Massively parallel read mapping on GPUs with the q-group index and PEANUT
We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best hits or all hits of a read. Our benchmarks show that PEANUT outperforms other state-of-the-art read mappers in terms of speed while maintaining or slightly increasing precision, recall and sensitivity.
Köster et al. (2014) Massively parallel read mapping on GPUs with the q-group index and PEANUT. PeerJ 2:e606 https://doi.org/10.7717/peerj.606
Effect of obesity and exercise on the expression of the novel myokines, Myonectin and Fibronectin type III domain containing 5
Metabolic dysfunction in skeletal muscle is a major contributor to the development of type 2 diabetes. Endurance exercise training has long been established as an effective means to directly restore skeletal muscle glucose and lipid uptake and metabolism. However, in addition to the direct effects of skeletal muscle on glucose and lipids, there is renewed interest in the ability of skeletal muscle to coordinate metabolic activity of other tissues, such as adipose tissue and liver. The purpose of this study was to examine the effects of endurance exercise on the expression level of two novel muscle-derived secreted factors, or myokines, Myonectin and Fibronectin type III domain containing 5 (FNDC5), the precursor for Irisin. Methods. We performed immunoblot analysis and quantitative real-time PCR analysis of Myonectin and FNDC5 in the diaphragm muscles of obese Zucker rat (OZR) and lean Zucker rat (LZR) with 9 weeks of aerobic training on a motorized treadmill. Results. We show that myonectin gene expression is increased in the OZR model of obesity and decreases with exercise in both lean and obese Zucker rats. Conversely, myonectin protein concentration was elevated with exercise. Similarly, FNDC5 mRNA levels are significantly higher in the OZR, however exercise training had no effect on the expression level of FNDC5 in either the LZR or OZR. We did not observe any difference in muscle protein content of Irisin with obesity or exercise. Conclusion. Our data shows that exercise training does not increase either FNDC5 or myonectin gene expression, indicating that increased transcriptional regulation of these myokines is not induced by exercise. However, our data also indicates a yet to be explored disconnect between myonectin gene expression and protein content. Further, this report highlights the importance of verifying reference genes when completing gene expression analysis. We found that many commonly used reference genes varied significantly by obesity and/or exercise and would have skewed the results of this study if used to normalize gene expression data. The unstable reference genes include: beta-Actin, beta-2-microglobulin, Non-POU domain containing, octamer-binding, Peptidylprolyl isomerase H, 18S ribosomal RNA, TATA box binding protein and Transferrin receptor.
Peterson et al. (2014) Effect of obesity and exercise on the expression of the novel myokines, Myonectin and Fibronectin type III domain containing 5. PeerJ 2:e605 https://doi.org/10.7717/peerj.605
Bumblebee size polymorphism and worker response to queen pheromone
Queen pheromones are chemical signals produced by reproductive individuals in social insect colonies. In many species they are key to the maintenance of reproductive division of labor, with workers beginning to reproduce individually once the queen pheromone disappears. Recently, a queen pheromone that negatively affects worker fecundity was discovered in the bumblebee Bombus terrestris, presenting an exciting opportunity for comparisons with analogous queen pheromones in independently-evolved eusocial lineages such as honey bees, ants, wasps and termites. I set out to replicate this discovery and verify its reproducibility. Using blind, controlled experiments, I found that n-pentacosane (C25) does indeed negatively affect worker ovary development. Moreover, the pheromone affects both large and small workers, and applies to workers from large, mature colonies as well as young colonies. Given that C25 is readily available and that bumblebees are popular study organisms, I hope that this replication will encourage other researchers to tackle the many research questions enabled by the discovery of a queen pheromone.
Holman (2014) Bumblebee size polymorphism and worker response to queen pheromone. PeerJ 2:e604 https://doi.org/10.7717/peerj.604
GroopM: an automated tool for the recovery of population genomes from related metagenomes
Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.
Imelfort et al. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2:e603 https://doi.org/10.7717/peerj.603
Eutrophication and the dietary promotion of sea turtle tumors
The tumor-forming disease fibropapillomatosis (FP) has afflicted sea turtle populations for decades with no clear cause. A lineage of α-herpesviruses associated with these tumors has existed for millennia, suggesting environmental factors are responsible for its recent epidemiology. In previous work, we described how herpesviruses could cause FP tumors through a metabolic influx of arginine. We demonstrated the disease prevails in chronically eutrophied coastal waters, and that turtles foraging in these sites might consume arginine-enriched macroalgae. Here, we test the idea using High-Performance Liquid Chromatography (HPLC) to describe the amino acid profiles of green turtle (Chelonia mydas) tumors and five common forage species of macroalgae from a range of eutrophic states. Tumors were notably elevated in glycine, proline, alanine, arginine, and serine and depleted in lysine when compared to baseline samples. All macroalgae from eutrophic locations had elevated arginine, and all species preferentially stored environmental nitrogen as arginine even at oligotrophic sites. From these results, we estimate adult turtles foraging at eutrophied sites increase their arginine intake 17–26 g daily, up to 14 times the background level. Arginine nitrogen increased with total macroalgae nitrogen and watershed nitrogen, and the invasive rhodophyte Hypnea musciformis significantly outperformed all other species in this respect. Our results confirm that eutrophication substantially increases the arginine content of macroalgae, which may metabolically promote latent herpesviruses and cause FP tumors in green turtles.
Van Houtan et al. (2014) Eutrophication and the dietary promotion of sea turtle tumors. PeerJ 2:e602 https://doi.org/10.7717/peerj.602
Nest-building behavior of Monk Parakeets and insights into potential mechanisms for reducing damage to utility poles
The Monk Parakeet (Myiopsitta monachus) commonly uses utility poles as a substrate for building large, bulky nests. These nests often cause fires and electric power outages, creating public safety risks and increasing liability and maintenance costs for electric companies. Previous research has focused on lethal methods and chemical contraception to prevent nesting on utility poles and electrical substations. However, implementation of lethal methods has led to public protests and lawsuits, while chemical contraception may affect other than the targeted species, and must be continually reapplied for effectiveness. One non-lethal alternative, nest removal, is costly and may not be a sustainable measure if Monk Parakeet populations continue to grow. In order to identify cost-effective non-lethal solutions to problems caused by Monk Parakeet nesting, we studied their behavior as they built nests on utility poles. Monk Parakeets initiate nests by attaching sticks at the intersection of the pole and electric lines. We found that parakeets use the electric lines exclusively to gain access to the intersection of lines and pole during nest initiation, and continue to use the lines intensively throughout construction. Monk Parakeets also have more difficulty attaching sticks during the early stages of nest construction than when the nest is nearing completion. These findings suggest that intervention during the earlier stages of nest building, by excluding Monk Parakeets from electric lines adjacent to poles, may be an effective, non-lethal method of reducing or eliminating parakeets nesting on, and damaging, utility poles.
Burgio et al. (2014) Nest-building behavior of Monk Parakeets and insights into potential mechanisms for reducing damage to utility poles. PeerJ 2:e601 https://doi.org/10.7717/peerj.601
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an equally comprehensive comparison for VarScan not yet been performed. More specifically, we compare (1) the effects of different pre-processing steps prior to variant calling with both GATK and VarScan, (2) VarScan variants called with increasingly conservative parameters, and (3) filtered and unfiltered GATK variant calls (for both the UnifiedGenotyper and the HaplotypeCaller). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. In most cases, pre-processing steps (e.g., indel realignment and quality score base recalibration using GATK) had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. Based upon concordance statistics presented in this study, we recommend GATK users focus on “high-quality” GATK variants by filtering out variants flagged as low-quality. We also found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a reproducible list of variants, with high concordance (>97%) to high-quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84–88% of the high-quality GATK SNPs in the exome datasets. This study also provides limited evidence that VarScan-Cons has a decreased false positive rate among novel variants (relative to high-quality GATK SNPs) and that the GATK HaplotypeCaller has an increased false positive rate for indels (relative to VarScan-Cons and high-quality GATK UnifiedGenotyper indels). More broadly, we believe the metrics used for comparison in this study can be useful in assessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.
Warden et al. (2014) Detailed comparison of two popular variant calling packages for exome and targeted exon studies. PeerJ 2:e600 https://doi.org/10.7717/peerj.600
Multi-decade biomass dynamics in an old-growth hemlock-northern hardwood forest, Michigan, USA
Trends in living aboveground biomass and inputs to the pool of coarse woody debris (CWD) in an undisturbed, old-growth hemlock-northern hardwood forest in northern MI were estimated from multi-decade observations of permanent plots. Growth and demographic data from seven plot censuses over 47 years (1962–2009), combined with one-time measurement of CWD pools, help assess biomass/carbon status of this landscape. Are trends consistent with traditional notions of late-successional forests as equilibrial ecosystems? Specifically, do biomass pools and CWD inputs show consistent long-term trends and relationships, and can living and dead biomass pools and trends be related to forest composition and history? Aboveground living biomass densities, estimated using standard allometric relationships, range from 360–450 Mg/ha among sampled stands and types; these values are among the highest recorded for northeastern North American forests. Biomass densities showed significant decade-scale variation, but no consistent trends over the full study period (one stand, originating following an 1830 fire, showed an aggrading trend during the first 25 years of the study). Even though total above-ground biomass pools are neither increasing nor decreasing, they have been increasingly dominated, over the full study period, by very large (>70 cm dbh) stems and by the most shade-tolerant species (Acer saccharum and Tsuga canadensis). CWD pools measured in 2007 averaged 151 m3/ha, with highest values in Acer-dominated stands. Snag densities averaged 27/ha, but varied nearly ten-fold with canopy composition (highest in Tsuga-dominated stands, lowest in Acer-dominated); snags constituted 10–50% of CWD biomass. Annualized CWD inputs from tree mortality over the full study period averaged 1.9–3.2 Mg/ha/yr, depending on stand and species composition. CWD input rates tended to increase over the course of the study. Input rates may be expected to increase over longer-term observations because, (a) living biomass is increasingly dominated by very large trees whose dead trunks have longer residence time in the CWD pool, and (b) infrequent major disturbances, thought to be important in the dynamics of these forests, have not occurred during the study period but would be expected to produce major, episodic pulses in CWD input. Few fragments of old-growth cool-temperate forests remain, but such forests can constitute a very large carbon pool on a per-area basis. The carbon sink/source status of these forests remains unclear. While aboveground living biomass at this study site shows no strong aggrading or declining trend over the last half-century, this remains a modest span in the innate time-scale of late-successional forest. The effects of rare disturbances, long-term shifts in composition and size structure, and changes in soil carbon and CWD pools may all influence long-term carbon status.
