Increasing the precision of orthology-based complex prediction through network alignment
Macromolecular assemblies play an important role in almost all cellular processes. However, despite several large-scale studies, our current knowledge about protein complexes is still quite limited, thus advocating the use of in silico predictions to gather information on complex composition in model organisms. Since protein–protein interactions present certain constraints on the functional divergence of macromolecular assemblies during evolution, it is possible to predict complexes based on orthology data. Here, we show that incorporating interaction information through network alignment significantly increases the precision of orthology-based complex prediction. Moreover, we performed a large-scale in silico screen for protein complexes in human, yeast and fly, through the alignment of hundreds of known complexes to whole organism interactomes. Systematic comparison of the resulting network alignments to all complexes currently known in those species revealed many conserved complexes, as well as several novel complex components. In addition to validating our predictions using orthogonal data, we were able to assign specific functional roles to the predicted complexes. In several cases, the incorporation of interaction data through network alignment allowed to distinguish real complex components from other orthologous proteins. Our analyses indicate that current knowledge of yeast protein complexes exceeds that in other organisms and that predicting complexes in fly based on human and yeast data is complementary rather than redundant. Lastly, assessing the conservation of protein complexes of the human pathogen Mycoplasma pneumoniae, we discovered that its complexes repertoire is different from that of eukaryotes, suggesting new points of therapeutic intervention, whereas targeting the pathogen’s Restriction enzyme complex might lead to adverse effects due to its similarity to ATP-dependent metalloproteases in the human host.
Pache et al. (2014) Increasing the precision of orthology-based complex prediction through network alignment. PeerJ 2:e413 https://doi.org/10.7717/peerj.413
Biogeographic patterns in the cartilaginous fauna (Pisces: Elasmobranchii and Holocephali) in the southeast Pacific Ocean
The abundance and species richness of the cartilaginous fish community of the continental shelf and slope off central Chile is described, based on fishery-independent trawl tows made in 2006 and 2007. A total of 194,705 specimens comprising 20 species (9 sharks, 10 skates, 1 chimaera) were caught at depths of 100–500 m along a 1,000 km transect between 29.5°S and 39°S. Sample site locations were grouped to represent eight geographical zones within this latitudinal range. Species richness fluctuated from 1 to 6 species per zone. There was no significant latitudinal trend for sharks, but skates showed an increased species richness with latitude. Standardised catch per unit effort (CPUE) increased with increasing depth for sharks, but not for skates, but the observed trend for increasing CPUE with latitude was not significant for either sharks or skates. A change in community composition occurred along the depth gradient with the skates, Psammobatis rudis, Zearaja chilensis and Dipturus trachyderma dominating communities between 100 and 300 m, but small-sized, deep-water dogfishes, such as Centroscyllium spp. dominated the catch between 300 and 500 m. Cluster and ordination analysis identified one widespread assemblage, grouping 58% of sites, and three shallow-water assemblages. Assemblages with low diversity (coldspots) coincided with highly productive fishing grounds for demersal crustaceans and bony fishes. The community distribution suggested that the differences between assemblages may be due to compensatory changes in mesopredator species abundance, as a consequence of continuous and unselective species removal. Distribution patterns and the quantitative assessment of sharks, skates and chimaeras presented here complement extant biogeographic knowledge and further the understanding of deep-water ecosystem dynamics in relation to fishing activity in the south-east Pacific Ocean.
Bustamante et al. (2014) Biogeographic patterns in the cartilaginous fauna (Pisces: Elasmobranchii and Holocephali) in the southeast Pacific Ocean. PeerJ 2:e416 https://doi.org/10.7717/peerj.416
New information on the anatomy of the Chinese Early Cretaceous Bohaiornithidae (Aves: Enantiornithes) from a subadult specimen of Zhouornis hani
Enantiornithines are the most diverse avian clade in the Cretaceous. However, morphological specializations indicative of specific ecological roles are not well known for this clade. Here we report on an exquisitely well-preserved specimen from the Lower Cretaceous Jehol Group of northeastern China, which pedal morphology is suggestive of a unique ecological specialization within Enantiornithes. The morphology of the new specimen is largely indistinguishable from that of the holotype of the bohaiornithid enantiornithine Zhouornis hani, albeit the latter is somewhat larger. The new specimen provides important and previously unknown details of the skull of Zhouornis hani, which add to the limited knowledge about the cranial anatomy and evolution of enantiornithines. The information offered by the new specimen also augments our understanding of the postcranial morphology of bohaiornithid enantiornithines, a clade that has been only recently recognized. With the description of this specimen, Zhouornis hani becomes one of the most anatomically complete known enantiornithine species, which will facilitate future morphological studies.
Zhang et al. (2014) New information on the anatomy of the Chinese Early Cretaceous Bohaiornithidae (Aves: Enantiornithes) from a subadult specimen of Zhouornis hani. PeerJ 2:e407 https://doi.org/10.7717/peerj.407
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a simple synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique.
Beitel et al. (2014) Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415 https://doi.org/10.7717/peerj.415
Contrasting effects of ocean acidification on tropical fleshy and calcareous algae
Despite the heightened awareness of ocean acidification (OA) effects on marine organisms, few studies empirically juxtapose biological responses to CO2 manipulations across functionally distinct primary producers, particularly benthic algae. Algal responses to OA may vary because increasing CO2 has the potential to fertilize photosynthesis but impair biomineralization. Using a series of repeated experiments on Palmyra Atoll, simulated OA effects were tested across a suite of ecologically important coral reef algae, including five fleshy and six calcareous species. Growth, calcification and photophysiology were measured for each species independently and metrics were combined from each experiment using a meta-analysis to examine overall trends across functional groups categorized as fleshy, upright calcareous, and crustose coralline algae (CCA). The magnitude of the effect of OA on algal growth response varied by species, but the direction was consistent within functional groups. Exposure to OA conditions generally enhanced growth in fleshy macroalgae, reduced net calcification in upright calcareous algae, and caused net dissolution in CCA. Additionally, three of the five fleshy seaweeds tested became reproductive upon exposure to OA conditions. There was no consistent effect of OA on algal photophysiology. Our study provides experimental evidence to support the hypothesis that OA will reduce the ability of calcareous algae to biomineralize. Further, we show that CO2 enrichment either will stimulate population or somatic growth in some species of fleshy macroalgae. Thus, our results suggest that projected OA conditions may favor non-calcifying algae and influence the relative dominance of fleshy macroalgae on reefs, perpetuating or exacerbating existing shifts in reef community structure.
Johnson et al. (2014) Contrasting effects of ocean acidification on tropical fleshy and calcareous algae. PeerJ 2:e411 https://doi.org/10.7717/peerj.411
Prey aggregation is an effective olfactory predator avoidance strategy
Predator–prey interactions have a major effect on species abundance and diversity, and aggregation is a well-known anti-predator behaviour. For immobile prey, the effectiveness of aggregation depends on two conditions: (a) the inability of the predator to consume all prey in a group and (b) detection of a single large group not being proportionally easier than that of several small groups. How prey aggregation influences predation rates when visual cues are restricted, such as in turbid water, has not been thoroughly investigated. We carried out foraging (predation) experiments using a fish predator and (dead) chironomid larvae as prey in both laboratory and field settings. In the laboratory, a reduction in visual cue availability (in turbid water) led to a delay in the location of aggregated prey compared to when visual cues were available. Aggregated prey suffered high mortality once discovered, leading to better survival of dispersed prey in the longer term. We attribute this to the inability of the dead prey to take evasive action. In the field (where prey were placed in feeding stations that allowed transmission of olfactory but not visual cues), aggregated (large groups) and semi-dispersed prey survived for longer than dispersed prey—including long term survival. Together, our results indicate that similar to systems where predators hunt using vision, aggregation is an effective anti-predator behaviour for prey avoiding olfactory predators.
