Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives
Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported. Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.
Strickler et al. (2015) Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PeerJ 3:e793 https://doi.org/10.7717/peerj.793
Patient exposure in the basic science classroom enhances differential diagnosis formation and clinical decision-making
Purpose. The authors proposed that introducing real patients into a pathology classroom early in medical education would help integrate fundamental principles and disease pathology with clinical presentation and medical history. Methods. Three patients with different pathologies described their history and presentation without revealing their diagnosis. Students were required to submit a differential diagnosis in writing, and then were able to ask questions to arrive at the correct diagnosis. Students were surveyed on the efficacy of patient-based learning. Results. Average student scores on the differential diagnosis assignments significantly improved 32% during the course. From the survey, 72% of students felt that patient encounters should be included in the pathology course next year. Seventy-four percent felt that the differential diagnosis assignments helped them develop clinical decision-making skills. Seventy-three percent felt that the experience helped them know what questions to ask patients. Eighty-six percent felt that they obtained a better understanding of patients’ social and emotional challenges. Discussion. Having students work through the process of differential diagnosis formulation when encountering a real patient and their clinical presentation improved clinical decision-making skills and integrated fundamental concepts with disease pathology during a basic science pathology course.
Peacock et al. (2015) Patient exposure in the basic science classroom enhances differential diagnosis formation and clinical decision-making. PeerJ 3:e809 https://doi.org/10.7717/peerj.809
Genetic divergence between populations of feral and domestic forms of a mosquito disease vector assessed by transcriptomics
Culex pipiens, an invasive mosquito and vector of West Nile virus in the US, has two morphologically indistinguishable forms that differ dramatically in behavior and physiology. Cx. pipiens form pipiens is primarily a bird-feeding temperate mosquito, while the sub-tropical Cx. pipiens form molestus thrives in sewers and feeds on mammals. Because the feral form can diapause during the cold winters but the domestic form cannot, the two Cx. pipiens forms are allopatric in northern Europe and, although viable, hybrids are rare. Cx. pipiens form molestus has spread across all inhabited continents and hybrids of the two forms are common in the US. Here we elucidate the genes and gene families with the greatest divergence rates between these phenotypically diverged mosquito populations, and discuss them in light of their potential biological and ecological effects. After generating and assembling novel transcriptome data for each population, we performed pairwise tests for nonsynonymous divergence (Ka) of homologous coding sequences and examined gene ontology terms that were statistically over-represented in those sequences with the greatest divergence rates. We identified genes involved in digestion (serine endopeptidases), innate immunity (fibrinogens and α-macroglobulins), hemostasis (D7 salivary proteins), olfaction (odorant binding proteins) and chitin binding (peritrophic matrix proteins). By examining molecular divergence between closely related yet phenotypically divergent forms of the same species, our results provide insights into the identity of rapidly-evolving genes between incipient species. Additionally, we found that families of signal transducers, ATP synthases and transcription regulators remained identical at the amino acid level, thus constituting conserved components of the Cx. pipiens proteome. We provide a reference with which to gauge the divergence reported in this analysis by performing a comparison of transcriptome sequences from conspecific (yet allopatric) populations of another member of the Cx. pipiens complex, Cx. quinquefasciatus.
Price et al. (2015) Genetic divergence between populations of feral and domestic forms of a mosquito disease vector assessed by transcriptomics. PeerJ 3:e807 https://doi.org/10.7717/peerj.807
Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria)
Marsupials or metatherians are a group of mammals that are distinct in giving birth to young at early stages of development and in having a prolonged investment in lactation. The group consists of nearly 350 extant species, including kangaroos, koala, possums, and their relatives. Marsupials are an old lineage thought to have diverged from early therian mammals some 160 million years ago in the Jurassic, and have a remarkable evolutionary and biogeographical history, with extant species restricted to the Americas, mostly South America, and to Australasia. Although the group has been the subject of decades of phylogenetic research, the marsupial tree of life remains controversial, with most studies focusing on only a fraction of the species diversity within the infraclass. Here we present the first Methaterian species-level phylogeny to include 80% of the extant marsupial species and five nuclear and five mitochondrial markers obtained from Genbank and a recently published retroposon matrix. Our primary goal is to provide a summary phylogeny that will serve as a tool for comparative research. We evaluate the extent to which the phylogeny recovers current phylogenetic knowledge based on the recovery of “benchmark clades” from prior studies—unambiguously supported key clades and undisputed traditional taxonomic groups. The Bayesian phylogenetic analyses recovered nearly all benchmark clades but failed to find support for the suborder Phalagiformes. The most significant difference with previous published topologies is the support for Australidelphia as a group containing Microbiotheriidae, nested within American marsupials. However, a likelihood ratio test shows that alternative topologies with monophyletic Australidelphia and Ameridelphia are not significantly different than the preferred tree. Although further data are needed to solidify understanding of Methateria phylogeny, the new phylogenetic hypothesis provided here offers a well resolved and detailed tool for comparative analyses, covering the majority of the known species richness of the group.
