Escape and avoidance learning in the earthworm Eisenia hortensis
Interest in instrumental learning in earthworms dates back to 1912 when Yerkes concluded that they can learn a spatial discrimination in a T-maze. Rosenkoetter and Boice determined in the 1970s that the “learning” that Yerkes observed was probably chemotaxis and not learning at all. We examined a different form of instrumental learning: the ability to learn both to escape and to avoid an aversive stimulus. Freely moving “master” worms could turn off an aversive white light by increasing their movement; the behavior of yoked controls had no effect on the light. We demonstrate that in as few as 12 trials the behavior of the master worms comes under the control of this contingency.
Wilson et al. (2014) Escape and avoidance learning in the earthworm Eisenia hortensis. PeerJ 2:e250 https://doi.org/10.7717/peerj.250
Sexual coevolution of spermatophore envelopes and female genital traits in butterflies: Evidence of male coercion?
Signa are sclerotized structures located on the inner wall of the corpus bursa of female Lepidoptera whose main function is tearing open spermatophores. The sexually antagonistic coevolution (SAC) hypothesis proposes that the thickness of spermatophore envelopes has driven the evolution of the females signa; this idea is based in the fact that in many lepidopterans female sexual receptivity is at least partially controlled by the volume of ejaculate remaining in the corpus bursa. According to the SAC hypothesis, males evolved thick spermatophore envelopes to delay the post-mating recovery of female sexual receptivity thus reducing sperm competition; in response, females evolved signa for breaking spermatophore envelopes faster, gaining access to the resources contained in them and reducing their intermating intervals; the evolution of signa, in turn, favored the evolution of even thicker spermatophore envelopes, and so on. We tested two predictions of the SAC hypothesis with comparative data on the thickness of spermatophore envelopes of eleven species of Heliconiinae butterflies. The first prediction is that the spermatophore envelopes of polyandrous species with signa will be thicker than those of monandrous species without signa. In agreement with this prediction, we found that the spermatophore envelopes of a polyandrous Heliconius species with signa are thicker than those of two monandrous Heliconius species without signa. The second prediction is that in some species with signa males could enforce monandry in females by evolving “very thick” spermatophore envelopes, in these species we predict that their spermatophore envelopes will be thicker than those of their closer polyandrous relatives with signa. In agreement with this prediction, we found that in two out of three comparisons, spermatophore envelopes of monandrous species with signa have thicker spermatophore envelopes than their closer polyandrous relatives with signa. Thus, our results support the idea that selective pressures arising from sexually antagonistic interactions have been important in the evolution of spermatophore envelopes, female signa and female mating patterns.
Sánchez et al. (2014) Sexual coevolution of spermatophore envelopes and female genital traits in butterflies: Evidence of male coercion?. PeerJ 2:e247 https://doi.org/10.7717/peerj.247
A new model for simulating growth in fish
A real dynamic population model calculates change in population sizes independent of time. The Beverton & Holt (B&H) model commonly used in fish assessment includes the von Bertalanffy growth function which has age or accumulated time as an independent variable. As a result the B&H model has to assume constant fish growth. However, growth in fish is highly variable depending on food availability and environmental conditions. We propose a new growth model where the length increment of fish living under constant conditions and unlimited food supply, decreases linearly with increasing fish length until it reaches zero at a maximal fish length. The model is independent of time and includes a term which accounts for the environmental variation. In the present study, the model was validated in zebrafish held at constant conditions. There was a good fit of the model to data on observed growth in Norwegian spring spawning herring, capelin from the Barents Sea, North Sea herring and in farmed coastal cod. Growth data from Walleye Pollock from the Eastern Bering Sea and blue whiting from the Norwegian Sea also fitted reasonably well to the model, whereas data from cod from the North Sea showed a good fit to the model only above a length of 70 cm. Cod from the Barents Sea did not grow according to the model. The last results can be explained by environmental factors and variable food availability in the time under study. The model implicates that the efficiency of energy conversion from food decreases as the individual animal approaches its maximal length and is postulated to represent a natural law of fish growth.