Johannesen et al. (2014) Prey aggregation is an effective olfactory predator avoidance strategy. PeerJ 2:e408 https://doi.org/10.7717/peerj.408
Aerosol delivery of synthetic lung surfactant
Background. Nasal continuous positive airway pressure (nCPAP) is a widely accepted technique of non-invasive respiratory support in premature infants with respiratory distress syndrome due to lack of lung surfactant. If this approach fails, the next step is often intubation, mechanical ventilation (MV) and intratracheal instillation of clinical lung surfactant. Objective. To investigate whether aerosol delivery of advanced synthetic lung surfactant, consisting of peptide mimics of surfactant proteins B and C (SP-B and SP-C) and synthetic lipids, during nCPAP improves lung function in surfactant-deficient rabbits. Methods. Experimental synthetic lung surfactants were produced by formulating 3% Super Mini-B peptide (SMB surfactant), a highly surface active SP-B mimic, and a combination of 1.5% SMB and 1.5% of the SP-C mimic SP-Css ion-lock 1 (BC surfactant), with a synthetic lipid mixture. After testing aerosol generation using a vibrating membrane nebulizer and aerosol conditioning (particle size, surfactant composition and surface activity), we investigated the effects of aerosol delivery of synthetic SMB and BC surfactant preparations on oxygenation and lung compliance in saline-lavaged, surfactant-deficient rabbits, supported with either nCPAP or MV. Results. Particle size distribution of the surfactant aerosols was within the 1–3 µm distribution range and surfactant activity was not affected by aerosolization. At a dose equivalent to clinical surfactant therapy in premature infants (100 mg/kg), aerosol delivery of both synthetic surfactant preparations led to a quick and clinically relevant improvement in oxygenation and lung compliance in the rabbits. Lung function recovered to a greater extent in rabbits supported with MV than with nCPAP. BC surfactant outperformed SMB surfactant in improving lung function and was associated with higher phospholipid values in bronchoalveolar lavage fluid; these findings were irrespective of the type of ventilatory support (nCPAP or MV) used. Conclusions. Aerosol delivery of synthetic lung surfactant with a combination of highly active second generation SP-B and SP-C mimics was effective as a therapeutic approach towards relieving surfactant deficiency in spontaneously breathing rabbits supported with nCPAP. To obtain similar results with nCPAP as with intratracheal instillation, higher dosage of synthetic surfactant and reduction of its retention by the delivery circuit will be needed to increase the lung dose.
Walther et al. (2014) Aerosol delivery of synthetic lung surfactant. PeerJ 2:e403 https://doi.org/10.7717/peerj.403
Diagnosing the dangerous demography of manta rays using life history theory
Background. The directed harvest and global trade in the gill plates of mantas, and devil rays, has led to increased fishing pressure and steep population declines in some locations. The slow life history, particularly of the manta rays, is cited as a key reason why such species have little capacity to withstand directed fisheries. Here, we place their life history and demography within the context of other sharks and rays. Methods. Despite the limited availability of data, we use life history theory and comparative analysis to estimate the intrinsic risk of extinction (as indexed by the maximum intrinsic rate of population increase rmax) for a typical generic manta ray using a variant of the classic Euler–Lotka demographic model. This model requires only three traits to calculate the maximum intrinsic population growth rate rmax: von Bertalanffy growth rate, annual pup production and age at maturity. To account for the uncertainty in life history parameters, we created plausible parameter ranges and propagate these uncertainties through the model to calculate a distribution of the plausible range of rmax values. Results. The maximum population growth rate rmax of manta ray is most sensitive to the length of the reproductive cycle, and the median rmax of 0.116 year−1 95th percentile [0.089–0.139] is one of the lowest known of the 106 sharks and rays for which we have comparable demographic information. Discussion. In common with other unprotected, unmanaged, high-value large-bodied sharks and rays the combination of very low population growth rates of manta rays, combined with the high value of their gill rakers and the international nature of trade, is highly likely to lead to rapid depletion and potential local extinction unless a rapid conservation management response occurs worldwide. Furthermore, we show that it is possible to derive important insights into the demography extinction risk of data-poor species using well-established life history theory.
Dulvy et al. (2014) Diagnosing the dangerous demography of manta rays using life history theory. PeerJ 2:e400 https://doi.org/10.7717/peerj.400
TGF-β1 of no avail as prognostic marker in lyme disease
Background. Within the present in vivo study using the wild type mouse strains C3H/HeN and FVB/N it was intended to (1) measure TGF-β1 expression in the course of lyme disease, (2) examine the potential correlation of TGF-β1 expression with the clinical outcome of a Borrelia infection (with a focus on lyme arthritis), (3) develop a diagnostic tool based on the endogenous factor TGF-β1 to predict the progressivity of lyme disease. Findings. In the course of lyme disease there was an increase in the serum content of active TGF-β1, which became significant 56 days post infection (p < 0.001). The serum concentration of total TGF-β1 in the course of infection initially decreased then rebounded and subsequently dropped again. Despite considerable individual variations in active TGF-β1 serum concentrations there were no identifiable dissimilarities in the clinical appearance of the mice. Likewise, no correlation could be seen between the serum content of active TGF-β1 and the severity of lyme arthritis of tibiotarsal joints of infected mice. Conclusions. The present study clearly shows that TGF-β1 is of no avail as prognostic marker in lyme disease. Hence, the search for an endogenous predictive factor, which can be determined in an easy and reliable manner, remains open.
Schumann (2014) TGF-β1 of no avail as prognostic marker in lyme disease. PeerJ 2:e398 https://doi.org/10.7717/peerj.398
Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss
Obesity in human populations, currently a serious health concern, is considered to be the consequence of an energy imbalance in which more energy in calories is consumed than is expended. We used interval mapping techniques to investigate the genetic basis of a number of energy balance traits in an F11 advanced intercross population of mice created from an original intercross of lines selected for increased and decreased heat loss. We uncovered a total of 137 quantitative trait loci (QTLs) for these traits at 41 unique sites on 18 of the 20 chromosomes in the mouse genome, with X-linked QTLs being most prevalent. Two QTLs were found for the selection target of heat loss, one on distal chromosome 1 and another on proximal chromosome 2. The number of QTLs affecting the various traits generally was consistent with previous estimates of heritabilities in the same population, with the most found for two bone mineral traits and the least for feed intake and several body composition traits. QTLs were generally additive in their effects, and some, especially those affecting the body weight traits, were sex-specific. Pleiotropy was extensive within trait groups (body weights, adiposity and organ weight traits, bone traits) and especially between body composition traits adjusted and not adjusted for body weight at sacrifice. Nine QTLs were found for one or more of the adiposity traits, five of which appeared to be unique. The confidence intervals among all QTLs averaged 13.3 Mb, much smaller than usually observed in an F2 cross, and in some cases this allowed us to make reasonable inferences about candidate genes underlying these QTLs. This study combined QTL mapping with genetic parameter analysis in a large segregating population, and has advanced our understanding of the genetic architecture of complex traits related to obesity.
Leamy et al. (2014) Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss. PeerJ 2:e392 https://doi.org/10.7717/peerj.392
Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change
We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-term responses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity–diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant–plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic.
