a trait that similarly occurs in the growth of other dinosaurs. Bone textural changes were found to be sufficient proxies for relative maturity in individuals that have not reached adult size. Additionally, frill length is congruent with relative maturity status and makes an acceptable proxy for ontogenetic status, especially in smaller individuals. In adult-sized individuals, the fusion of the epiparietals and episquamosals and the orientation of the nasal horn are the best indicators of relative maturity. This study recovers no clear evidence for sexually specific display structures or size dimorphism in C. apertus.
Frederickson et al. (2014) Craniofacial ontogeny in Centrosaurus apertus. PeerJ 2:e252 https://doi.org/10.7717/peerj.252
Absence of Helicobacter pylori is not protective against peptic ulcer bleeding in elderly on offending agents: lessons from an exceptionally low prevalence population
Aim. Helicobacter pylori (H. pylori) infection is exceptionally rare in population from the north-eastern region of Peninsular Malaysia. This provides us an opportunity to contemplate the future without H. pylori in acute non-variceal upper gastrointestinal (GI) bleeding. Methods. All cases in the GI registry with GI bleeding between 2003 and 2006 were reviewed. Cases with confirmed non-variceal aetiology were analysed. Rockall score > 5 was considered high risk for bleeding and primary outcomes studied were in-hospital mortality, recurrent bleeding and need for surgery. Results. The incidence of non-variceal upper GI bleeding was 2.2/100,000 person-years. Peptic ulcer bleeding was the most common aetiology (1.8/100,000 person-years). In-hospital mortality (3.6%), recurrent bleeding (9.6%) and need for surgery (4.0%) were uncommon in this population with a largely low risk score (85.2% with score ≤5). Elderly were at greater risk for bleeding (mean 68.5 years, P = 0.01) especially in the presence of duodenal ulcers (P = 0.04) despite gastric ulcers being more common. NSAIDs, aspirin and co-morbidities were the main risk factors. Conclusions. The absence of H. pylori infection may not reduce the risk of peptic ulcer bleeding in the presence of risk factors especially offending drugs in the elderly.
Lee et al. (2014) Absence of Helicobacter pylori is not protective against peptic ulcer bleeding in elderly on offending agents: lessons from an exceptionally low prevalence population. PeerJ 2:e257 https://doi.org/10.7717/peerj.257
Existence of benefit finding and posttraumatic growth in people treated for head and neck cancer: a systematic review
Background. The impact of head and neck cancer (HNC) in long-term survivors differs widely among individuals, and a significant number of them suffer from the negative effects of disease, whereas others report significant positive effect. This systematic review investigated the evidence the implications of treatment for HNC and subsequent development of Benefit Finding (BF) or Posttraumatic Growth (PTG). Purpose. To understand how differing medical, psychological and social characteristics of HNC may lead to BF/PTG and subsequently inform post-treatment interventions to encourage positive outcomes. Method. In February 2012, five databases including Pubmed, and Psych Info, were searched, for peer-reviewed English-language publications. Search strings included key words pertaining to HNC, BF, and PTG. One thousand three hundred and sixty three publications were identified, reviewed, and reduced following Cochrane guidelines and inclusion/exclusion criteria specified by a group of maxillofacial consultants and psychologists. Publications were then quality assessed using the CASP Cohort Critical Appraisal tool. Findings. Five manuscripts met the search and selection criteria, and were sourced for review. All studies were identified as being level IIb evidence which is a medium level of quality. The majority of studies investigated benefit finding (80%) and were split between recruiting participant via cancer clinics and postal survey. They focused on the medical, psychological and social characteristics of the patient following completion of treatment for HNC. Conclusion. Demographic factors across the papers showed similar patterns of relationships across BF and PTG; that higher education/qualification and cohabitation/marriage are associated with increased BF/PTG. Similarly, overlap with disease characteristics and psychosocial factors where hope and optimism were both positively correlated with increased reported BF/PTG.