Woods (2014) Multi-decade biomass dynamics in an old-growth hemlock-northern hardwood forest, Michigan, USA. PeerJ 2:e598 https://doi.org/10.7717/peerj.598
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism that typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases chain length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a new, tractable chassis for engineering compression sensitive organisms. Second, the sensitivity of colony morphology to media compression in Bacillus can be modulated by altering a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
Polka et al. (2014) Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression. PeerJ 2:e597 https://doi.org/10.7717/peerj.597
One pair of hands is not like another: caudate BOLD response in dogs depends on signal source and canine temperament
Having previously used functional MRI to map the response to a reward signal in the ventral caudate in awake unrestrained dogs, here we examined the importance of signal source to canine caudate activation. Hand signals representing either incipient reward or no reward were presented by a familiar human (each dog’s respective handler), an unfamiliar human, and via illustrated images of hands on a computer screen to 13 dogs undergoing voluntary fMRI. All dogs had received extensive training with the reward and no-reward signals from their handlers and with the computer images and had minimal exposure to the signals from strangers. All dogs showed differentially higher BOLD response in the ventral caudate to the reward versus no reward signals, and there was a robust effect at the group level. Further, differential response to the signal source had a highly significant interaction with a dog’s general aggressivity as measured by the C-BARQ canine personality assessment. Dogs with greater aggressivity showed a higher differential response to the reward signal versus no-reward signal presented by the unfamiliar human and computer, while dogs with lower aggressivity showed a higher differential response to the reward signal versus no-reward signal from their handler. This suggests that specific facets of canine temperament bear more strongly on the perceived reward value of relevant communication signals than does reinforcement history, as each of the dogs were reinforced similarly for each signal, regardless of the source (familiar human, unfamiliar human, or computer). A group-level psychophysiological interaction (PPI) connectivity analysis showed increased functional coupling between the caudate and a region of cortex associated with visual discrimination and learning on reward versus no-reward trials. Our findings emphasize the sensitivity of the domestic dog to human social interaction, and may have other implications and applications pertinent to the training and assessment of working and pet dogs.
Cook et al. (2014) One pair of hands is not like another: caudate BOLD response in dogs depends on signal source and canine temperament. PeerJ 2:e596 https://doi.org/10.7717/peerj.596
Spatial genetic structure across a hybrid zone between European rabbit subspecies
The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioral and molecular, that hierarchically interact through time and space.
Alda et al. (2014) Spatial genetic structure across a hybrid zone between European rabbit subspecies. PeerJ 2:e582 https://doi.org/10.7717/peerj.582
Fibrochondrogenic potential of synoviocytes from osteoarthritic and normal joints cultured as tensioned bioscaffolds for meniscal tissue engineering in dogs
Meniscal tears are a common cause of stifle lameness in dogs. Use of autologous synoviocytes from the affected stifle is an attractive cell source for tissue engineering replacement fibrocartilage. However, the diseased state of these cells may impede in vitro fibrocartilage formation. Synoviocytes from 12 osteoarthritic (“oaTSB”) and 6 normal joints (“nTSB”) were cultured as tensioned bioscaffolds and compared for their ability to synthesize fibrocartilage sheets. Gene expression of collagens type I and II were higher and expression of interleukin-6 was lower in oaTSB versus nTSB. Compared with nTSB, oaTSB had more glycosaminoglycan and alpha smooth muscle staining and less collagen I and II staining on histologic analysis, whereas collagen and glycosaminoglycan quantities were similar. In conclusion, osteoarthritic joint—origin synoviocytes can produce extracellular matrix components of meniscal fibrocartilage at similar levels to normal joint—origin synoviocytes, which makes them a potential cell source for canine meniscal tissue engineering.
Warnock et al. (2014) Fibrochondrogenic potential of synoviocytes from osteoarthritic and normal joints cultured as tensioned bioscaffolds for meniscal tissue engineering in dogs. PeerJ 2:e581 https://doi.org/10.7717/peerj.581
Case based rubella surveillance in Abia State, South East Nigeria, 2007–2011
Introduction. Rubella infection has the potential of causing severe fetal birth defects collectively called congenital rubella syndrome (CRS) if the mother is infected early in pregnancy. However, little is known about rubella and CRS epidemiology in Nigeria and rubella vaccines are still not part of routine childhood immunization in Nigeria. Methods. Analysis of confirmed cases of rubella in Abia State, Nigeria from 2007 to 2011 detected through Abia State Integrated Disease Surveillance and Response system. Results. Of the 757 febrile rash cases, 81(10.7%) tested positive for rubella immunoglobulin M (IgM). New rubella infection decreased from 6.81/1,000,000 population in 2007 to 2.28/1,000,000 in 2009 and increased to 6.34/1,000,000 in 2011. The relative risk of rubella was 1.5 (CI [0.98–2.28]) times as high in females compared to males and 1.6 times (CI [0.90–2.91]) as high in rural areas compared to urban areas. Eighty six percent of rubella infections occurred in children less than 15 years with a high proportion of cases occurring between 5 and 14 years. Conclusion. Rubella infection in Abia State, Nigeria is predominantly in those who are younger than 15 years old. It is also more prevalent in females and in those living in rural areas of the state. Unfortunately, there is no surveillance of CRS in Nigeria and so the public health impact of rubella infection in the state is not known. Efforts should be made to expand the rubella surveillance in Nigeria to incorporate surveillance for CRS.
Umeh et al. (2014) Case based rubella surveillance in Abia State, South East Nigeria, 2007–2011. PeerJ 2:e580 https://doi.org/10.7717/peerj.580
A candidate multimodal functional genetic network for thermal adaptation
Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken. We first established a framework of candidate functions for such markers, and then compiled the literature on genes known to adapt to the thermal environment in different lineages of vertebrates. We then identified them in the genomes of human, chicken, and the lizard Anolis carolinensis, and established a functional genetic interaction network in the chicken. Surprisingly, markers initially identified from diverse lineages of vertebrates such as human and fish were all in close functional relationship with each other and more associated than expected by chance. This indicates that the general genetic functional network for thermoregulation and/or thermal adaptation to the environment might be regulated via similar evolutionarily conserved pathways in different vertebrate lineages. We were able to identify seven functions that were statistically overrepresented in this network, corresponding to four of our originally predicted functions plus three unpredicted functions. We describe this network as multimodal: central regulator genes with the function of relaying thermal signal (1), affect genes with different cellular functions, namely (2) lipoprotein metabolism, (3) membrane channels, (4) stress response, (5) response to oxidative stress, (6) muscle contraction and relaxation, and (7) vasodilation, vasoconstriction and regulation of blood pressure. This network constitutes a novel resource for the study of thermal adaptation in the closely related nonavian reptiles and other vertebrate ectotherms.
Wollenberg Valero et al. (2014) A candidate multimodal functional genetic network for thermal adaptation. PeerJ 2:e578 https://doi.org/10.7717/peerj.578
Factors associated with leisure time physical inactivity in black individuals: hierarchical model
Background. A number of studies have shown that the black population exhibits higher levels of leisure-time physical inactivity (LTPI), but few have investigated the factors associated with this behavior. Objective. The aim of this study was to analyze associated factors and the explanatory model proposed for LTPI in black adults. Methods. The design was cross-sectional with a sample of 2,305 adults from 20–96 years of age, 902 (39.1%) men, living in the city of Salvador, Brazil. LTPI was analyzed using the International Physical Activity Questionnaire (IPAQ). A hierarchical model was built with the possible factors associated with LTPI, distributed in distal (age and sex), intermediate 1 (socioeconomic status, educational level and marital status), intermediate 2 (perception of safety/violence in the neighborhood, racial discrimination in private settings and physical activity at work) and proximal blocks (smoking and participation in Carnival block rehearsals). We estimated crude and adjusted odds ratio (OR) using logistic regression. Results. The variables inversely associated with LTPI were male gender, socioeconomic status and secondary/university education, although the proposed model explains only 4.2% of LTPI. Conclusions. We conclude that male gender, higher education and socioeconomic status can reduce LTPI in black adults.
Pitanga et al. (2014) Factors associated with leisure time physical inactivity in black individuals: hierarchical model. PeerJ 2:e577 https://doi.org/10.7717/peerj.577
Species and size diversity in protective services offered by coral guard-crabs
Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo’orea, French Polynesia showed the Trapezia—coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.