Hamre et al. (2014) A new model for simulating growth in fish. PeerJ 2:e244 https://doi.org/10.7717/peerj.244
Ligand determinants of fatty acid activation of the pronociceptive ion channel TRPA1
Background and purpose. Arachidonic acid (AA) and its derivatives are important modulators of cellular signalling. The transient receptor potential cation channel subfamily A, member 1 (TRPA1) is a cation channel with important functions in mediating cellular responses to noxious stimuli and inflammation. There is limited information about the interactions between AA itself and TRPA1, so we investigated the effects of AA and key ethanolamide and amino acid/neurotransmitter derivatives of AA on hTRPA1. Experimental approach. HEK 293 cells expressing hTRPA1 were studied by measuring changes in intracellular calcium ([Ca]i) with a fluorescent dye and by standard whole cell patch clamp recordings. Key results. AA (30 μM) increased fluorescence in hTRPA1 expressing cells by 370% (notional EC50 13 μM). The covalent TRPA1 agonist cinnamaldehyde (300 μM) increased fluorescence by 430% (EC50, 11 μM). Anandamide (230%) and N-arachidonoyl tyrosine (170%) substantially activated hTRPA1 at 30 μM, however, N-arachidonoyl conjugates of glycine and taurine were less effective while N-acyl conjugates of 5-HT did not affect hTRPA1. Changing the acyl chain length or the number and position of double bonds reduced fatty acid efficacy at hTRPA1. Mutant hTRPA1 (Cys621, Cys641 and Cys665 changed to Ser) could be activated by AA (100 μM, 40% of wild type) but not by cinnamaldehyde (300 μM). Conclusions and implications. AA is a more potent activator of TRPA1 than its ethanolamide or amino acid/neurotransmitter derivatives and acts via a mechanism distinct from that of cinnamaldehyde, further underscoring the likelyhood of multiple pharmacologically exploitable sites on hTRPA1.
Redmond et al. (2014) Ligand determinants of fatty acid activation of the pronociceptive ion channel TRPA1. PeerJ 2:e248 https://doi.org/10.7717/peerj.248
Plant compensation to grazing and soil carbon dynamics in a tropical grassland
The effects of grazing on soil organic carbon (SOC) dynamics, particularly in the tropics, are still poorly understood. Plant compensation to grazing, whereby plants maintain leaf area (C input capacity) despite consumption (C removal) by grazers, has been demonstrated in tropical grasslands but its influence on SOC is largely unexplored. Here, the effect of grazing on plant leaf area index (LAI) was measured in a field experiment in Serengeti National Park, Tanzania. LAI changed little for grazing intensities up to 70%. The response curve of LAI versus grazing intensity was used in a mass balance model, called SNAP, of SOC dynamics based on previous data from the Serengeti. The model predicted SOC to increase at intermediate grazing intensity, but then to decline rapidly at the highest grazing intensities. The SNAP model predictions were compared with observed SOC stocks in the 24 grazed plots of a 10-year grazing exclosure experiment at eight sites across the park that varied in mean annual rainfall, soil texture, grazing intensity and plant lignin and cellulose. The model predicted current SOC stocks very well (R2 > 0.75), and suggests that compensatory plant responses to grazing are an important means of how herbivores might maintain or increase SOC in tropical grasslands.