Harding et al. (2014) Existence of benefit finding and posttraumatic growth in people treated for head and neck cancer: a systematic review. PeerJ 2:e256 https://doi.org/10.7717/peerj.256
Comparison of lodgepole and jack pine resin chemistry: implications for range expansion by the mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae)
The mountain pine beetle, Dendroctonus ponderosae, is a significant pest of lodgepole pine in British Columbia (BC), where it has recently reached an unprecedented outbreak level. Although it is native to western North America, the beetle can now be viewed as a native invasive because for the first time in recorded history it has begun to reproduce in native jack pine stands within the North American boreal forest. The ability of jack pine trees to defend themselves against mass attack and their suitability for brood success will play a major role in the success of this insect in a putatively new geographic range and host. Lodgepole and jack pine were sampled along a transect extending from the beetle’s historic range (central BC) to the newly invaded area east of the Rocky Mountains in north-central Alberta (AB) in Canada for constitutive phloem resin terpene levels. In addition, two populations of lodgepole pine (BC) and one population of jack pine (AB) were sampled for levels of induced phloem terpenes. Phloem resin terpenes were identified and quantified using gas chromatography. Significant differences were found in constitutive levels of terpenes between the two species of pine. Constitutive α-pinene levels – a precursor in the biosynthesis of components of the aggregation and antiaggregation pheromones of mountain pine beetle – were significantly higher in jack pine. However, lower constitutive levels of compounds known to be toxic to bark beetles, e.g., 3-carene, in jack pine suggests that this species could be poorly defended. Differences in wounding-induced responses for phloem accumulation of five major terpenes were found between the two populations of lodgepole pine and between lodgepole and jack pine. The mountain pine beetle will face a different constitutive and induced phloem resin terpene environment when locating and colonizing jack pine in its new geographic range, and this may play a significant role in the ability of the insect to persist in this new host.
Clark et al. (2014) Comparison of lodgepole and jack pine resin chemistry: implications for range expansion by the mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae). PeerJ 2:e240 https://doi.org/10.7717/peerj.240
Ankyrin (ANK) repeats are one of the most common amino acid sequence motifs that mediate interactions between proteins of myriad sizes, shapes and functions. We assess their widespread abundance in Bacteria and Archaea for the first time and demonstrate in Bacteria that lifestyle, rather than phylogenetic history, is a predictor of ANK repeat abundance. Unrelated organisms that forge facultative and obligate symbioses with eukaryotes show enrichment for ANK repeats in comparison to free-living bacteria. The reduced genomes of obligate intracellular bacteria remarkably contain a higher fraction of ANK repeat proteins than other lifestyles, and the number of ANK repeats in each protein is augmented in comparison to other bacteria. Taken together, these results reevaluate the concept that ANK repeats are signature features of eukaryotic proteins and support the hypothesis that intracellular bacteria broadly employ ANK repeats for structure-function relationships with the eukaryotic host cell.
Jernigan et al. (2014) Ankyrin domains across the Tree of Life. PeerJ 2:e264 https://doi.org/10.7717/peerj.264
The rediscovery and redescription of the holotype of the Late Jurassic turtle Plesiochelys etalloni
Plesiochelyidae are a major component of Late Jurassic shallow marine environments throughout Europe. However, the taxonomy of plesiochelyid turtles is rather confused. Over the years, many taxa have been synonymized with Plesiochelys etalloni, one of the first described species. However, the holotype of P. etalloni (and only specimen known from Lect, the type locality) was lost for more than 150 years. This specimen has been recently rediscovered in the collections of the Musée d’archéologie du Jura in Lons-le-Saunier, France. For the first time since its original description in 1857, the holotype of P. etalloni is redescribed and compared to relevant material. The taxonomic status of this taxon is revised accordingly. Based on the morphology of the newly rediscovered holotype and on a reassessment of specimens from Solothurn (Switzerland), the species P. solodurensis, P. sanctaeverenae and P. langii are synonymized with P. etalloni. Known skull-shell associations for P. etalloni are re-evaluated in light of the new morphological information available since the rediscovery of this holotype specimen. Finally, we confirm that Plesiochelys is represented by a single species in the Late Jurassic of the Jura Mountains.