Alatalo et al. (2014) Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change. PeerJ 2:e406 https://doi.org/10.7717/peerj.406
Carbapenem-resistant enterobacteriaceae: analyzing knowledge and practice in healthcare providers
Background. Gram negative antibiotic resistance is increasing worldwide as both carbapenem-resistant enterobacteriaceae (CREs) and Enterobacteriaceae producing extended spectrum ß-lactamases (ESBLs) become more common. Objective. We analyzed clinicians’ knowledge regarding resistant gram-negative organisms with respect to infection control practices, prescribing practices and assessment of their patients’ risk for resistant infections. Design. Online survey. Participants. Target population included clinicians who prescribe antibiotics i.e., medical doctors and mid-level practitioners, at three Massachusetts hospitals. Methods. Questionnaires were sent to 3 Tufts-affiliated teaching hospitals to assess level of knowledge and elucidate perceptions about gram-negative resistance. Results. We received 434 responses from 3332 non-infectious disease clinicians (13%) surveyed at the three hospitals. 51.1% of clinicians correctly scored 50% or greater on the knowledge questions. Internal medicine clinicians had higher knowledge scores than non-internal medicine clinicians (62% vs 45%; OR = 1.67, p = 0.02). Clinicians within three years of training had higher scores than those with more than 10 years of training (64.3% vs 44%; OR = 2.3, p = 0.002). Clinicians with fewer years since training and those with higher knowledge scores were more likely to appropriately consider certain patients at risk for resistant infections (p < 0.05). 54.4% of clinicians were very concerned about gram-negative antibiotic resistance. 64.6% of clinicians felt comfortable de-escalating antibiotics as cultures are available. Conclusion. We found overall low knowledge scores and much variability in the way clinicians assess whether certain patient populations are at risk for antibiotic resistance. Internal medicine clinicians and those with fewer years since completion of their training scored higher and more appropriately considered patients at risk for resistance. The majority of clinicians are concerned about gram-negative resistance and indicated they would de-escalate antibiotic therapy if they had susceptibility information. These results will help focus and target our teaching and awareness-raising strategies.
Thibodeau et al. (2014) Carbapenem-resistant enterobacteriaceae: analyzing knowledge and practice in healthcare providers. PeerJ 2:e405 https://doi.org/10.7717/peerj.405
Growth and metal bioconcentration by conspecific freshwater macroalgae cultured in industrial waste water
The bioremediation of industrial waste water by macroalgae is a sustainable and renewable approach to the treatment of waste water produced by multiple industries. However, few studies have tested the bioremediation of complex multi-element waste streams from coal-fired power stations by live algae. This study compares the ability of three species of green freshwater macroalgae from the genus Oedogonium, isolated from different geographic regions, to grow in waste water for the bioremediation of metals. The experiments used Ash Dam water from Tarong power station in Queensland, which is contaminated by multiple metals (Al, Cd, Ni and Zn) and metalloids (As and Se) in excess of Australian water quality guidelines. All species had consistent growth rates in Ash Dam water, despite significant differences in their growth rates in “clean” water. A species isolated from the Ash Dam water itself was not better suited to the bioremediation of that waste water. While there were differences in the temporal pattern of the bioconcentration of metals by the three species, over the course of the experiment, all three species bioconcentrated the same elements preferentially and to a similar extent. All species bioconcentrated metals (Cu, Mn, Ni, Cd and Zn) more rapidly than metalloids (As, Mo and Se). Therefore, bioremediation in situ will be most rapid and complete for metals. Overall, all three species of freshwater macroalgae had the ability to grow in waste water and bioconcentrate elements, with a consistent affinity for the key metals that are regulated by Australian and international water quality guidelines. Together, these characteristics make Oedogonium a clear target for scaled bioremediation programs across a range of geographic regions.
Ellison et al. (2014) Growth and metal bioconcentration by conspecific freshwater macroalgae cultured in industrial waste water. PeerJ 2:e401 https://doi.org/10.7717/peerj.401
Spatial and temporal distribution of the invasive lionfish Pterois volitans in coral reefs of Tayrona National Natural Park, Colombian Caribbean
The lionfish Pterois volitans is an invasive species throughout the Western Atlantic that disturbs functioning of local ecosystems such as coral reefs via fast and intense consumption of small fish and invertebrates. In 2009, lionfish populated the bays of Tayrona National Natural Park (TNNP), a biodiversity hotspot in the Colombian Caribbean that is strongly influenced by changing environmental conditions due to a rainy and dry season. So far, the spatial and temporal distribution of P. volitans in the bays of TNNP is unknown. Therefore, this study assessed the abundance and body lengths of P. volitans during monthly surveys throughout the year 2012 in four bays (thereof two bays where lionfish removals were undertaken) of TNNP at 10 m water depth in coral reefs using transect tools. Findings revealed lionfish abundances of 2.9 ± 0.9 individuals ha−1 with lengths of 20–25 cm for TNNP, hinting to an established, mostly adult local population. Actual TNNP lionfish abundances are thereby very similar to those at Indo–Pacific reef locations where the invasive lionfish formerly originated from. Significant spatial differences for lionfish abundances and body lengths between different bays in TNNP suggest habitat preferences of P. volitans depending on age. Lionfish abundances were highly variable over time, but without significant differences between seasons. Removals could not reduce lionfish abundances significantly during the period of study. This study therefore recommends improved management actions in order to control the already established invasive lionfish population in TNNP.
Bayraktarov et al. (2014) Spatial and temporal distribution of the invasive lionfish Pterois volitans in coral reefs of Tayrona National Natural Park, Colombian Caribbean. PeerJ 2:e397 https://doi.org/10.7717/peerj.397
Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior
Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as an important determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.
Balakrishnan et al. (2014) Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior. PeerJ 2:e396 https://doi.org/10.7717/peerj.396
Synthetic surfactant containing SP-B and SP-C mimics is superior to single-peptide formulations in rabbits with chemical acute lung injury
Background. Chemical spills are on the rise and inhalation of toxic chemicals may induce chemical acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). Although the pathophysiology of ALI/ARDS is well understood, the absence of specific antidotes has limited the effectiveness of therapeutic interventions. Objectives. Surfactant inactivation and formation of free radicals are important pathways in (chemical) ALI. We tested the potential of lipid mixtures with advanced surfactant protein B and C (SP-B and C) mimics to improve oxygenation and lung compliance in rabbits with lavage- and chemical-induced ALI/ARDS. Methods. Ventilated young adult rabbits underwent repeated saline lung lavages or underwent intratracheal instillation of hydrochloric acid to induce ALI/ARDS. After establishment of respiratory failure rabbits were treated with a single intratracheal dose of 100 mg/kg of synthetic surfactant composed of 3% Super Mini-B (S-MB), a SP-B mimic, and/or SP-C33 UCLA, a SP-C mimic, in a lipid mixture (DPPC:POPC:POPG 5:3:2 by weight), the clinical surfactant Infasurf®, a bovine lung lavage extract with SP-B and C, or synthetic lipids alone. End-points consisted of arterial oxygenation, dynamic lung compliance, and protein and lipid content in bronchoalveolar lavage fluid. Potential mechanism of surfactant action for S-MB and SP-C33 UCLA were investigated with captive bubble surfactometry (CBS) assays. Results. All three surfactant peptide/lipid mixtures and Infasurf equally lowered the minimum surface tension on CBS, and also improved oxygenation and lung compliance. In both animal models, the two-peptide synthetic surfactant with S-MB and SP-C33 UCLA led to better arterial oxygenation and lung compliance than single peptide synthetic surfactants and Infasurf. Synthetic surfactants and Infasurf improved lung function further in lavage- than in chemical-induced respiratory failure, with the difference probably due to greater capillary-alveolar protein leakage and surfactant dysfunction after HCl instillation than following lung lavage. At the end of the duration of the experiments, synthetic surfactants provided more clinical stability in ALI/ARDS than Infasurf, and the protein content of bronchoalveolar lavage fluid was lowest for the two-peptide synthetic surfactant with S-MB and SP-C33 UCLA. Conclusion. Advanced synthetic surfactant with robust SP-B and SP-C mimics is better equipped to tackle surfactant inactivation in chemical ALI than synthetic surfactant with only a single surfactant peptide or animal-derived surfactant.