McKeon et al. (2014) Species and size diversity in protective services offered by coral guard-crabs. PeerJ 2:e574 https://doi.org/10.7717/peerj.574
Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids
Atoposaurid crocodyliforms represent an important faunal component of Late Jurassic to Early Cretaceous Laurasian semi-aquatic to terrestrial ecosystems, with numerous spatiotemporally contemporaneous atoposaurids known from western Europe. In particular, the Late Jurassic of France and Germany records evidence for high diversity and possible sympatric atoposaurid species belonging to Alligatorellus, Alligatorium and Atoposaurus. However, atoposaurid taxonomy has received little attention, and many species are in need of revision. As such, this potentially high European diversity within a narrow spatiotemporal range might be a taxonomic artefact. Here we provide a taxonomic and anatomical revision of the Late Jurassic atoposaurid Alligatorellus. Initially described as A. beaumonti from the Kimmeridgian of Cerin, eastern France, additional material from the Tithonian of Solnhofen, south-eastern Germany, was subsequently referred to this species, with the two occurrences differentiated as A. beaumonti beaumonti and A. beaumonti bavaricus, respectively. We provide a revised diagnosis for the genus Alligatorellus, and note a number of anatomical differences between the French and German specimens, including osteoderm morphology and the configuration and pattern of sculpting of cranial elements. Consequently, we restrict the name Alligatorellus beaumonti to include only the French remains, and raise the rank of the German material to a distinct species: Alligatorellus bavaricus. A new diagnosis is provided for both species, and we suggest that a recently referred specimen from a coeval German locality cannot be conclusively referred to Alligatorellus. Although it has previously been suggested that Alligatorellus, Alligatorium and Atoposaurus might represent a single growth series of one species, we find no conclusive evidence to support this proposal, and provide a number of morphological differences to distinguish these three taxa that appear to be independent of ontogeny. Consequently, we interpret high atoposaurid diversity in the Late Jurassic island archipelago of western Europe as a genuine biological signal, with closely related species of Alligatorellus, Alligatorium and Atoposaurus in both French and German basins providing evidence for allopatric speciation, potentially driven by fluctuating highstand sea levels.
Tennant et al. (2014) Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids. PeerJ 2:e599 https://doi.org/10.7717/peerj.599
The self prefers itself? Self-referential versus parental standards in face attractiveness
Preference for phenotypic similarity in assortative mating may be influenced by either a preference for self-similarity or parent-similarity. The aim of the current study was to assess whether people’s preference in face attractiveness is influenced by resemblance to the opposite sex parent’s face (parental phenotype) or their own face (self-based phenotype or “self-imprinting”). We used computerized image manipulations of facial photographs of participants, their mothers and fathers. The original photographs were combined with 78% of the participants’ opposite sex prototype face (i.e., male and female prototypes made from equal contributions of a hundred faces), creating morphs where the contribution from the familiar faces went unnoticed. Female and male participants ranked these images together with the opposite-sex prototype different familiar morphs. Each participant did the same for the morphs generated with other same-sex participants’ faces and of their parents. We found that the female participants preferred the self-based morphs to the prototype faces. Male participants showed a general tendency towards self-referential standard. Parental face morphs were ranked low in attractiveness, which may be accounted for by the age difference of the faces blended into the self-based versus parental face morphs, since we used present-time photographs of both the participants and their parents.
Sulutvedt et al. (2014) The self prefers itself? Self-referential versus parental standards in face attractiveness. PeerJ 2:e595 https://doi.org/10.7717/peerj.595
Chronic playback of boat noise does not impact hatching success or post-hatching larval growth and survival in a cichlid fish
Anthropogenic (man-made) noise has been shown to have a negative impact on the behaviour and physiology of a range of terrestrial and aquatic animals. However, direct assessments of fitness consequences are rare. Here we examine the effect of additional noise on early life stages in the model cichlid fish, Neolamprologus pulcher. Many fishes use and produce sounds, they are crucial elements of aquatic ecosystems, and there is mounting evidence that they are vulnerable to anthropogenic noise; adult N. pulcher have recently been shown to change key behaviours during playback of motor boat noise. Using a split-brood design to eliminate potential genetic effects, we exposed half of the eggs and fry from each clutch to four weeks of playbacks of noise originally recorded from small motor boats with the other half acting as a control (receiving no noise playback). There was no significant effect of additional noise on hatching success or fry survival, length or weight at the end of the exposure period. Although care should be taken not to generalize these findings on a single species from a laboratory study, our data suggest that moderate noise increases do not necessarily have direct negative impacts on early-life survival and growth. Further studies on a range of species in natural conditions are urgently needed to inform conservation efforts and policy decisions about the consequences of anthropogenic noise.
Bruintjes et al. (2014) Chronic playback of boat noise does not impact hatching success or post-hatching larval growth and survival in a cichlid fish. PeerJ 2:e594 https://doi.org/10.7717/peerj.594
Swarm: robust and fast clustering method for amplicon-based studies
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
Mahé et al. (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2:e593 https://doi.org/10.7717/peerj.593
Habitat creation and biodiversity maintenance in mangrove forests: teredinid bivalves as ecosystem engineers
Substantial amounts of dead wood in the intertidal zone of mature mangrove forests are tunnelled by teredinid bivalves. When the tunnels are exposed, animals are able to use tunnels as refuges. In this study, the effect of teredinid tunnelling upon mangrove forest faunal diversity was investigated. Mangrove forests exposed to long emersion times had fewer teredinid tunnels in wood and wood not containing teredinid tunnels had very few species and abundance of animals. However, with a greater cross-sectional percentage surface area of teredinid tunnels, the numbers of species and abundance of animals was significantly higher. Temperatures within teredinid-attacked wood were significantly cooler compared with air temperatures, and animal abundance was greater in wood with cooler temperatures. Animals inside the tunnels within the wood may avoid desiccation by escaping the higher temperatures. Animals co-existing in teredinid tunnelled wood ranged from animals found in terrestrial ecosystems including centipedes, crickets and spiders, and animals found in subtidal marine ecosystems such as fish, octopods and polychaetes. There was also evidence of breeding within teredinid-attacked wood, as many juvenile individuals were found, and they may also benefit from the cooler wood temperatures. Teredinid tunnelled wood is a key low-tide refuge for cryptic animals, which would otherwise be exposed to fishes and birds, and higher external temperatures. This study provides evidence that teredinids are ecosystem engineers and also provides an example of a mechanism whereby mangrove forests support intertidal biodiversity and nurseries through the wood-boring activity of teredinids.
Hendy et al. (2014) Habitat creation and biodiversity maintenance in mangrove forests: teredinid bivalves as ecosystem engineers. PeerJ 2:e591 https://doi.org/10.7717/peerj.591
Synergy as a rationale for phage therapy using phage cocktails
Where phages are used to treat bacterial contaminations and infections, multiple phages are typically applied at once as a cocktail. When two or more phages in the cocktail attack the same bacterium, the combination may produce better killing than any single phage (synergy) or the combination may be worse than the best single phage (interference). Synergy is of obvious utility, especially if it can be predicted a priori, but it remains poorly documented with few examples known. This study addresses synergy in which one phage improves adsorption by a second phage. It first presents evidence of synergy from an experimental system of two phages and a mucoid E. coli host. The synergy likely stems from a tailspike enzyme produced by one of the phages. We then offer mathematical models and simulations to understand the dynamics of synergy and the enhanced magnitude of bacterial control possible. The models and observations complement each other and suggest that synergy may be of widespread utility and may be predictable from easily observed phenotypes.
Schmerer et al. (2014) Synergy as a rationale for phage therapy using phage cocktails. PeerJ 2:e590 https://doi.org/10.7717/peerj.590
Fast and accurate estimation of the covariance between pairwise maximum likelihood distances
Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.
Gil (2014) Fast and accurate estimation of the covariance between pairwise maximum likelihood distances. PeerJ 2:e583 https://doi.org/10.7717/peerj.583
Shared phylogeographic patterns between the ectocommensal flatworm Temnosewellia albata and its host, the endangered freshwater crayfish Euastacus robertsi
Comparative phylogeography of commensal species may show congruent patterns where the species involved share a common history. Temnosewellia is a genus of flatworms, members of which live in commensal relationships with host freshwater crustaceans. By constructing phylogenetic trees based on mitochondrial COI and 28S nuclear ribosomal gene sequences, this study investigated how evolutionary history has shaped patterns of intraspecific molecular variation in two such freshwater commensals. This study concentrates on the flatworm Temnosewellia albata and its critically endangered crayfish host Euastacus robertsi, which have a narrow climatically-restricted distribution on three mountaintops. The genetic data expands upon previous studies of Euastacus that suggested several vicariance events have led to the population subdivision of Euastacus robertsi. Further, our study compared historical phylogeographic patterning of these species. Our results showed that phylogeographic patterns shared among these commensals were largely congruent, featuring a shared history of limited dispersal between the mountaintops. Several hypotheses were proposed to explain the phylogeographic points of differences between the species. This study contributes significantly to understanding evolutionary relationships of commensal freshwater taxa.
Hurry et al. (2014) Shared phylogeographic patterns between the ectocommensal flatworm Temnosewellia albata and its host, the endangered freshwater crayfish Euastacus robertsi. PeerJ 2:e552 https://doi.org/10.7717/peerj.552
Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture
Growth of ice on surfaces poses a challenge for both organisms and for devices that come into contact with liquids below the freezing point. Resistance of some organisms to ice formation and growth, either in subtidal environments (e.g., Antarctic anchor ice), or in environments with moisture and cold air (e.g., plants, intertidal) begs examination of how this is accomplished. Several factors may be important in promoting or mitigating ice formation. As a start, here we examine the effect of surface texture alone. We tested four candidate surfaces, inspired by hard-shelled marine invertebrates and constructed using a three-dimensional printing process. We examined sub-polar marine organisms to develop sample textures and screened them for ice formation and accretion in submerged conditions using previous methods for comparison to data for Antarctic organisms. The sub-polar organisms tested were all found to form ice readily. We also screened artificial 3-D printed samples using the same previous methods, and developed a new test to examine ice formation from surface droplets as might be encountered in environments with moist, cold air. Despite limitations inherent to our techniques, it appears surface texture plays only a small role in delaying the onset of ice formation: a stripe feature (corresponding to patterning found on valves of blue mussels, Mytilus edulis, or on the spines of the Antarctic sea urchin Sterechinus neumayeri) slowed ice formation an average of 25% compared to a grid feature (corresponding to patterning found on sub-polar butterclams, Saxidomas nuttalli). The geometric dimensions of the features have only a small (∼6%) effect on ice formation. Surface texture affects ice formation, but does not explain by itself the large variation in ice formation and species-specific ice resistance observed in other work. This suggests future examination of other factors, such as material elastic properties and surface coatings, and their interaction with surface pattern.