Ritchie (2014) Plant compensation to grazing and soil carbon dynamics in a tropical grassland. PeerJ 2:e233 https://doi.org/10.7717/peerj.233
Snake venomics of Bothrops punctatus, a semiarboreal pitviper species from Antioquia, Colombia
Bothrops punctatus is an endangered, semi-arboreal pitviper species distributed in Panamá, Colombia, and Ecuador, whose venom is poorly characterized. In the present work, the protein composition of this venom was profiled using the ‘snake venomics’ analytical strategy. Decomplexation of the crude venom by RP-HPLC and SDS-PAGE, followed by tandem mass spectrometry of tryptic digests, showed that it consists of proteins assigned to at least nine snake toxin families. Metalloproteinases are predominant in this secretion (41.5% of the total proteins), followed by C-type lectin/lectin-like proteins (16.7%), bradykinin-potentiating peptides (10.7%), phospholipases A2 (93%), serine proteinases (5.4%), disintegrins (38%), L-amino acid oxidases (3.1%), vascular endothelial growth factors (17%), and cysteine-rich secretory proteins (1.2%). Altogether, 6.6% of the proteins were not identified. In vitro, the venom exhibited proteolytic, phospholipase A2, and L-amino acid oxidase activities, as well as angiotensin-converting enzyme (ACE)-inhibitory activity, in agreement with the obtained proteomic profile. Cytotoxic activity on murine C2C12 myoblasts was negative, suggesting that the majority of venom phospholipases A2 likely belong to the acidic type, which often lack major toxic effects. The protein composition of B. punctatus venom shows a good correlation with toxic activities here and previously reported, and adds further data in support of the wide diversity of strategies that have evolved in snake venoms to subdue prey, as increasingly being revealed by proteomic analyses.
Fernández Culma et al. (2014) Snake venomics of Bothrops punctatus, a semiarboreal pitviper species from Antioquia, Colombia. PeerJ 2:e246 https://doi.org/10.7717/peerj.246
Perioperative morbidity and mortality of cardiothoracic surgery in patients with a do-not-resuscitate order
Background. Do-not-resuscitate (DNR) orders are often active in patients with multiple comorbidities and a short natural life expectancy, but limited information exists as to how often these patients undergo high-risk operations and of the perioperative outcomes in this population. Methods. Using comprehensive inpatient administrative data from the Public Discharge Data file (years 2005 through 2010) of the California Office of Statewide Health Planning and Development, which includes a dedicated variable recording DNR status, we identified cohorts of DNR patients who underwent major cardiac or thoracic operations and compared themto age- and procedure-matched comparison cohorts. The primary study outcome was in-hospital mortality. Results. DNR status was not uncommon in cardiac (n = 2,678, 1.1% of all admissions for cardiac surgery, age 71.6 ± 15.9 years) and thoracic (n = 3,129, 3.7% of all admissions for thoracic surgery, age 73.8 ± 13.6 years) surgical patient populations. Relative to controls, patients who were DNR experienced significantly greater inhospital mortality after cardiac (37.5% vs. 11.2%, p < 0.0001 and thoracic (25.4% vs. 6.4%) operations. DNR status remained an independent predictor of in-hospital mortality onmultivariate analysis after adjustment for baseline and comorbid conditions in both the cardiac (OR 4.78, 95% confidence interval 4.21–5.41, p < 0.0001) and thoracic (OR 6.11, 95% confidence interval 5.37–6.94, p < 0.0001) cohorts. Conclusions. DNR status is associated with worse outcomes of cardiothoracic surgery even when controlling for age, race, insurance status, and serious comorbid disease. DNR status appears to be a marker of substantial perioperative risk, and may warrant substantial consideration when framing discussions of surgical risk and benefit, resource utilization, and biomedical ethics surrounding end-of-life care.