Walther et al. (2014) Synthetic surfactant containing SP-B and SP-C mimics is superior to single-peptide formulations in rabbits with chemical acute lung injury. PeerJ 2:e393 https://doi.org/10.7717/peerj.393
The role of a water bug, Sigara striata, in freshwater food webs
Freshwater food webs are dominated by aquatic invertebrates whose trophic relationships are often poorly known. Here, I used laboratory experiments to study the role of a water bug, Sigara striata, as a potential predator and prey in food webs of stagnant waters. Multiple-choice predation experiment revealed that Sigara, which had been considered mostly herbivorous, also consumed larvae of Chironomus midges. Because they often occur in high densities and are among the most ubiquitous aquatic insects, Sigara water bugs may be important predators in fresh waters. A second experiment tested the role of Sigara as a potential prey for 13 common invertebrate predators. Mortality of Sigara inflicted by different predators varied widely, especially depending on body mass, foraging mode (ambush/searching) and feeding mode (chewing/suctorial) of the predators. Sigara was highly vulnerable to ambush predators, while searching predators caused on average 8.1 times lower mortality of Sigara. Additionally, suctorial predators consumed on average 6.6 times more Sigara individuals than chewing predators, which supports previous results hinting on potentially different predation pressures of these two types of predators on prey populations. The importance of these two foraging-related traits demonstrates the need to move from body mass based to multiple trait based descriptions of food web structure. Overall, the results suggests that detailed experimental studies of common but insufficiently known species can significantly enhance our understanding of food web structure.
Klecka (2014) The role of a water bug, Sigara striata, in freshwater food webs. PeerJ 2:e389 https://doi.org/10.7717/peerj.389
Organic carbon inventories in natural and restored Ecuadorian mangrove forests
Mangroves can capture and store organic carbon and their protection and therefore their restoration is a component of climate change mitigation. However, there are few empirical measurements of long-term carbon storage in mangroves or of how storage varies across environmental gradients. The context dependency of this process combined with geographically limited field sampling has made it difficult to generalize regional and global rates of mangrove carbon sequestration. This has in turn hampered the inclusion of sequestration by mangroves in carbon cycle models and in carbon offset markets. The purpose of this study was to estimate the relative carbon capture and storage potential in natural and restored mangrove forests. We measured depth profiles of soil organic carbon content in 72 cores collected from six sites (three natural, two restored, and one afforested) surrounding Muisne, Ecuador. Samples up to 1 m deep were analyzed for organic matter content using loss-on-ignition and values were converted to organic carbon content using an accepted ratio of 1.72 (g/g). Results suggest that average soil carbon storage is 0.055 ± 0.002 g cm−3 (11.3 ± 0.8% carbon content by dry mass, mean ± 1 SE) up to 1 m deep in natural sites, and 0.058 ± 0.002 g cm−3 (8.0 ± 0.3%) in restored sites. These estimates are concordant with published global averages. Evidence of equivalent carbon stocks in restored and afforested mangrove patches emphasizes the carbon sink potential for reestablished mangrove systems. We found no relationship between sediment carbon storage and aboveground biomass, forest structure, or within-patch location. Our results demonstrate the long-term carbon storage potential of natural mangroves, high effectiveness of mangrove restoration and afforestation, a lack of predictability in carbon storage strictly based on aboveground parameters, and the need to establish standardized protocol for quantifying mangrove sediment carbon stocks.
DelVecchia et al. (2014) Organic carbon inventories in natural and restored Ecuadorian mangrove forests. PeerJ 2:e388 https://doi.org/10.7717/peerj.388
Retrospective cohort study of anti-tumor necrosis factor agent use in a veteran population
Introduction. Anti-tumor necrosis factor (TNF) agents are effective for several immunologic conditions (rheumatoid arthritis (RA), Crohn’s disease (CD), and psoriasis). The purpose of this study was to evaluate the efficacy and safety of anti-TNF agents via chart review. Methods. Single-site, retrospective cohort study that evaluated the efficacy and safety of anti-TNF agents in veterans initiated between 2010 and 2011. Primary aim evaluated response at 12 months post-index date. Secondary aims evaluated initial response prior to 12 months post-index date and infection events. Results. A majority of patients were prescribed anti-TNF agents for CD (27%) and RA (24%). Patients were initiated on etanercept (41%), adalimumab (40%), and infliximab (18%) between 2010 and 2011. No differences in patient demographics were reported. Response rates were high overall. Sixty-five percent of etanercept patients, 82% of adalimumab patients, and 59% of infliximab patients were either partial or full responders, respectively. Approximately 16%, 11%, and 12% of etanercept, adalimumab, and infliximab were non-responders, respectively. Infections between the groups were non-significant. Etanercept and adalimumab patients had higher but non-significant odds of being a responder relative to infliximab. Conclusions. Most patients initiated with anti-TNF agent were responders at 12 months follow-up for all indications in a veteran population.
Bounthavong et al. (2014) Retrospective cohort study of anti-tumor necrosis factor agent use in a veteran population. PeerJ 2:e385 https://doi.org/10.7717/peerj.385
Coral-algae metabolism and diurnal changes in the CO2-carbonate system of bulk sea water
Precise measurements were conducted in continuous flow seawater mesocosms located in full sunlight that compared metabolic response of coral, coral-macroalgae and macroalgae systems over a diurnal cycle. Irradiance controlled net photosynthesis (Pnet), which in turn drove net calcification (Gnet), and altered pH. Pnet exerted the dominant control on [CO32−] and aragonite saturation state (Ωarag) over the diel cycle. Dark calcification rate decreased after sunset, reaching zero near midnight followed by an increasing rate that peaked at 03:00 h. Changes in Ωarag and pH lagged behind Gnet throughout the daily cycle by two or more hours. The flux rate Pnet was the primary driver of calcification. Daytime coral metabolism rapidly removes dissolved inorganic carbon (DIC) from the bulk seawater and photosynthesis provides the energy that drives Gnet while increasing the bulk water pH. These relationships result in a correlation between Gnet and Ωarag, with Ωarag as the dependent variable. High rates of H+ efflux continued for several hours following mid-day peak Gnet suggesting that corals have difficulty in shedding waste protons as described by the Proton Flux Hypothesis. DIC flux (uptake) followed Pnet and Gnet and dropped off rapidly following peak Pnet and peak Gnet indicating that corals can cope more effectively with the problem of limited DIC supply compared to the problem of eliminating H+. Over a 24 h period the plot of total alkalinity (AT) versus DIC as well as the plot of Gnet versus Ωarag revealed a circular hysteresis pattern over the diel cycle in the coral and coral-algae mesocosms, but not the macroalgae mesocosm. Presence of macroalgae did not change Gnet of the corals, but altered the relationship between Ωarag and Gnet. Predictive models of how future global changes will effect coral growth that are based on oceanic Ωarag must include the influence of future localized Pnet on Gnet and changes in rate of reef carbonate dissolution. The correlation between Ωarag and Gnet over the diel cycle is simply the response of the CO2-carbonate system to increased pH as photosynthesis shifts the equilibria and increases the [CO32−] relative to the other DIC components of [HCO3−] and [CO2]. Therefore Ωarag closely tracked pH as an effect of changes in Pnet, which also drove changes in Gnet. Measurements of DIC flux and H+ flux are far more useful than concentrations in describing coral metabolism dynamics. Coral reefs are systems that exist in constant disequilibrium with the water column.