Mehrabani et al. (2014) Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture. PeerJ 2:e588 https://doi.org/10.7717/peerj.588
Differences in healthcare expenditures for inflammatory bowel disease by insurance status, income, and clinical care setting
Background. Socioeconomic factors and insurance status have not been correlated with differential use of healthcare services in inflammatory bowel disease (IBD). Aim. To describe IBD-related expenditures based on insurance and household income with the use of inpatient, outpatient, emergency, and office-based services, and prescribed medications in the United States (US). Methods. We evaluated the Medical Expenditure Panel Survey from 1996 to 2011 of individuals with Crohn’s disease (CD) or ulcerative colitis (UC). Nationally weighted means, proportions, and multivariate regression models examined the relationships between income and insurance status with expenditures. Results. Annual per capita mean expenditures for CD, UC, and all IBD were $10,364 (N = 238), $7,827 (N = 95), and $9,528, respectively, significantly higher than non-IBD ($4,314, N = 276, 372, p < 0.05). Publicly insured patients incurred the highest costs ($18,067) over privately insured ($8,014, p < 0.05) or uninsured patients ($5,129, p < 0.05). Among all IBD patients, inpatient care composed the highest proportion of costs ($3,392, p < 0.05). Inpatient costs were disproportionately higher for publicly insured patients. Public insurance had higher odds of total costs than private (OR 2.13, CI [1.08–4.19]) or no insurance (OR 4.94, CI [1.26–19.47]), with increased odds for inpatient and emergency care. Private insurance had higher costs associated with outpatient care, office-based care, and prescribed medicines. Low-income patients had lower costs associated with outpatient (OR 0.38, CI [0.15–0.95]) and office-based care (OR 0.21, CI [0.07–0.62]). Conclusions. In the US, high inpatient utilization among publicly insured patients is a previously unrecognized driver of high IBD costs. Bridging this health services gap between SES strata for acute care services may curtail direct IBD-related costs.
Park et al. (2014) Differences in healthcare expenditures for inflammatory bowel disease by insurance status, income, and clinical care setting. PeerJ 2:e587 https://doi.org/10.7717/peerj.587
A simple non-invasive method for measuring gross brain size in small live fish with semi-transparent heads
This paper describes a non-invasive method for estimating gross brain size in small fish with semi-transparent heads, using system camera equipment. Macro-photographs were taken from above on backlit free-swimming fish undergoing light anaesthesia. From the photographs, the width of the optic tectum was measured. This measure (TeO-measure) correlates well with the width of the optic tectum as measured from out-dissected brains in both brown trout fry and zebrafish (Pearson r > 0.90). The TeO-measure also correlates well with overall brain wet weight in brown trout fry (r = 0.90), but less well for zebrafish (r = 0.79). A non-invasive measure makes it possible to quickly assess brain size from a large number of individuals, as well as repeatedly measuring brain size of live individuals allowing calculation of brain growth.
Näslund (2014) A simple non-invasive method for measuring gross brain size in small live fish with semi-transparent heads. PeerJ 2:e586 https://doi.org/10.7717/peerj.586
Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of “modern” M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence-based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplification steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
Doughty et al. (2014) Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ 2:e585 https://doi.org/10.7717/peerj.585
The impact of atypical early histories on pet or performer chimpanzees
It is widely accepted that an animal’s early history, including but not limited to its rearing history, can have a profound impact on later behavior. In the case of captive animals, many studies have used categorical measures such as mother reared or human reared that do not account for both the influence of human and conspecific interaction. In order to account for the influence of both human and conspecific early exposure to later behavior, we collected 1385 h of data on 60 chimpanzees, of which 36 were former pets or performers, currently housed at accredited zoos or sanctuaries. We developed a unique metric, the Chimpanzee-Human Interaction (CHI) Index that represented a continuous measure of the proportion of human and chimpanzee exposure subjects experienced and here focused on their exposure during the first four years of life. We found that chimpanzees who experienced less exposure to other chimpanzees as infants showed a lower frequency of grooming and sexual behaviors later in life which can influence social dynamics within groups. We also found chimpanzees who experienced more exposure to other chimpanzees as infants showed a higher frequency of coprophagy, suggesting coprophagy could be a socially-learned behavior. These results help characterize some of the long-term effects borne by chimpanzees maintained as pets and performers and may help inform managers seeking to integrate these types of chimpanzees into larger social groups, as in zoos and sanctuaries. In addition, these results highlight the necessity of taking into account the time-weighted influence of human and conspecific interactions when assessing the impact that humans can have on animals living in captivity.
Freeman et al. (2014) The impact of atypical early histories on pet or performer chimpanzees. PeerJ 2:e579 https://doi.org/10.7717/peerj.579
Error estimates for the analysis of differential expression from RNA-seq count data
Background. A number of algorithms exist for analysing RNA-sequencing data to infer profiles of differential gene expression. Problems inherent in building algorithms around statistical models of over dispersed count data are formidable and frequently lead to non-uniform p-value distributions for null-hypothesis data and to inaccurate estimates of false discovery rates (FDRs). This can lead to an inaccurate measure of significance and loss of power to detect differential expression. Results. We use synthetic and real biological data to assess the ability of several available R packages to accurately estimate FDRs. The packages surveyed are based on statistical models of overdispersed Poisson data and include edgeR, DESeq, DESeq2, PoissonSeq and QuasiSeq. Also tested is an add-on package to edgeR and DESeq which we introduce called Polyfit. Polyfit aims to address the problem of a non-uniform null p-value distribution for two-class datasets by adapting the Storey–Tibshirani procedure. Conclusions. We find the best performing package in the sense that it achieves a low FDR which is accurately estimated over the full range of p-values, albeit with a very slow run time, is the QLSpline implementation of QuasiSeq. This finding holds provided the number of biological replicates in each condition is at least 4. The next best performing packages are edgeR and DESeq2. When the number of biological replicates is sufficiently high, and within a range accessible to multiplexed experimental designs, the Polyfit extension improves the performance DESeq (for approximately 6 or more replicates per condition), making its performance comparable with that of edgeR and DESeq2 in our tests with synthetic data.
Burden et al. (2014) Error estimates for the analysis of differential expression from RNA-seq count data. PeerJ 2:e576 https://doi.org/10.7717/peerj.576
Livestock as a potential biological control agent for an invasive wetland plant
Invasive species threaten biodiversity and incur costs exceeding billions of US$. Eradication efforts, however, are nearly always unsuccessful. Throughout much of North America, land managers have used expensive, and ultimately ineffective, techniques to combat invasive Phragmites australis in marshes. Here, we reveal that Phragmites may potentially be controlled by employing an affordable measure from its native European range: livestock grazing. Experimental field tests demonstrate that rotational goat grazing (where goats have no choice but to graze Phragmites) can reduce Phragmites cover from 100 to 20% and that cows and horses also readily consume this plant. These results, combined with the fact that Europeans have suppressed Phragmites through seasonal livestock grazing for 6,000 years, suggest Phragmites management can shift to include more economical and effective top-down control strategies. More generally, these findings support an emerging paradigm shift in conservation from high-cost eradication to economically sustainable control of dominant invasive species.
Silliman et al. (2014) Livestock as a potential biological control agent for an invasive wetland plant. PeerJ 2:e567 https://doi.org/10.7717/peerj.567
Removing batch effects for prediction problems with frozen surrogate variable analysis
Batch effects are responsible for the failure of promising genomic prognostic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to remove these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where samples are analyzed one at a time for diagnostic, prognostic, and predictive applications. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction accuracy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package.
Parker et al. (2014) Removing batch effects for prediction problems with frozen surrogate variable analysis. PeerJ 2:e561 https://doi.org/10.7717/peerj.561
Anopheles gambiae densovirus (AgDNV) has negligible effects on adult survival and transcriptome of its mosquito host
Mosquito densoviruses (DNVs) are candidate agents for paratransgenic control of malaria and other vector-borne diseases. Unlike other mosquito DNVs, the Anopheles gambiae DNV (AgDNV) is non-pathogenic to larval mosquitoes. However, the cost of infection upon adults and the molecular mechanisms underpinning infection in the mosquito host are unknown. Using life table analysis, we show that AgDNV infection has minimal effects on An. gambiae survival (no significant effect in 2 replicates and a slight 2 day survival decrease in the third replicate). Using microarrays, we show that AgDNV has very minimal effect on the adult mosquito transcriptome, with only 4–15 genes differentially regulated depending on the statistical criteria imposed. The minimal impact upon global transcription provides some mechanistic understanding of lack of virus pathogenicity, suggesting a long co-evolutionary history that has shifted towards avirulence. From an applied standpoint, lack of strong induced fitness costs makes AgDNV an attractive agent for paratransgenic malaria control.