Maxwell et al. (2014) Perioperative morbidity and mortality of cardiothoracic surgery in patients with a do-not-resuscitate order. PeerJ 2:e245 https://doi.org/10.7717/peerj.245
Being there: a brief visit to a neighbourhood induces the social attitudes of that neighbourhood
There are differences between human groups in social behaviours and the attitudes that underlie them, such as trust. However, the psychological mechanisms that produce and reproduce this variation are not well understood. In particular, it is not clear whether assimilation to the social culture of a group requires lengthy socialization within that group, or can be more rapidly and reversibly evoked by exposure to the group’s environment and the behaviour of its members. Here, we report the results of a two-part study in two neighbourhoods of a British city, one economically deprived with relatively high crime, and the other affluent and lower in crime. In the first part of the study, we surveyed residents and found that the residents of the deprived neighbourhood had lower levels of social trust and higher levels of paranoia than the residents of the affluent neighbourhood. In the second part, we experimentally transported student volunteers who resided in neither neighbourhood to one or the other, and had them walk around delivering questionnaires to houses. We surveyed their trust and paranoia, and found significant differences according to which neighbourhood they had been sent to. The differences in the visitors mirrored the differences seen in the residents, with visitors to the deprived neighbourhood reporting lower social trust and higher paranoia than visitors to the affluent one. The magnitudes of the neighbourhood differences in the visitors, who only spent up to 45 min in the locations, were nearly as great as the magnitudes of those amongst the residents. We discuss the relevance of our findings to differential psychology, neighbourhood effects on social outcomes, and models of cultural evolution.
Nettle et al. (2014) Being there: a brief visit to a neighbourhood induces the social attitudes of that neighbourhood. PeerJ 2:e236 https://doi.org/10.7717/peerj.236
PhyloSift: phylogenetic analysis of genomes and metagenomes
Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
Darling et al. (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243 https://doi.org/10.7717/peerj.243
The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles
Pattern recognition receptors (PRRs) play an important role in detecting invading pathogens and mounting a robust defense response to restrict infection. In rice, one of the best characterized PRRs is XA21, a leucine rich repeat receptor-like kinase that confers broad-spectrum resistance to multiple strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). In 2009 we reported that an Xoo protein, called Ax21, is secreted by a type I-secretion system and that it serves to activate XA21-mediated immunity. This report has recently been retracted. Here we present data that corrects our previous model. We first show that Ax21 secretion does not depend on the predicted type I secretion system and that it is processed by the general secretion (Sec) system. We further show that Ax21 is an outer membrane protein, secreted in association with outer membrane vesicles. Finally, we provide data showing that ax21 knockout strains do not overcome XA21-mediated immunity.
Bahar et al. (2014) The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PeerJ 2:e242 https://doi.org/10.7717/peerj.242
Composable languages for bioinformatics: the NYoSh experiment
Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is distributed at http://nyosh.campagnelab.org.
Simi et al. (2014) Composable languages for bioinformatics: the NYoSh experiment. PeerJ 2:e241 https://doi.org/10.7717/peerj.241
Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves
Several clinical scoring systems for diagnosis of bovine respiratory disease (BRD) in calves have been proposed. However, such systems were based on subjective judgment, rather than statistical methods, to weight scores. Data from a pair-matched case-control study on a California calf raising facility was used to develop three novel scoring systems to diagnose BRD in preweaned dairy calves. Disease status was assigned using both clinical signs and diagnostic test results for BRD-associated pathogens. Regression coefficients were used to weight score values. The systems presented use nasal and ocular discharge, rectal temperature, ear and head carriage, coughing, and respiratory quality as predictors. The systems developed in this research utilize fewer severity categories of clinical signs, require less calf handling, and had excellent agreement (Kappa > 0.8) when compared to an earlier scoring system. The first scoring system dichotomized all clinical predictors but required inducing a cough. The second scoring system removed induced cough as a clinical abnormality but required distinguishing between three levels of nasal discharge severity. The third system removed induced cough and forced a dichotomized variable