Anquetin et al. (2014) The rediscovery and redescription of the holotype of the Late Jurassic turtle Plesiochelys etalloni. PeerJ 2:e258 https://doi.org/10.7717/peerj.258
Regulation of antimycin biosynthesis by the orphan ECF RNA polymerase sigma factor σAntA
Antimycins are an extended family of depsipeptides that are made by filamentous actinomycete bacteria and were first isolated more than 60 years ago. Recently, antimycins have attracted renewed interest because of their activities against the anti-apoptotic machineries inside human cells which could make them promising anti-cancer compounds. The biosynthetic pathway for antimycins was recently characterised but very little is known about the organisation and regulation of the antimycin (ant) gene cluster. Here we report that the ant gene cluster in Streptomyces albus is organized into four transcriptional units; the antBA, antCDE, antGF and antHIJKLMNO operons. Unusually for secondary metabolite clusters, the antG and antH promoters are regulated by an extracytoplasmic function (ECF) RNA polymerase sigma factor named σAntA which represents a new sub-family of ECF σ factors that is only found in antimycin producing strains. We show that σAntA controls production of the unusual precursor 3-aminosalicylate which is absolutely required for the production of antimycins. σAntA is highly conserved in antimycin producing strains and the −10 and −35 elements at the σAntA regulated antG and antH promoters are also highly conserved suggesting a common mechanism of regulation. We also demonstrate that altering the C-terminal Ala-Ala residues found in all σAntA proteins to Asp-Asp increases expression of the antFG and antGHIJKLMNO operons and we speculate that this Ala-Ala motif may be a signal for the protease ClpXP.
Seipke et al. (2014) Regulation of antimycin biosynthesis by the orphan ECF RNA polymerase sigma factor σAntA. PeerJ 2:e253 https://doi.org/10.7717/peerj.253
Alkalinity to calcium flux ratios for corals and coral reef communities: variances between isolated and community conditions
Calcification in reef corals and coral reefs is widely measured using the alkalinity depletion method which is based on the fact that two protons are produced for every mole of CaCO3 precipitated. This assumption was tested by measuring the total alkalinity (TA) flux and Ca2+ flux of isolated components (corals, alga, sediment and plankton) in reference to that of a mixed-community. Experiments were conducted in a flume under natural conditions of sunlight, nutrients, plankton and organic matter. A realistic hydrodynamic regime was provided. Groups of corals were run separately and in conjunction with the other reef components in a mixed-community. The TA flux to Ca2+ flux ratio (ΔTA: ΔCa2+) was consistently higher in the coral-only run (2.06 ± 0.19) than in the mixed-community run (1.60 ± 0.14, p-value = 0.011). The pH was higher and more stable in the mixed-community run (7.94 ± 0.03 vs. 7.52 ± 0.07, p-value = 3 × 10−5). Aragonite saturation state (Ωarag) was also higher in the mixed-community run (2.51 ± 0.2 vs. 1.12 ± 0.14, p-value = 2 × 10−6). The sediment-only run revealed that sediment is the source of TA that can account for the lower ΔTA: ΔCa2+ ratio in the mixed-community run. The macroalgae-only run showed that algae were responsible for the increased pH in the mixed-community run. Corals growing in a mixed-community will experience an environment that is more favorable to calcification (higher daytime pH due to algae photosynthesis, additional TA and inorganic carbon from sediments, higher Ωarag). A paradox is that the alkalinity depletion method will yield a lower net calcification for a mixed-community versus a coral-only community due to TA recycling, even though the corals may be calcifying at a higher rate due to a more optimal environment.
Murillo et al. (2014) Alkalinity to calcium flux ratios for corals and coral reef communities: variances between isolated and community conditions. PeerJ 2:e249 https://doi.org/10.7717/peerj.249
When is an ecological network complex? Connectance drives degree distribution and emerging network properties
Connectance and degree distributions are important components of the structure of ecological networks. In this contribution, we use a statistical argument and simple network generating models to show that properties of the degree distribution are driven by network connectance. We discuss the consequences of this finding for (1) the generation of random networks in null-model analyses, and (2) the interpretation of network structure and ecosystem properties in relationship with degree distribution.
Poisot et al. (2014) When is an ecological network complex? Connectance drives degree distribution and emerging network properties. PeerJ 2:e251 https://doi.org/10.7717/peerj.251