Ren et al. (2014) Anopheles gambiae densovirus (AgDNV) has negligible effects on adult survival and transcriptome of its mosquito host. PeerJ 2:e584 https://doi.org/10.7717/peerj.584
MicroRNAs expression profile in CCR6+ regulatory T cells
Backgroud. CCR6+ CD4+ regulatory T cells (CCR6+ Tregs), a distinct Tregs subset, played an important role in various immune diseases. Recent evidence showed that microRNAs (miRNAs) are vital regulators in the function of immune cells. However, the potential role of miRNAs in the function of CCR6+ Tregs remains largely unknown. In this study, we detected the expression profile of miRNAs in CCR6+ Tregs. Materials and Methods. The expression profile of miRNAs as well as genes in CCR6+ Tregs or CCR6- Tregs from Balb/c mice were detected by microarray. The signaling pathways were analyzed using the Keggs pathway library. Results. We found that there were 58 miRNAs significantly upregulated and 62 downregulated up to 2 fold in CCR6+ Tregs compared with CCR6- Tregs. Moreover, 1,391 genes were observed with 3 fold change and 20 signaling pathways were enriched using the Keggs pathway library. Conclusion. The present data showed CCR6+ Tregs expressed specific miRNAs pattern, which provides insight into the role of miRNAs in the biological function of distinct Tregs subsets.
Zhao et al. (2014) MicroRNAs expression profile in CCR6+ regulatory T cells. PeerJ 2:e575 https://doi.org/10.7717/peerj.575
Students distracted by electronic devices perform at the same level as those who are focused on the lecture
Background. Little is known about the characteristics of internet distractions that students may engage in during lecture. The objective of this pilot study is to identify some of the internet-based distractions students engage in during in-person lectures. The findings will help identify what activities most commonly cause students to be distracted from the lecture and if these activities impact student learning. Methods. This study is a quasi-experimental pilot study of 26 students from a single institution. In the current study, one class of third-year students were surveyed after a lecture on special needs dentistry. The survey identified self-reported utilization patterns of “smart” devices during the lecture. Additionally, twelve quiz-type questions were given to assess the students’ recall of important points in the lecture material that had just been covered. Results. The sample was comprised of 26 students. Of these, 17 were distracted in some form (either checking email, sending email, checking Facebook, or sending texts). The overall mean score on the test was 9.85 (9.53 for distracted students and 10.44 for non-distracted students). There were no significant differences in test scores between distracted and non-distracted students (p = 0.652). Gender and types of distractions were not significantly associated with test scores (p > 0.05). All students believed that they understood all the important points from the lecture. Conclusions. Every class member felt that they acquired the important learning points during the lecture. Those who were distracted by electronic devices during the lecture performed similarly to those who were not. However, results should be interpreted with caution as this study was a small quasi-experimental design and further research should examine the influence of different types of distraction on different types of learning.
Nalliah et al. (2014) Students distracted by electronic devices perform at the same level as those who are focused on the lecture. PeerJ 2:e572 https://doi.org/10.7717/peerj.572
Turf algae-mediated coral damage in coastal reefs of Belize, Central America
Many coral reefs in the Caribbean experienced substantial changes in their benthic community composition during the last decades. This often resulted in phase shifts from scleractinian coral dominance to that by other benthic invertebrate or algae. However, knowledge about how the related role of coral-algae contacts may negatively affect corals is scarce. Therefore, benthic community composition, abundance of algae grazers, and the abundance and character of coral-algae contacts were assessed in situ at 13 Belizean reef sites distributed along a distance gradient to the Belizean mainland (12–70 km): Mesoamerican Barrier Reef (inshore), Turneffe Atoll (inner and outer midshore), and Lighthouse Reef (offshore). In situ surveys revealed significantly higher benthic cover by scleractinian corals at the remote Lighthouse Reef (26–29%) when compared to the other sites (4–19%). The abundance of herbivorous fish and the sea urchin Diadema antillarum significantly increased towards the offshore reef sites, while the occurrence of direct coral-algae contacts consequently increased significantly with decreasing distance to shore. About 60% of these algae contacts were harmful (exhibiting coral tissue damage, pigmentation change, or overgrowth) for corals (mainly genera Orbicella and Agaricia), particularly when filamentous turf algae were involved. These findings provide support to the hypothesis that (turf) algae-mediated coral damage occurs in Belizean coastal, near-shore coral reefs.
Wild et al. (2014) Turf algae-mediated coral damage in coastal reefs of Belize, Central America. PeerJ 2:e571 https://doi.org/10.7717/peerj.571
What’s for dinner? Undescribed species of porcini in a commercial packet
Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.
Dentinger et al. (2014) What’s for dinner? Undescribed species of porcini in a commercial packet. PeerJ 2:e570 https://doi.org/10.7717/peerj.570
Role of enzymatic activity in muscle damage and cytotoxicity induced by Bothrops asper Asp49 phospholipase A2 myotoxins: are there additional effector mechanisms involved?
Viperid venoms often contain mixtures of Asp49 and Lys49 PLA2 myotoxin isoforms, relevant to development of myonecrosis. Given their difference in catalytic activity, mechanistic studies on each type require highly purified samples. Studies on Asp49 PLA2s have shown that enzyme inactivation using p-bromophenacyl bromide (p-BPB) drastically affects toxicity. However, based on the variable levels of residual toxicity observed in some studies, it has been suggested that effector mechanisms independent of catalysis may additionally be involved in the toxicity of these enzymes, possibly resembling those of the enzymatically inactive Lys49 myotoxins. A possibility that Lys49 isoforms could be present in Asp49 PLA2 preparations exists and, if undetected in previous studies, could explain the variable residual toxicity. This question is here addressed by using an enzyme preparation ascertained to be free of Lys49 myotoxins. In agreement with previous reports, inactivation of the catalytic activity of an Asp49 myotoxin preparation led to major inhibition of toxic effects in vitro and in vivo. The very low residual levels of myotoxicity (7%) and cytotoxicity (4%) observed can be attributed to the low, although detectable, enzyme remaining active after p-BPB treatment (2.7%), and would be difficult to reconcile with the proposed existence of additional catalytic-independent toxic mechanisms. These findings favor the concept that the effector mechanism of toxicity of Asp49 PLA2 myotoxins from viperids fundamentally relies on their ability to hydrolyze phospholipids, arguing against the proposal that membrane disruption may also be caused by additional mechanisms that are independent of catalysis.
Mora-Obando et al. (2014) Role of enzymatic activity in muscle damage and cytotoxicity induced by Bothrops asper Asp49 phospholipase A2 myotoxins: are there additional effector mechanisms involved?. PeerJ 2:e569 https://doi.org/10.7717/peerj.569
Nestling activity levels during begging behaviour predicts activity level and body mass in adulthood
Across a range of species including humans, personality traits, or differences in behaviour between individuals that are consistent over time, have been demonstrated. However, few studies have measured whether these consistent differences are evident in very young animals, and whether they persist over an individual’s entire lifespan. Here we investigated the begging behaviour of very young cross-fostered zebra finch nestlings and the relationship between that and adult activity levels. We found a link between the nestling activity behaviour head movements during begging, measured at just five and seven days after hatching, and adult activity levels, measured when individuals were between three and three and a half years old. Moreover, body mass was found to be negatively correlated with both nestling and adult activity levels, suggesting that individuals which carry less body fat as adults are less active both as adults and during begging as nestlings. Our work suggests that the personality traits identified here in both very young nestlings and adults may be linked to physiological factors such as metabolism or environmental sources of variation. Moreover, our work suggests it may be possible to predict an individual’s future adult personality at a very young age, opening up new avenues for future work to explore the relationship between personality and a number of aspects of individual life history and survival.
McCowan et al. (2014) Nestling activity levels during begging behaviour predicts activity level and body mass in adulthood. PeerJ 2:e566 https://doi.org/10.7717/peerj.566
Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: a cross-sectional study
Background. Researchers have emphasized a need to identify predictors that can explain the variability in weight management after bariatric surgery. Eating self-efficacy has demonstrated predictive impact on patients’ adherence to recommended eating habits following multidisciplinary treatment programs, but has to a limited extent been subject for research after bariatric surgery. Recently an American short form version (WEL-SF) of the commonly used Weight Efficacy Lifestyle Questionnaire (WEL) was available for research and clinical purposes. Objectives. We intended to translate and culturally adapt the WEL-SF to Norwegian conditions, and to evaluate the new versions’ psychometrical properties in a Norwegian population of morbidly obese patients eligible for bariatric surgery. Design. Cross-sectional Methods. A total of 225 outpatients selected for Laparoscopic sleeve gastrectomy (LSG) were recruited; 114 non-operated and 111 operated patients, respectively. The questionnaire was translated through forward and backward procedures. Structural properties were assessed performing principal component analysis (PCA), correlation and regression analysis were conducted to evaluate convergent validity and sensitivity, respectively. Data was assessed by mean, median, item response, missing values, floor- and ceiling effect, Cronbach’s alpha and alpha if item deleted. Results. The PCA resulted in one factor with eigenvalue > 1, explaining 63.0% of the variability. The WEL-SF sum scores were positively correlated with the Self-efficacy and quality of life instruments (p < 0.001). The WEL-SF was associated with body mass index (BMI) (p < 0.001) and changes in BMI (p = 0.026). A very high item response was obtained with only one missing value (0.4%). The ceiling effect was in average 0.9 and 17.1% in the non-operated and operated sample, respectively. Strong internal consistency (r = 0.92) was obtained, and Cronbach’s alpha remained high (0.86–0.92) if single items were deleted. Conclusion. The Norwegian version of WEL-SF appears to be a valid questionnaire on eating self-efficacy, with acceptable psychometrical properties in a population of morbidly obese patients.