for nasal discharge. The first system presented in this study used the following predictors and assigned values: coughing (induced or spontaneous coughing, 2 points), nasal discharge (any discharge, 3 points), ocular discharge (any discharge, 2 points), ear and head carriage (ear droop or head tilt, 5 points), fever (≥39.2°C or 102.5°F, 2 points), and respiratory quality (abnormal respiration, 2 points). Calves were categorized “BRD positive” if their total score was ≥4. This system correctly classified 95.4% cases and 88.6% controls. The second presented system categorized the predictors and assigned weights as follows: coughing (spontaneous only, 2 points), mild nasal discharge (unilateral, serous, or watery discharge, 3 points), moderate to severe nasal discharge (bilateral, cloudy, mucoid, mucopurlent, or copious discharge, 5 points), ocular discharge (any discharge, 1 point), ear and head carriage (ear droop or head tilt, 5 points), fever (≥39.2°C, 2 points), and respiratory quality (abnormal respiration, 2 points). Calves were categorized “BRD positive” if their total score was ≥4. This system correctly classified 89.3% cases and 92.8% controls. The third presented system used the following predictors and scores: coughing (spontaneous only, 2 points), nasal discharge (any, 4 points), ocular discharge (any, 2 points), ear and head carriage (ear droop or head tilt, 5 points), fever (≥39.2°C, 2 points), and respiratory quality (abnormal respiration, 2 points). Calves were categorized “BRD positive” if their total score was ≥5. This system correctly classified 89.4% cases and 90.8% controls. Each of the proposed systems offer few levels of clinical signs and data-based weights for on-farm diagnosis of BRD in dairy calves.
Love et al. (2014) Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves. PeerJ 2:e238 https://doi.org/10.7717/peerj.238
Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae
While shifts from coral to seaweed dominance have become increasingly common on coral reefs and factors triggering these shifts successively identified, the primary mechanisms involved in coral-algae interactions remain unclear. Amongst various potential mechanisms, algal exudates can mediate increases in microbial activity, leading to localized hypoxic conditions which may cause coral mortality in the direct vicinity. Most of the processes likely causing such algal exudate induced coral mortality have been quantified (e.g., labile organic matter release, increased microbial metabolism, decreased dissolved oxygen availability), yet little is known about how reduced dissolved oxygen concentrations affect competitive dynamics between seaweeds and corals. The goals of this study were to investigate the effects of different levels of oxygen including hypoxic conditions on a common hermatypic coral Acropora yongei and the common green alga Bryopsis pennata. Specifically, we examined how photosynthetic oxygen production, dark and daylight adapted quantum yield, intensity and anatomical distribution of the coral innate fluorescence, and visual estimates of health varied with differing background oxygen conditions. Our results showed that the algae were significantly more tolerant to extremely low oxygen concentrations (2–4 mg L−1) than corals. Furthermore corals could tolerate reduced oxygen concentrations, but only until a given threshold determined by a combination of exposure time and concentration. Exceeding this threshold led to rapid loss of coral tissue and mortality. This study concludes that hypoxia may indeed play a significant role, or in some cases may even be the main cause, for coral tissue loss during coral-algae interaction processes.
Haas et al. (2014) Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae. PeerJ 2:e235 https://doi.org/10.7717/peerj.235
A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph
The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds.
Chiappe et al. (2014) A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph. PeerJ 2:e234 https://doi.org/10.7717/peerj.234
Inter-annual variability influences the eco-evolutionary dynamics of range-shifting
Understanding the eco-evolutionary dynamics of species under rapid climate change is vital for both accurate forecasting of biodiversity responses and for developing effective management strategies. Using an individual-based model we demonstrate that the presence and form (colour) of inter-annual variability in environmental conditions can impact the evolution of dispersal during range shifts. Under stable climate, temporal variability typically results in higher dispersal. However, at expanding margins, inter-annual variability actually inhibits the evolution of higher emigration propensities by disrupting the spatial sorting and natural selection processes. These results emphasize the need for future theoretical studies, as well as predictive modelling, to account for the potential impacts of inter-annual variability.
Henry et al. (2014) Inter-annual variability influences the eco-evolutionary dynamics of range-shifting. PeerJ 1:e228 https://doi.org/10.7717/peerj.228