Jokiel et al. (2014) Coral-algae metabolism and diurnal changes in the CO2-carbonate system of bulk sea water. PeerJ 2:e378 https://doi.org/10.7717/peerj.378
Formation of 1-octen-3-ol from Aspergillus flavus conidia is accelerated after disruption of cells independently of Ppo oxygenases, and is not a main cause of inhibition of germination
Eight-carbon (C8) volatiles, such as 1-octen-3-ol, are ubiquitous among fungi. They are the volatiles critical for aroma and flavor of fungi, and assumed to be signals controlling germination of several fungi. In this study, we found that intact Aspergillus flavus conidia scarcely synthesized C8 volatiles but repeated freeze-thaw treatment that made the cell membrane permeable promoted (R)-1-octen-3-ol formation. Loss or down regulation of any one of five fatty acid oxygenases (PpoA, PpoB, PpoC, PpoD or lipoxygenase) hypothesized contribute to 1-octen-3-ol formation had little impact on production of this volatile. This suggested that none of the oxygenases were directly involved in the formation of 1-octen-3-ol or that compensatory pathways exist in the fungus. Germination of the conidia was markedly inhibited at high density (1.0 × 109spores mL−1). It has been postulated that 1-octen-3-ol is an autoinhibitor suppressing conidia germination at high density. 1-Octen-3-ol at concentration of no less than 10 mM was needed to suppress the germination while the concentration of 1-octen-3-ol in the suspension at 1.0 × 109 mL−1 was under the detection limit (<1 µM). Thus, 1-octen-3-ol was not the principal component responsible for inhibition of germination. Instead, it was evident that the other heat-labile factor(s) suppressed conidial germination.
Miyamoto et al. (2014) Formation of 1-octen-3-ol from Aspergillus flavus conidia is accelerated after disruption of cells independently of Ppo oxygenases, and is not a main cause of inhibition of germination. PeerJ 2:e395 https://doi.org/10.7717/peerj.395
Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution
Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.
Pochon et al. (2014) Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution. PeerJ 2:e394 https://doi.org/10.7717/peerj.394
Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
Allopolyploidy combines two progenitor genomes in the same nucleus. It is a common speciation process, especially in plants. Deciphering the origins of polyploid species is a complex problem due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. Among the perennial species of Glycine, the plant genus that includes the cultivated soybean (G. max), are eight allopolyploid species, three of which are studied here. Previous crossing studies and molecular systematic results from two nuclear gene sequences led to hypotheses of origin for these species from among extant diploid species. We use several phylogenetic and population genomics approaches to clarify the origins of the genomes of three of these allopolyploid species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that all three polyploid species are fixed hybrids combining the genomes of the two putative parents hypothesized on the basis of previous work. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also are consistent with multiple origins for these allopolyploid species, and suggest that origins occurred within the last several hundred thousand years.
Bombarely et al. (2014) Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ 2:e391 https://doi.org/10.7717/peerj.391
Violent deaths of media workers associated with conflict in Iraq, 2003–2012
Background. The violent deaths of media workers is a critical issue worldwide, especially in areas of political and social instability. Such deaths can be a particular concern as they may undermine the development and functioning of an open and democratic society. Method. Data on the violent deaths of media workers in Iraq for ten years (2003–2012) were systematically collated from five international databases. Analyses included time trends, weapons involved, nationality of the deceased, outcome for perpetrators and location of death. Results. During this ten-year period, there were 199 violent deaths of media workers in Iraq. The annual number increased substantially after the invasion in 2003 (peaking at n = 47 in 2007) and then declined (n = 5 in 2012). The peak years (2006–2007) for these deaths matched the peak years for estimated violent deaths among civilians. Most of the media worker deaths (85%) were Iraqi nationals. Some were killed whilst on assignment in the field (39%) and 28% involved a preceding threat. Common perpetrators of the violence were: political groups (45%), and coalition forces (9%), but the source of the violence was often unknown (29%). None of the perpetrators have subsequently been prosecuted (as of April 2014). For each violent death of a media worker, an average of 3.1 other people were also killed in the same attack (range 0–100 other deaths). Discussion. This analysis highlights the high number of homicides of media workers in Iraq in this conflict period, in addition to the apparently total level of impunity. One of the potential solutions may be establishing a functioning legal system that apprehends offenders and puts them on trial. The relatively high quality of data on violent deaths in this occupational group, suggests that it could act as one sentinel population within a broader surveillance system of societal violence in conflict zones.
Collinson et al. (2014) Violent deaths of media workers associated with conflict in Iraq, 2003–2012. PeerJ 2:e390 https://doi.org/10.7717/peerj.390
Effects of terrigenous sediment on settlement and survival of the reef coral Pocillopora damicornis
Survival and settlement of Pocillopora damicornis larvae on hard surfaces covered with fine (<63 µm) terrigenous red clay was measured in laboratory Petri dishes. The dishes were prepared with sediment films of various thicknesses covering the bottoms. Coral larvae were incubated in the dishes for two weeks and the percent that settled on the bottom was determined. There was a statistically significant relationship between the amount of sediment and coral recruitment on the bottom, with no recruitment on surfaces having a sediment cover above 0.9 mg cm−2. Experimental conditions for the delicate coral larvae were favorable in these experiments. Total survival over the two week settlement tests expressed as the sum of coral recruits and live larvae at the end of the experiment did not show a significant decline, so the major impact of the sediment was on successful settlement rather than on mortality. Larval substrate selection behavior was the primary factor in the observed result.
Perez et al. (2014) Effects of terrigenous sediment on settlement and survival of the reef coral Pocillopora damicornis. PeerJ 2:e387 https://doi.org/10.7717/peerj.387
On growth and form of irregular coiled-shell of a terrestrial snail: Plectostoma concinnum (Fulton, 1901) (Mollusca: Caenogastropoda: Diplommatinidae)
The molluscan shell can be viewed as a petrified representation of the organism’s ontogeny and thus can be used as a record of changes in form during growth. However, little empirical data is available on the actual growth and form of shells, as these are hard to quantify and examine simultaneously. To address these issues, we studied the growth and form of a land snail that has an irregularly coiled and heavily ornamented shell–Plectostoma concinnum. The growth data were collected in a natural growth experiment and the actual form changes of the aperture during shell ontogeny were quantified. We used an ontogeny axis that allows data of growth and form to be analysed simultaneously. Then, we examined the association between the growth and the form during three different whorl growing phases, namely, the regular coiled spire phase, the transitional constriction phase, and the distortedly-coiled tuba phase. In addition, we also explored the association between growth rate and the switching between whorl growing mode and rib growing mode. As a result, we show how the changes in the aperture ontogeny profiles in terms of aperture shape, size and growth trajectory, and the changes in growth rates, are associated with the different shell forms at different parts of the shell ontogeny. These associations suggest plausible constraints that underlie the three different shell ontogeny phases and the two different growth modes. We found that the mechanism behind the irregularly coiled-shell is the rotational changes of the animal’s body and mantle edge with respect to the previously secreted shell. Overall, we propose that future study should focus on the role of the mantle and the columellar muscular system in the determination of shell form.
Liew et al. (2014) On growth and form of irregular coiled-shell of a terrestrial snail: Plectostoma concinnum (Fulton, 1901) (Mollusca: Caenogastropoda: Diplommatinidae). PeerJ 2:e383 https://doi.org/10.7717/peerj.383
Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico
The genetic composition of the resident Symbiodinium endosymbionts can strongly modulate the physiological performance of reef-building corals. Here, we used quantitative metabarcoding to investigate Symbiodinium genetic diversity in two species of mountainous star corals, Orbicella franksi and Orbicella faveolata, from two reefs separated by 19 km of deep water. We aimed to determine if the frequency of different symbiont genotypes varied with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained seven haplotypes of Symbiodinium, all identifiable as clade B and most closely related to type B1. Five of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No significant differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were detected between the east and west banks for three background haplotypes comprising 0.1%–10% of the total. The quantitative metabarcoding approach described here can help to sensitively characterize cryptic genetic diversity of Symbiodinium and potentially contribute to the understanding of physiological variations among coral populations.