Flølo et al. (2014) Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: a cross-sectional study. PeerJ 2:e565 https://doi.org/10.7717/peerj.565
Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines
This study represents the first description of whale sharks, Rhincodon typus, occurring at a provisioning site in Oslob, Cebu, Philippines. Frequent observations of sharks are often difficult, even at tourism sites, giving rise to provisioning activities to attract them. The present study provides repeated longitudinal data at a site where daily provisioning activities took place, and whale sharks were present every day. A total of 158 individual whale sharks were photographically identified between Mar 2012 and Dec 2013, with 129 males (82%), 19 females (12%) and 10 (6%) of undetermined sex. Mean estimated total length was 5.5 m (±1.3 m S.D.). Twenty individuals were measured with laser photogrammetry to validate researchers’ estimated sizes, yielding a good correlation (r2 = 0.83). Fifty-four (34%) individuals were observed being hand-fed by local fishermen (provisioned), through in-water behavioural observations. Maximum likelihood methods were used to model mean residency time of 44.9 days (±20.6 days S.E.) for provisioned R. typus contrasting with 22.4 days (±8.9 days S.E.) for non-provisioned individuals. Propeller scars were observed in 47% of the animals. A mean of 12.7 (±4.3 S.D.) R. typus were present in the survey area daily, with a maximum of 26 individuals (Aug 10 2013) and a minimum of 2 (Dec 6 2012). Twelve (8%) individuals were seen on at least 50% of survey days (n = 621), with a maximum residency of 572 days for one individual (P-396). Twenty four individuals were photographically identified across regional hotsposts, highlighting the species’ migratory nature and distribution. Extended residency and differences in lagged identification rates suggest behavioural modification on provisioned individuals, underlying the necessity for proper management of this tourism activity.
Araujo et al. (2014) Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines. PeerJ 2:e543 https://doi.org/10.7717/peerj.543
Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity
The role of species’ interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran’s eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners’ genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.
Buckley et al. (2014) Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity. PeerJ 2:e573 https://doi.org/10.7717/peerj.573
Tracheostomy in children with congenital heart disease: a national analysis of the Kids’ Inpatient Database
Background. While single-institution studies reported the indications and outcomes of tracheostomy in children with congenital heart disease (CHD), no national analyses have been performed. We sought to examine the indications, performance, outcomes, and resource utilization of tracheostomy in children with CHD using a nationally representative database. Methods. We identified all children undergoing tracheostomy in the Kids’ Inpatient Database 1997 through 2009, and we compared children with CHD to children without CHD. Within the CHD group, we compared children whose tracheostomy occurred in the same hospital admission as a cardiac operation to those whose tracheostomy occurred without a cardiac operation in the same admission. Results. Tracheostomy was performed in n = 2,495 children with CHD, which represents 9.6% of all tracheostomies performed in children (n = 25,928), and 3.5% of all admissions for children with CHD (n = 355,460). Over the study period, there was an increasing trend in the proportion of all tracheostomies that were done in children with CHD (p < 0.0001) and an increasing trend in the proportion of admissions for children with CHD that involved a tracheostomy (p < 0.0001). The population of children with CHD undergoing tracheostomy differed markedly in baseline characteristics, outcomes, and resource utilization. Similarly, the subgroup of children whose tracheostomy was performed in the same admission as a cardiac operation differed significantly from those whose tracheostomy was not. Conclusions. Tracheostomy is an increasingly common procedure in children with CHD despite being associated with significantly greater resource utilization and in-hospital mortality. The population of children with CHD who undergo tracheostomy differs markedly from that of children without CHD who undergo tracheostomy, and important differences are observed between children who undergo tracheostomy in the same admission as a cardiac surgical procedure and those who undergo tracheostomy in a nonsurgical admission, as well as between children with single-ventricle physiology and children with two-ventricle physiology.
Maxwell et al. (2014) Tracheostomy in children with congenital heart disease: a national analysis of the Kids’ Inpatient Database. PeerJ 2:e568 https://doi.org/10.7717/peerj.568
Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation
Interleukin-18 (IL-18) is a pro-inflammatory cytokine which stimulates activation of the nuclear factor kappa beta (NF-κB) pathway via interaction with the IL-18 receptor. The receptor itself is formed from a dimer of two subunits, with the ligand-binding IL-18Rα subunit being encoded by the IL18R1 gene. A splice variant of murine IL18r1, which has been previously described, is formed by transcription of an unspliced intron (forming a ‘type II’ IL18r1 transcript) and is predicted to encode a receptor with a truncated intracellular domain lacking the capacity to generate downstream signalling. In order to examine the relevance of this finding to human IL-18 function, we assessed the presence of a homologous transcript by reverse transcription-polymerase chain reaction (RT-PCR) in the human and rat as another common laboratory animal. We present evidence for type II IL18R1 transcripts in both species. While the mouse and rat transcripts are predicted to encode a truncated receptor with a novel 5 amino acid C-terminal domain, the human sequence is predicted to encode a truncated protein with a novel 22 amino acid sequence bearing resemblance to the ‘Box 1’ motif of the Toll/interleukin-1 receptor (TIR) domain, in a similar fashion to the inhibitory interleukin-1 receptor 2. Given that transcripts from these three species are all formed by inclusion of homologous unspliced intronic regions, an analysis of homologous introns across a wider array of 33 species with available IL18R1 gene records was performed, which suggests similar transcripts may encode truncated type II IL-18Rα subunits in other species. This splice variant may represent a conserved evolutionary mechanism for regulating IL-18 activity.
Booker et al. (2014) Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation. PeerJ 2:e560 https://doi.org/10.7717/peerj.560
Modelling foraging movements of diving predators: a theoretical study exploring the effect of heterogeneous landscapes on foraging efficiency
Foraging in the marine environment presents particular challenges for air-breathing predators. Information about prey capture rates, the strategies that diving predators use to maximise prey encounter rates and foraging success are still largely unknown and difficult to observe. As well, with the growing awareness of potential climate change impacts and the increasing interest in the development of renewable sources it is unknown how the foraging activity of diving predators such as seabirds will respond to both the presence of underwater structures and the potential corresponding changes in prey distributions. Motivated by this issue we developed a theoretical model to gain general understanding of how the foraging efficiency of diving predators may vary according to landscape structure and foraging strategy. Our theoretical model highlights that animal movements, intervals between prey capture and foraging efficiency are likely to critically depend on the distribution of the prey resource and the size and distribution of introduced underwater structures. For multiple prey loaders, changes in prey distribution affected the searching time necessary to catch a set amount of prey which in turn affected the foraging efficiency. The spatial aggregation of prey around small devices (∼ 9 × 9 m) created a valuable habitat for a successful foraging activity resulting in shorter intervals between prey captures and higher foraging efficiency. The presence of large devices (∼ 24 × 24 m) however represented an obstacle for predator movement, thus increasing the intervals between prey captures. In contrast, for single prey loaders the introduction of spatial aggregation of the resources did not represent an advantage suggesting that their foraging efficiency is more strongly affected by other factors such as the timing to find the first prey item which was found to occur faster in the presence of large devices. The development of this theoretical model represents a useful starting point to understand the energetic reasons for a range of potential predator responses to spatial heterogeneity and environmental uncertainties in terms of search behaviour and predator–prey interactions. We highlight future directions that integrated empirical and modelling studies should take to improve our ability to predict how diving predators will be impacted by the deployment of manmade structures in the marine environment.
Chimienti et al. (2014) Modelling foraging movements of diving predators: a theoretical study exploring the effect of heterogeneous landscapes on foraging efficiency. PeerJ 2:e544 https://doi.org/10.7717/peerj.544
Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals
There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250 bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
Wares (2014) Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals. PeerJ 2:e564 https://doi.org/10.7717/peerj.564
Estimating the prevalence of researcher misconduct: a study of UK academics within biological sciences
Misconduct in academic research is undoubtedly increasing, but studies estimating the prevalence of such behaviour suffer from biases inherent in researching sensitive topics. We compared the unmatched-count technique (UCT) and the crosswise-model (CM), two methods specifically designed to increase honest reporting to sensitive questions, with direct questioning (DQ) for five types of misconduct in the biological sciences. UCT performed better than CM and either outperformed or produced similar estimates to DQ depending on the question. Estimates of academic misconduct increased with decreasing seriousness of the behaviour, from c. 0% for data fabrication to >68% for inappropriate co-authorship. Results show that research into even minor issues of misconduct, is sensitive, suggesting that future studies should consider using specialised questioning techniques as they are more likely to yield accurate figures.
Roberts et al. (2014) Estimating the prevalence of researcher misconduct: a study of UK academics within biological sciences. PeerJ 2:e562 https://doi.org/10.7717/peerj.562
Psoralidin induces autophagy through ROS generation which inhibits the proliferation of human lung cancer A549 cells
Psoralidin (PSO), a natural furanocoumarin, is isolated from Psoralea corylifolia L. possessing anti-cancer properties. However, the mechanisms of its effects remain unclear. Herein, we investigated its anti-proliferative effect and potential approaches of action on human lung cancer A549 cells. Cell proliferation and death were measured by MTT and LDH assay respectively. Apoptosis was detected with Hoechst 33342 staining by fluorescence microscopy, Annexin V-FITC by flow cytometry and Western blot analysis for apoptosis-related proteins. The autophagy was evaluated using MDC staining, immunofluorescence assay and Western blot analyses for LC3-I and LC3-II. In addition, the reactive oxygen species (ROS) generation was measured by DCFH2-DA with flow cytometry. PSO dramatically decreased the cell viabilities in dose- and time-dependent manner. However, no significant change was observed between the control group and the PSO-treated groups in Hoechst 33342 and Annexin V-FITC staining. The expression of apoptosis-related proteins was not altered significantly either. While the MDC-fluorescence intensity and the expression ratio of LC3-II/LC3-I was remarkably increased after PSO treatment. Autophagy inhibitor 3-MA blocked the production of LC3-II and reduced the cytotoxicity in response to PSO. Furthermore, PSO increased intracellular ROS level which was correlated to the elevation of LC3-II. ROS scavenger N-acetyl cysteine pretreatment not only decreased the ROS level, reduced the expression of LC3-II but also reversed PSO induced cytotoxicity. PSO inhibited the proliferation of A549 cells through autophagy but not apoptosis, which was mediated by inducing ROS production.
Hao et al. (2014) Psoralidin induces autophagy through ROS generation which inhibits the proliferation of human lung cancer A549 cells. PeerJ 2:e555 https://doi.org/10.7717/peerj.555
Digging the pupfish out of its hole: risk analyses to guide harvest of Devils Hole pupfish for captive breeding
The Devils Hole pupfish is restricted to one wild population in a single aquifer-fed thermal pool in the Desert National Wildlife Refuge Complex. Since 1995 the pupfish has been in a nearly steady decline, where it was perched on the brink of extinction at 35–68 fish in 2013. A major strategy for conserving the pupfish has been the establishment of additional captive or “refuge” populations, but all ended in failure. In 2013 a new captive propagation facility designed specifically to breed pupfish was opened. I examine how a captive population can be initiated by removing fish from the wild without unduly accelerating extinction risk for the pupfish in Devils Hole. I construct a count-based PVA model, parameterized from estimates of the intrinsic rate of increase and its variance using counts in spring and fall from 1995–2013, to produce the first risk assessment for the pupfish. Median time to extinction was 26 and 27 years from spring and fall counts, respectively, and the probability of extinction in 20 years was 26–33%. Removing individuals in the fall had less risk to the wild population than harvest in spring. For both spring and fall harvest, risk increased rapidly when levels exceeded six adult pupfish per year for three years. Extinction risk was unaffected by the apportionment of total harvest among years. A demographic model was used to examine how removal of different stage classes affects the dynamics of the wild population based on reproductive value (RV) and elasticity. Removing eggs had the least impact on the pupfish in Devils Hole; RV of an adult was roughly 25 times that of an egg. To evaluate when it might be prudent to remove all pupfish from Devils Hole for captive breeding, I used the count-based model to examine how extinction risk related to pupfish population size. Risk accelerated when initial populations were less than 30 individuals. Results are discussed in relation to the challenges facing pupfish recovery compared to management of other highly endangered species.
Beissinger (2014) Digging the pupfish out of its hole: risk analyses to guide harvest of Devils Hole pupfish for captive breeding. PeerJ 2:e549 https://doi.org/10.7717/peerj.549
Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent
Ocean acidification (OA) is not an isolated threat, but acts in concert with other impacts on ecosystems and species. Coastal marine invertebrates will have to face the synergistic interactions of OA with other global and local stressors. One local factor, common in coastal environments, is trace element contamination. CO2 vent sites are extensively studied in the context of OA and are often considered analogous to the oceans in the next few decades. The CO2 vent found at Levante Bay (Vulcano, NE Sicily, Italy) also releases high concentrations of trace elements to its surrounding seawater, and is therefore a unique site to examine the effects of long-term exposure of nearby organisms to high pCO2 and trace element enrichment in situ. The sea anemone Anemonia viridis is prevalent next to the Vulcano vent and does not show signs of trace element poisoning/stress. The aim of our study was to compare A. viridis trace element profiles and compartmentalization between high pCO2 and control environments. Rather than examining whole anemone tissue, we analyzed two different body compartments—the pedal disc and the tentacles, and also examined the distribution of trace elements in the tentacles between the animal and the symbiotic algae. We found dramatic changes in trace element tissue concentrations between the high pCO2/high trace element and control sites, with strong accumulation of iron, lead, copper and cobalt, but decreased concentrations of cadmium, zinc and arsenic proximate to the vent. The pedal disc contained substantially more trace elements than the anemone’s tentacles, suggesting the pedal disc may serve as a detoxification/storage site for excess trace elements. Within the tentacles, the various trace elements displayed different partitioning patterns between animal tissue and algal symbionts. At both sites iron was found primarily in the algae, whereas cadmium, zinc and arsenic were primarily found in the animal tissue. Our data suggests that A. viridis regulates its internal trace element concentrations by compartmentalization and excretion and that these features contribute to its resilience and potential success at the trace element-rich high pCO2 vent.
Horwitz et al. (2014) Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent. PeerJ 2:e538 https://doi.org/10.7717/peerj.538
Alterations in fiber pathways reveal brain tumor typology: a diffusion tractography study
Conventional structural Magnetic Resonance (MR) techniques can accurately identify brain tumors but do not provide exhaustive information about the integrity of the surrounding/embedded white matter (WM). In this study, we used Diffusion-Weighted (DW) MRI tractography to explore tumor-induced alterations of WM architecture without any a priori knowledge about the fiber paths under consideration. We used deterministic multi-fiber tractography to analyze 16 cases of histologically classified brain tumors (meningioma, low-grade glioma, high-grade glioma) to evaluate the integrity of WM bundles in the tumoral region, in relation to the contralateral unaffected hemisphere. Our new tractographic approach yielded measures of WM involvement which were strongly correlated with the histopathological features of the tumor (r = 0.83, p = 0.0001). In particular, the number of affected fiber tracts were significantly (p = 0.0006) different among tumor types. Our method proposes a new application of diffusion tractography for the detection of tumor aggressiveness in those cases in which the lesion does not involve any major/known WM paths and when a priori information about the local fiber anatomy is lacking.
Campanella et al. (2014) Alterations in fiber pathways reveal brain tumor typology: a diffusion tractography study. PeerJ 2:e497 https://doi.org/10.7717/peerj.497
Metagenome fragment classification based on multiple motif-occurrence profiles
A vast amount of metagenomic data has been obtained by extracting multiple genomes simultaneously from microbial communities, including genomes from uncultivable microbes. By analyzing these metagenomic data, novel microbes are discovered and new microbial functions are elucidated. The first step in analyzing these data is sequenced-read classification into reference genomes from which each read can be derived. The Naïve Bayes Classifier is a method for this classification. To identify the derivation of the reads, this method calculates a score based on the occurrence of a DNA sequence motif in each reference genome. However, large differences in the sizes of the reference genomes can bias the scoring of the reads. This bias might cause erroneous classification and decrease the classification accuracy. To address this issue, we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence. This multiple profile strategy improves the accuracy of the results generated by the Naïve Bayes Classifier method for simulated and Sargasso Sea datasets.
Matsushita et al. (2014) Metagenome fragment classification based on multiple motif-occurrence profiles. PeerJ 2:e559 https://doi.org/10.7717/peerj.559
Protein kinase C in the wood frog, Rana sylvatica: reassessing the tissue-specific regulation of PKC isozymes during freezing
The wood frog, Rana sylvatica, survives whole-body freezing and thawing each winter. The extensive adaptations required at the biochemical level are facilitated by alterations to signaling pathways, including the insulin/Akt and AMPK pathways. Past studies investigating changing tissue-specific patterns of the second messenger IP3 in adapted frogs have suggested important roles for protein kinase C (PKC) in response to stress. In addition to their dependence on second messengers, phosphorylation of three PKC sites by upstream kinases (most notably PDK1) is needed for full PKC activation, according to widely-accepted models. The present study uses phospho-specific immunoblotting to investigate phosphorylation states of PKC—as they relate to distinct tissues, PKC isozymes, and phosphorylation sites—in control and frozen frogs. In contrast to past studies where second messengers of PKC increased during the freezing process, phosphorylation of PKC tended to generally decline in most tissues of frozen frogs. All PKC isozymes and specific phosphorylation sites detected by immunoblotting decreased in phosphorylation levels in hind leg skeletal muscle and hearts of frozen frogs. Most PKC isozymes and specific phosphorylation sites detected in livers and kidneys also declined; the only exceptions were the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641) antibody, which remained unchanged from control to frozen frogs. Changes in brains of frozen frogs were unique; no decreases were observed in the phosphorylation levels of any of the PKC isozymes and/or specific phosphorylation sites detected by immunoblotting. Rather, increases were observed for the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641), phospho-PKCδ (Thr505), and phospho-PKCθ (Thr538) antibodies; all other isozymes/phosphorylation sites detected in brain remained unchanged from control to frozen frogs. The results of this study indicate a potential important role for PKC in cerebral protection during wood frog freezing. Our findings also call for a reassessment of the previously-inferred importance of PKC in other tissues, particularly in liver; a more thorough investigation is required to determine whether PKC activity in this physiological situation is indeed dependent on phosphorylation, or whether it deviates from the generally-accepted model and can be “overridden” by exceedingly high levels of second messengers, as has been demonstrated with certain PKC isozymes (e.g., PKCδ).
Dieni et al. (2014) Protein kinase C in the wood frog, Rana sylvatica: reassessing the tissue-specific regulation of PKC isozymes during freezing. PeerJ 2:e558 https://doi.org/10.7717/peerj.558
Effects of low and high dose intraarticular tiludronate on synovial fluid and clinical variables in healthy horses—a preliminary investigation
To determine effects of intraarticularly administered tiludronate on articular cartilage in vivo, eight healthy horses were injected once with tiludronate (low dose tiludronate [LDT] 0.017 mg, n = 4; high dose tiludronate [HDT] 50 mg, n = 4) into one middle carpal joint and with saline into the contralateral joint. Arthrocentesis of both middle carpal joints was performed pre-treatment, and 10 min, 24 h, 48 h, 7 and 14 days after treatment. Synovial nucleated cell counts and total solids, tiludronate, sulfated glycosaminoglycan (sGAG), chondroitin sulfate 846 epitope (CS-846, a measure of aggrecan synthesis), and collagen type II cleavage neoepitope (C2C) concentrations were determined. Histologic analysis of joint tissues and sGAG quantitation in cartilage was performed at 14 days in HDT horses. Data were analyzed by repeated measures non-parametric ANOVA and Wilcoxon signed-rank test. High dose tiludronate administration produced synovial fluid tiludronate concentrations of 2,677,500 ng/mL, exceeding concentrations that were safe for cartilage in vitro, and LDT administration produced synovial fluid concentrations of 1,353 ng/mL, remaining below concentrations considered potentially detrimental to cartilage. With HDT, synovial fluid total solids concentration was higher at 24 h and 7 days and sGAG concentration was higher at 48 h, compared to control joints. Synovial fluid CS-846 concentration was increased over pre-treatment values in HDT control but not in HDT treated joints at 24 and 48 h. All joints (HDT and LDT control and treated) showed a temporary decrease in synovial fluid C2C concentration, compared to pre-treatment values. Histologic features of articular cartilage and synovial membrane did not differ between HDT treated and control joints. High dose tiludronate treatment caused a transient increase in synovial total solids and temporarily increased proteoglycan degradation in cartilage. Although clinical significance of these changes are questionable, as they did not result in articular cartilage damage, further investigation of the safety of intraarticular HDT in a larger number of horses is warranted.