Green et al. (2014) Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ 2:e386 https://doi.org/10.7717/peerj.386
Effect of nutrition survey ‘cleaning criteria’ on estimates of malnutrition prevalence and disease burden: secondary data analysis
Tackling childhood malnutrition is a global health priority. A key indicator is the estimated prevalence of malnutrition, measured by nutrition surveys. Most aspects of survey design are standardised, but data ‘cleaning criteria’ are not. These aim to exclude extreme values which may represent measurement or data-entry errors. The effect of different cleaning criteria on malnutrition prevalence estimates was unknown. We applied five commonly used data cleaning criteria (WHO 2006; EPI-Info; WHO 1995 fixed; WHO 1995 flexible; SMART) to 21 national Demographic and Health Survey datasets. These included a total of 163,228 children, aged 6–59 months. We focused on wasting (low weight-for-height), a key indicator for treatment programmes. Choice of cleaning criteria had a marked effect: SMART were least inclusive, resulting in the lowest reported malnutrition prevalence, while WHO 2006 were most inclusive, resulting in the highest. Across the 21 countries, the proportion of records excluded was 3 to 5 times greater when using SMART compared to WHO 2006 criteria, resulting in differences in the estimated prevalence of total wasting of between 0.5 and 3.8%, and differences in severe wasting of 0.4–3.9%. The magnitude of difference was associated with the standard deviation of the survey sample, a statistic that can reflect both population heterogeneity and data quality. Using these results to estimate case-loads for treatment programmes resulted in large differences for all countries. Wasting prevalence and caseload estimations are strongly influenced by choice of cleaning criterion. Because key policy and programming decisions depend on these statistics, variations in analytical practice could lead to inconsistent and potentially inappropriate implementation of malnutrition treatment programmes. We therefore call for mandatory reporting of cleaning criteria use so that results can be compared and interpreted appropriately. International consensus is urgently needed regarding choice of criteria to improve the comparability of nutrition survey data.
Crowe et al. (2014) Effect of nutrition survey ‘cleaning criteria’ on estimates of malnutrition prevalence and disease burden: secondary data analysis. PeerJ 2:e380 https://doi.org/10.7717/peerj.380
Light enhanced calcification in Stylophora pistillata: effects of glucose, glycerol and oxygen
Zooxanthellate corals have long been known to calcify faster in the light than in the dark, however the mechanism underlying this process has been uncertain. Here we tested the effects of oxygen under controlled pCO2 conditions and fixed carbon sources on calcification in zooxanthellate and bleached microcolonies of the branching coral Stylophora pistillata. In zooxanthellate microcolonies, oxygen increased dark calcification rates to levels comparable to those measured in the light. However in bleached microcolonies oxygen alone did not enhance calcification, but when combined with a fixed carbon source (glucose or glycerol), calcification increased. Respiration rates increased in response to oxygen with greater increases when oxygen is combined with fixed carbon. ATP content was largely unaffected by treatments, with the exception of glycerol which decreased ATP levels.
Holcomb et al. (2014) Light enhanced calcification in Stylophora pistillata: effects of glucose, glycerol and oxygen. PeerJ 2:e375 https://doi.org/10.7717/peerj.375
The impact of social context on learning and cognitive demands for interactive virtual human simulations
Interactive virtual human (IVH) simulations offer a novel method for training skills involving person-to-person interactions. This article examines the effectiveness of an IVH simulation for teaching medical students to assess rare cranial nerve abnormalities in both individual and small-group learning contexts. Individual (n = 26) and small-group (n = 30) interaction with the IVH system was manipulated to examine the influence on learning, learner engagement, perceived cognitive demands of the learning task, and instructional efficiency. Results suggested the IVH activity was an equally effective and engaging instructional tool in both learning structures, despite learners in the group learning contexts having to share hands-on access to the simulation interface. Participants in both conditions demonstrated a significant increase in declarative knowledge post-training. Operation of the IVH simulation technology imposed moderate cognitive demand but did not exceed the demands of the task content or appear to impede learning.
Lyons et al. (2014) The impact of social context on learning and cognitive demands for interactive virtual human simulations. PeerJ 2:e372 https://doi.org/10.7717/peerj.372
A taxonomic review of the Late Jurassic eucryptodiran turtles from the Jura Mountains (Switzerland and France)
Background. Eucryptodiran turtles from the Late Jurassic (mainly Kimmeridgian) deposits of the Jura Mountains (Switzerland and France) are among the earliest named species traditionally referred to the Plesiochelyidae, Thalassemydidae, and Eurysternidae. As such, they are a reference for the study of Late Jurassic eucryptodires at the European scale. Fifteen species and four genera have been typified based on material from the Late Jurassic of the Jura Mountains. In the past 50 years, diverging taxonomic reassessments have been proposed for these turtles with little agreement in sight. In addition, there has been a shift of focus from shell to cranial anatomy in the past forty years, although most of these species are only represented by shell material. As a result, the taxonomic status of many of these 15 species remains ambiguous, which prevents comprehensive comparison of Late Jurassic turtle assemblages throughout Europe and hinders description of new discoveries, such as the new assemblage recently unearthed in the vicinity of Porrentruy, Switzerland. Methods. An exhaustive reassessment of the available material provides new insights into the comparative anatomy of these turtles. The taxonomic status of each of the 15 species typified based on material from the Late Jurassic of the Jura Mountains is evaluated. New diagnoses and general descriptions are provided for each valid taxon. Results. Six out of the 15 available species names are recognized as valid: Plesiochelys etalloni, Craspedochelys picteti, Craspedochelys jaccardi, Tropidemys langii, Thalassemys hugii, and ‘Thalassemys’ moseri. The intraspecific variability of the shell of P. etalloni is discussed based on a sample of about 30 relatively complete specimens from Solothurn, Switzerland. New characters are proposed to differentiate P. etalloni, C. picteti, and C. jaccardi, therefore rejecting the previously proposed synonymy of these forms. Based partly on previously undescribed specimens, the plastral morphology of Th. hugii is redescribed. The presence of lateral plastral fontanelles is notably revealed in this species, which calls into question the traditional definitions of the Thalassemydidae and Eurysternidae. Based on these new data, Eurysternum ignoratum is considered a junior synonym of Th. hugii. The Eurysternidae are therefore only represented by Solnhofia parsonsi in the Late Jurassic of the Jura Mountains. Finally, ‘Th.’ moseri is recognized as a valid species, although a referral to the genus Thalassemys is refuted.
Anquetin et al. (2014) A taxonomic review of the Late Jurassic eucryptodiran turtles from the Jura Mountains (Switzerland and France). PeerJ 2:e369 https://doi.org/10.7717/peerj.369
Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss
Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype.
Pique et al. (2014) Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss. PeerJ 2:e384 https://doi.org/10.7717/peerj.384
Linking a genetic defect in migraine to spreading depression in a computational model
Familial hemiplegic migraine (FHM) is a rare subtype of migraine with aura. A mutation causing FHM type 3 (FHM3) has been identified in SCN1A encoding the Nav1.1 Na+ channel. This genetic defect affects the inactivation gate. While the Na+ tail currents following voltage steps are consistent with both hyperexcitability and hypoexcitability, in this computational study, we investigate functional consequences beyond these isolated events. Our extended Hodgkin–Huxley framework establishes a connection between genotype and cellular phenotype, i.e., the pathophysiological dynamics that spans over multiple time scales and is relevant to migraine with aura. In particular, we investigate the dynamical repertoire from normal spiking (milliseconds) to spreading depression and anoxic depolarization (tens of seconds) and show that FHM3 mutations render gray matter tissue more vulnerable to spreading depression despite opposing effects associated with action potential generation. We conclude that the classification in terms of hypoexcitability vs. hyperexcitability is too simple a scheme. Our mathematical analysis provides further basic insight into also previously discussed criticisms against this scheme based on psychophysical and clinical data.