Duesterdieck-Zellmer et al. (2014) Effects of low and high dose intraarticular tiludronate on synovial fluid and clinical variables in healthy horses—a preliminary investigation. PeerJ 2:e534 https://doi.org/10.7717/peerj.534
Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene
An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.
Taylor et al. (2014) Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene. PeerJ 2:e556 https://doi.org/10.7717/peerj.556
Benthic primary production in an upwelling-influenced coral reef, Colombian Caribbean
In Tayrona National Natural Park (Colombian Caribbean), abiotic factors such as light intensity, water temperature, and nutrient availability are subjected to high temporal variability due to seasonal coastal upwelling. These factors are the major drivers controlling coral reef primary production as one of the key ecosystem services. This offers the opportunity to assess the effects of abiotic factors on reef productivity. We therefore quantified primary net (Pn) and gross production (Pg) of the dominant local primary producers (scleractinian corals, macroalgae, algal turfs, crustose coralline algae, and microphytobenthos) at a water current/wave-exposed and-sheltered site in an exemplary bay of Tayrona National Natural Park. A series of short-term incubations was conducted to quantify O2 fluxes of the different primary producers during non-upwelling and the upwelling event 2011/2012, and generalized linear models were used to analyze group-specific O2 production, their contribution to benthic O2 fluxes, and total daily benthic O2 production. At the organism level, scleractinian corals showed highest Pn and Pg rates during non-upwelling (16 and 19 mmol O2 m−2 specimen area h−1), and corals and algal turfs dominated the primary production during upwelling (12 and 19 mmol O2 m−2 specimen area h−1, respectively). At the ecosystem level, corals contributed most to total Pn and Pg during non-upwelling, while during upwelling, corals contributed most to Pn and Pg only at the exposed site and macroalgae at the sheltered site, respectively. Despite the significant spatial and temporal differences in individual productivity of the investigated groups and their different contribution to reef productivity, differences for daily ecosystem productivity were only present for Pg at exposed with higher O2 fluxes during non-upwelling compared to upwelling. Our findings therefore indicate that total benthic primary productivity of local autotrophic reef communities is relatively stable despite the pronounced fluctuations of environmental key parameters. This may result in higher resilience against anthropogenic disturbances and climate change and Tayrona National Natural Park should therefore be considered as a conservation priority area.
Eidens et al. (2014) Benthic primary production in an upwelling-influenced coral reef, Colombian Caribbean. PeerJ 2:e554 https://doi.org/10.7717/peerj.554
Effects of deuterium oxide on cell growth and vesicle speed in RBL-2H3 cells
For the first time we show the effects of deuterium oxide on cell growth and vesicle transport in rat basophilic leukemia (RBL-2H3) cells. RBL-2H3 cells cultured with 15 moles/L deuterium showed decreased cell growth which was attributed to cells not doubling their DNA content. Experimental observations also showed an increase in vesicle speed for cells cultured in deuterium oxide. This increase in vesicle speed was not observed in deuterium oxide cultures treated with a microtubule-destabilizing drug, suggesting that deuterium oxide affects microtubule-dependent vesicle transport.
Kalkur et al. (2014) Effects of deuterium oxide on cell growth and vesicle speed in RBL-2H3 cells. PeerJ 2:e553 https://doi.org/10.7717/peerj.553
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe–4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe–4S], yielding a negatively-charged intermediate. Depending on the rate of Fe–S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe–S cluster re-reduction should be the rate-limiting stage of the process. Poisson–Boltzmann computations on the full enzyme–substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe–S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjuntion with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction intermediates with those of common biochemical redox intermediates suggest a surprisingly simple explanation for the mechanistic differences between the dark-catalyzed and light-dependent enzyme reaction mechanisms.
Silva (2014) With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase. PeerJ 2:e551 https://doi.org/10.7717/peerj.551
The effect of cigarette smoking habits on the outcome of dental implant treatment
The aim of this study was to analyze the influence of smoking habits and other possibly relevant factors on dental implant survival. The study population included all patients who underwent dental implants between the years 1999 and 2008 at a large military dental clinic and were examined in the periodic medical examination center. Correlation between implant characteristics and patients’ smoking habits, as mentioned in the questionnaire answered by patients in the periodic examination, was performed. Besides standard statistical methods, multiple linear regression models were constructed for estimation of the relative influence of some factors on implant survival rate. The long-term results of the implant treatment were good. The study refers to 7,680 implants. 7,359 (95.8%) survived and 321 (4.2%) did not survive. Concerning smoking habits, in a uni-variable analysis, factors found to have an association with implant survival were the smoking status of the patients (smoking/no smoking), the amount of smoking, passive smoking, and the time elapsed in ex-smokers from the time they ceased smoking to the time of implantation. In a multi-variable analysis, factors found to have an association with implant survival were smoking status (smoking/no smoking) and amounts of smoking as expressed in pack years.
Twito et al. (2014) The effect of cigarette smoking habits on the outcome of dental implant treatment. PeerJ 2:e546 https://doi.org/10.7717/peerj.546
Too big to be noticed: cryptic invasion of Asian camel crickets in North American houses
Despite the rapid expansion of the built environment, we know little about the biology of species living in human-constructed habitats. Camel crickets (Rhaphidophoridae) are commonly observed in North American houses and include a range of native taxa as well as the Asian Diestrammena asynamora (Adelung), a species occasionally reported from houses though considered to be established only in greenhouses. We launched a continental-scale citizen science campaign to better understand the relative distributions and frequency of native and nonnative camel crickets in human homes across North America. Participants contributed survey data about the presence or absence of camel crickets in homes, as well as photographs and specimens of camel crickets allowing us to identify the major genera and/or species in and around houses. Together, these data offer insight into the geographical distribution of camel crickets as a presence in homes, as well as the relative frequency and distribution of native and nonnative camel crickets encountered in houses. In so doing, we show that the exotic Diestrammena asynamora not only has become a common presence in eastern houses, but is found in these environments far more frequently than native camel crickets. Supplemental pitfall trapping along transects in 10 urban yards in Raleigh, NC revealed that D. asynamora can be extremely abundant locally around some homes, with as many as 52 individuals collected from pitfalls in a single yard over two days of sampling. The number of D. asynamora individuals present in a trap was negatively correlated with the trap’s distance from a house, suggesting that these insects may be preferentially associated with houses but also are present outside. In addition, we report the establishment in the northeastern United States of a second exotic species, putatively Diestrammena japanica Blatchley, which was previously undocumented in the literature. Our results offer new insight into the relative frequency and distribution of camel crickets living in human homes, and emphasize the importance of the built environment as habitat for two little-known invading species of Orthoptera.
Epps et al. (2014) Too big to be noticed: cryptic invasion of Asian camel crickets in North American houses. PeerJ 2:e523 https://doi.org/10.7717/peerj.523
Hand infections: a retrospective analysis
Purpose. Hand infections are common, usually resulting from an untreated injury. In this retrospective study, we report on hand infection cases needing surgical drainage in order to assess patient demographics, causation of infection, clinical course, and clinical management. Methods. Medical records of patients presenting with hand infections, excluding post-surgical infections, treated with incision and debridement over a one-year period were reviewed. Patient demographics; past medical history; infection site(s) and causation; intervals between onset of infection, hospital admission, surgical intervention and days of hospitalization; gram stains and cultures; choice of antibiotics; complications; and outcomes were reviewed. Results. Most infections were caused by laceration and the most common site of infection was the palm or dorsum of the hand. Mean length of hospitalization was 6 days. Methicillin-resistant Staphylococcus aureus, beta-hemolytic Streptococcus and methicillin-susceptible Staphylococcus aureus were the most commonly cultured microorganisms. Cephalosporins, clindamycin, amoxicillin/clavulanate, penicillin, vancomycin, and trimethoprim/sulfamethoxazole were major antibiotic choices. Amputations and contracture were the primary complications. Conclusions. Surgery along with medical management were key to treatment and most soft tissue infections resolved without further complications. With prompt and appropriate care, most hand infection patients can achieve full resolution of their infection.
Türker et al. (2014) Hand infections: a retrospective analysis. PeerJ 2:e513 https://doi.org/10.7717/peerj.513
Exceptionally preserved insect fossils in the Late Jurassic lagoon of Orbagnoux (Rhône Valley, France)
The Late Kimmeridgian marine limestones of the area around Orbagnoux (Rhône, France) are well known for their fish fauna and terrestrial flora. Here we record the first insects and their activities (mines on leaves and trails in sediments) from these layers, including the oldest record of the gerromorphan bugs, as a new genus and species Gallomesovelia grioti, attributed to the most basal family Mesoveliidae and subfamily Madeoveliinae. These new fossils suggest the presence of a complex terrestrial palaeoecosystem on emerged lands near the lagoon where the limestones were deposited. The exquisite state of preservation of these fossils also suggests that these outcrops can potentially become an important Konservat-Lagerstätte for the Late Jurassic of Western Europe.
Nel et al. (2014) Exceptionally preserved insect fossils in the Late Jurassic lagoon of Orbagnoux (Rhône Valley, France). PeerJ 2:e510 https://doi.org/10.7717/peerj.510