Dahlem et al. (2014) Linking a genetic defect in migraine to spreading depression in a computational model. PeerJ 2:e379 https://doi.org/10.7717/peerj.379
How long is enough to detect terrestrial animals? Estimating the minimum trapping effort on camera traps
Camera traps is an important wildlife inventory tool for estimating species diversity at a site. Knowing what minimum trapping effort is needed to detect target species is also important to designing efficient studies, considering both the number of camera locations, and survey length. Here, we take advantage of a two-year camera trapping dataset from a small (24-ha) study plot in Gutianshan National Nature Reserve, eastern China to estimate the minimum trapping effort actually needed to sample the wildlife community. We also evaluated the relative value of adding new camera sites or running cameras for a longer period at one site. The full dataset includes 1727 independent photographs captured during 13,824 camera days, documenting 10 resident terrestrial species of birds and mammals. Our rarefaction analysis shows that a minimum of 931 camera days would be needed to detect the resident species sufficiently in the plot, and c. 8700 camera days to detect all 10 resident species. In terms of detecting a diversity of species, the optimal sampling period for one camera site was c. 40, or long enough to record about 20 independent photographs. Our analysis of evaluating the increasing number of additional camera sites shows that rotating cameras to new sites would be more efficient for measuring species richness than leaving cameras at fewer sites for a longer period.
Si et al. (2014) How long is enough to detect terrestrial animals? Estimating the minimum trapping effort on camera traps. PeerJ 2:e374 https://doi.org/10.7717/peerj.374
Characterisation of the horse transcriptome from immunologically active tissues
The immune system of the horse has not been well studied, despite the fact that the horse displays several features such as sensitivity to bacterial lipopolysaccharide that make them in many ways a more suitable model of some human disorders than the current rodent models. The difficulty of working with large animal models has however limited characterisation of gene expression in the horse immune system with current annotations for the equine genome restricted to predictions from other mammals and the few described horse proteins. This paper outlines sequencing of 184 million transcriptome short reads from immunologically active tissues of three horses including the genome reference “Twilight”. In a comparison with the Ensembl horse genome annotation, we found 8,763 potentially novel isoforms.
Moreton et al. (2014) Characterisation of the horse transcriptome from immunologically active tissues. PeerJ 2:e382 https://doi.org/10.7717/peerj.382
Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting
Histopathology is the most useful tool for diagnosis of a number of diseases, especially cancer. To be effective, histopathology requires that tissues be fixed prior to processing. Formalin is currently the most common histologic fixative, offering many advantages: it is cheap, readily available, and pathologists are routinely trained to examine tissues fixed in formalin. However, formalin fixation substantially degrades tissue DNA, hindering subsequent use in diagnostics and research. We therefore evaluated three alternative fixatives, TissueTek® Xpress® Molecular Fixative, modified methacarn, and PAXgene®, all of which have been proposed as formalin alternatives, to determine their suitability for routine use in a veterinary diagnostic laboratory. This was accomplished by examining the histomorphology of sections produced from fixed tissues as well as the ability to amplify fragments from extracted DNA. Tissues were sampled from two dogs and four cats, fixed for 24–48 h, and processed routinely. While all fixatives produced acceptable histomorphology, formalin had significantly better morphologic characteristics than the other three fixatives. Alternative fixatives generally had better DNA amplification than formalin, although results varied somewhat depending on the tissue examined. While no fixative is yet ready to replace formalin, the alternative fixatives examined may be useful as adjuncts to formalin in diagnostic practices.
Craft et al. (2014) Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting. PeerJ 2:e377 https://doi.org/10.7717/peerj.377
Variable effects of temperature on insect herbivory
Rising temperatures can influence the top-down control of plant biomass by increasing herbivore metabolic demands. Unfortunately, we know relatively little about the effects of temperature on herbivory rates for most insect herbivores in a given community. Evolutionary history, adaptation to local environments, and dietary factors may lead to variable thermal response curves across different species. Here we characterized the effect of temperature on herbivory rates for 21 herbivore-plant pairs, encompassing 14 herbivore and 12 plant species. We show that overall consumption rates increase with temperature between 20 and 30 °C but do not increase further with increasing temperature. However, there is substantial variation in thermal responses among individual herbivore-plant pairs at the highest temperatures. Over one third of the herbivore-plant pairs showed declining consumption rates at high temperatures, while an approximately equal number showed increasing consumption rates. Such variation existed even within herbivore species, as some species exhibited idiosyncratic thermal response curves on different host plants. Thus, rising temperatures, particularly with respect to climate change, may have highly variable effects on plant-herbivore interactions and, ultimately, top-down control of plant biomass.
Lemoine et al. (2014) Variable effects of temperature on insect herbivory. PeerJ 2:e376 https://doi.org/10.7717/peerj.376
The complex hybrid origins of the root knot nematodes revealed through comparative genomics
Root knot nematodes (RKN) can infect most of the world’s agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of their extreme polyphagy. The most damaging pathogens reproduce by obligatory mitotic parthenogenesis and it has been suggested that these species originated from interspecific hybridizations between unknown parental taxa. We have sequenced the genome of the diploid meiotic parthenogen Meloidogyne floridensis, and use a comparative genomic approach to test the hypothesis that this species was involved in the hybrid origin of the tropical mitotic parthenogen Meloidogyne incognita. Phylogenomic analysis of gene families from M. floridensis, M. incognita and an outgroup species Meloidogyne hapla was carried out to trace the evolutionary history of these species’ genomes, and we demonstrate that M. floridensis was one of the parental species in the hybrid origins of M. incognita. Analysis of the M. floridensis genome itself revealed many gene loci present in divergent copies, as they are in M. incognita, indicating that it too had a hybrid origin. The triploid M. incognita is shown to be a complex double-hybrid between M. floridensis and a third, unidentified, parent. The agriculturally important RKN have very complex origins involving the mixing of several parental genomes by hybridization and their extreme polyphagy and success in agricultural environments may be related to this hybridization, producing transgressive variation on which natural selection can act. It is now clear that studying RKN variation via individual marker loci may fail due to the species’ convoluted origins, and multi-species population genomics is essential to understand the hybrid diversity and adaptive variation of this important species complex. This comparative genomic analysis provides a compelling example of the importance and complexity of hybridization in generating animal species diversity more generally.
Lunt et al. (2014) The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PeerJ 2:e356 https://doi.org/10.7717/peerj.356
Heritability estimation of osteoarthritis in the pig-tailed macaque (Macaca nemestrina) with a look toward future data collection
We examine heritability estimation of an ordinal trait for osteoarthritis, using a population of pig-tailed macaques from the Washington National Primate Research Center (WaNPRC). This estimation is non-trivial, as the data consist of ordinal measurements on 16 intervertebral spaces throughout each macaque’s spinal cord, with many missing values. We examine the resulting heritability estimates from different model choices, and also perform a simulation study to compare the performance of heritability estimation with these different models under specific known parameter values. Under both the real data analysis and the simulation study, we find that heritability estimates from an assumption of normality of the trait differ greatly from those of ordered probit regression, which considers the ordinality of the trait. This finding indicates that some caution should be observed regarding model selection when estimating heritability of an ordinal quantity. Furthermore, we find evidence that our real data have little information for valid heritability estimation under ordered probit regression. We thus conclude with an exploration of sample size requirements for heritability estimation under this model. For an ordinal trait, an incorrect assumption of normality can lead to severely biased heritability estimation. Sample size requirements for heritability estimation of an ordinal trait under the threshold model depends on the pedigree structure, trait distribution and the degree of relatedness between each phenotyped individual. Our sample of 173 monkeys did not have enough information from which to estimate heritability, but estimable heritability can be obtained with as few as 180 related individuals under certain scenarios examined here.
Chi et al. (2014) Heritability estimation of osteoarthritis in the pig-tailed macaque (Macaca nemestrina) with a look toward future data collection. PeerJ 2:e373 https://doi.org/10.7717/peerj.373
Distinct expression patterns of Notch ligands, Dll1 and Dll4, in normal and inflamed mice intestine
Reports have suggested that the two Notch ligands, Dll1 and Dll4, are indispensable to maintain the homeostasis of the intestinal epithelium. However, within the intestinal epithelium, the precise distribution of the cells that express those ligands at the protein level remains largely unknown. Here, we show a series of immunohistochemical analysis through which we successfully identified mice intestinal epithelial cells (IECs) that endogenously express Dll1 or Dll4. Results showed that Dll1-positive (Dll1+ve) IECs reside exclusively within the crypt, whereas Dll4-positive (Dll4+ve) IECs can locate both in the crypt and in the villus of the small intestine. Also in the colon, Dll1+ve IECs resided at the lower part of the crypt, whereas Dll4+ve IECs resided at both upper and lower part of the crypt, including the surface epithelium. Both Dll1+ve and Dll4+ve IECs were ATOH1-positive, but Hes1-negative cells, and located adjacent to Hes1-positive cells within the crypts. A sub-population of both Dll1+ve and Dll4+ve IECs appeared to co-express Muc2, but rarely co-expressed other secretory lineage markers. However, as compared to Dll1+ve IECs, Dll4+ve IECs included larger number of Muc2-postive IECs, suggesting that Dll4 is more preferentially expressed by goblet cells. Also, we identified that Dll4 is expressed in the Paneth cells of the small intestine, whereas Dll1 and Dll4 is expressed in the c-kit-positive IECs of the colon, indicating that Dll1+ve and Dll4+ve IECs may contribute to constitute the intestinal stem cell niche. Compared to the normal colon, analysis of DSS-colitis showed that number of Dll1+ve IECs significantly decrease in the elongated crypts of the inflamed colonic mucosa. In sharp contrast, number of Dll4+ve IECs showed a significant increase in those crypts, which was accompanied by the increase in number of Hes1-positive IECs. Those Dll4+ve IECs were mostly found adjacent to the Hes1-positive IECs, suggesting that Dll4 may act as a major Notch ligand in the crypts of the inflamed colonic mucosa. Our results illustrate distinct expression patterns of Dll1 and Dll4 within the intestinal epithelium, and suggest that these two ligands may have different roles in normal and inflamed mucosa.
Shimizu et al. (2014) Distinct expression patterns of Notch ligands, Dll1 and Dll4, in normal and inflamed mice intestine. PeerJ 2:e370 https://doi.org/10.7717/peerj.370
Modulatory interactions between the default mode network and task positive networks in resting-state
The two major brain networks, i.e., the default mode network (DMN) and the task positive network, typically reveal negative and variable connectivity in resting-state. In the present study, we examined whether the connectivity between the DMN and different components of the task positive network were modulated by other brain regions by using physiophysiological interaction (PPI) on resting-state functional magnetic resonance imaging data. Spatial independent component analysis was first conducted to identify components that represented networks of interest, including the anterior and posterior DMNs, salience, dorsal attention, left and right executive networks. PPI analysis was conducted between pairs of these networks to identify networks or regions that showed modulatory interactions with the two networks. Both network-wise and voxel-wise analyses revealed reciprocal positive modulatory interactions between the DMN, salience, and executive networks. Together with the anatomical properties of the salience network regions, the results suggest that the salience network may modulate the relationship between the DMN and executive networks. In addition, voxel-wise analysis demonstrated that the basal ganglia and thalamus positively interacted with the salience network and the dorsal attention network, and negatively interacted with the salience network and the DMN. The results demonstrated complex modulatory interactions among the DMNs and task positive networks in resting-state, and suggested that communications between these networks may be modulated by some critical brain structures such as the salience network, basal ganglia, and thalamus.
Di et al. (2014) Modulatory interactions between the default mode network and task positive networks in resting-state. PeerJ 2:e367 https://doi.org/10.7717/peerj.367
Assessing the impact of human trampling on vegetation: a systematic review and meta-analysis of experimental evidence
Vegetation trampling resulting from recreation can adversely impact natural habitats, leading to the loss of vegetation and the degradation of plant communities. A considerable primary literature exists on this topic, therefore it is important to assess whether this accumulated evidence can be used to reach general conclusions concerning vegetation vulnerability to inform conservation management decisions. Experimental trampling studies on a global scale were retrieved using a systematic review methodology and synthesised using random effects meta-analysis. The relationships between vegetation recovery and each of initial vegetation resistance, trampling intensity, time for recovery, Raunkiaer life-form (perennating bud position), and habitat were tested using random effects multiple meta-regressions and subgroup analyses. The systematic search yielded 304 studies; of these, nine reported relevant randomized controlled experiments, providing 188 vegetation recovery effect sizes for analysis. The synthesis indicated there was significant heterogeneity in the impact of trampling on vegetation recovery. This was related to resistance and recovery time, and the interactions of these variables with Raunkiaer life-form, but was not strongly dependent on the intensity of the trampling experienced. The available evidence suggests that vegetation dominated by hemicryptophytes and geophytes recovers from trampling to a greater extent than vegetation dominated by other life-forms. Variation in effect within the chamaephyte, hemicryptophyte and geophyte life-form sub-groups was also explained by the initial resistance of vegetation to trampling, but not by trampling intensity. Intrinsic properties of plant communities appear to be the most important factors determining the response of vegetation to trampling disturbance. Specifically, the dominant Raunkiaer life-form of a plant community accounts for more variation in the resilience of communities to trampling than the intensity of the trampling experienced, suggesting that simple assessments based on this trait could guide decisions concerning sustainable access to natural areas. Methodological and reporting limitations must be overcome before more disparate types of evidence can be synthesised; this would enable more reliable extrapolation to non-study situations, and a more comprehensive understanding of how assessments of intrinsic plant traits can be used to underpin conservation management decisions concerning access.
Pescott et al. (2014) Assessing the impact of human trampling on vegetation: a systematic review and meta-analysis of experimental evidence. PeerJ 2:e360 https://doi.org/10.7717/peerj.360
An interactive three dimensional approach to anatomical description—the jaw musculature of the Australian laughing kookaburra (Dacelo novaeguineae)
The investigation of form-function relationships requires a detailed understanding of anatomical systems. Here we document the 3-dimensional morphology of the cranial musculoskeletal anatomy in the Australian Laughing Kookaburra Dacelo novaeguineae, with a focus upon the geometry and attachments of the jaw muscles in this species. The head of a deceased specimen was CT scanned, and an accurate 3D representation of the skull and jaw muscles was generated through manual segmentation of the CT scan images, and augmented by dissection of the specimen. We identified 14 major jaw muscles: 6 in the temporal group (M. adductor mandibulae and M. pseudotemporalis), 7 in the pterygoid group (M. pterygoideus dorsalis and M. pterygoideus ventralis), and the single jaw abductor M. depressor mandibulae. Previous descriptions of avian jaw musculature are hindered by limited visual representation and inconsistency in the nomenclature. To address these issues, we: (1) present the 3D model produced from the segmentation process as a digital, fully interactive model in the form of an embedded 3D image, which can be viewed from any angle, and within which major components can be set as opaque, transparent, or hidden, allowing the anatomy to be visualised as required to provide a detailed understanding of the jaw anatomy; (2) provide a summary of the nomenclature used throughout the avian jaw muscle literature. The approach presented here provides considerable advantages for the documentation and communication of detailed anatomical structures in a wide range of taxa.
Quayle et al. (2014) An interactive three dimensional approach to anatomical description—the jaw musculature of the Australian laughing kookaburra (Dacelo novaeguineae). PeerJ 2:e355 https://doi.org/10.7717/peerj.355