May-Collado et al. (2015) Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria). PeerJ 3:e805 https://doi.org/10.7717/peerj.805
Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities
Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed–Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy–Leucanthemum vulgare and Alsike clover–Trifolium hybridum). Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca) still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition.
Aleklett et al. (2015) Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities. PeerJ 3:e804 https://doi.org/10.7717/peerj.804
Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease–substrate interactions
Noroviruses are positive-sense single-stranded RNA viruses. They encode an NS6 protease that cleaves a viral polyprotein at specific sites to produce mature viral proteins. In an earlier study we obtained crystals of murine norovirus (MNV) NS6 protease in which crystal contacts were mediated by specific insertion of the C-terminus of one protein (which contains residues P5-P1 of the NS6-7 cleavage junction) into the peptide binding site of an adjacent molecule, forming an adventitious protease-product complex. We sought to reproduce this crystal form to investigate protease–substrate complexes by extending the C-terminus of NS6 construct to include residues on the C-terminal (P′) side of the cleavage junction. We report the crystallization and crystal structure determination of inactive mutants of murine norovirus NS6 protease with C-terminal extensions of one, two and four residues from the N-terminus of the adjacent NS7 protein (NS6 1′, NS6 2′, NS6 4′). We also determined the structure of a chimeric extended NS6 protease in which the P4-P4′ sequence of the NS6-7 cleavage site was replaced with the corresponding sequence from the NS2-3 cleavage junction (NS6 4′ 2|3).The constructs NS6 1′ and NS6 2′ yielded crystals that diffracted anisotropically. We found that, although the uncorrected data could be phased by molecular replacement, refinement of the structures stalled unless the data were ellipsoidally truncated and corrected with anisotropic B-factors. These corrections significantly improved phasing by molecular replacement and subsequent refinement.The refined structures of all four extended NS6 proteases are very similar in structure to the mature MNV NS6—and in one case reveal additional details of a surface loop. Although the packing arrangement observed showed some similarities to those observed in the adventitious protease-product crystals reported previously, in no case were specific protease–substrate interactions observed.
Fernandes et al. (2015) Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease–substrate interactions. PeerJ 3:e798 https://doi.org/10.7717/peerj.798
Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours
CITED1 is a non-DNA binding transcriptional co-regulator whose expression can distinguish the ‘proliferative’ from ‘invasive’ signature in the phenotype-switching model of melanoma. We have found that, in addition to other ‘proliferative’ signature genes, CITED1 expression is repressed by TGFβ while the ‘invasive’ signature genes are upregulated. In agreement, CITED1 positively correlates with MITF expression and can discriminate the MITF-high/pigmentation tumour molecular subtype in a large cohort (120) of melanoma cell lines. Interestingly, CITED1 overexpression significantly suppressed MITF promoter activation, mRNA and protein expression levels while MITF was transiently upregulated following siRNA mediated CITED1 silencing. Conversely, MITF siRNA silencing resulted in CITED1 downregulation indicating a reciprocal relationship. Whole genome expression analysis identified a phenotype shift induced by CITED1 silencing and driven mainly by expression of MITF and a cohort of MITF target genes that were significantly altered. Concomitantly, we found changes in the cell-cycle profile that manifest as transient G1 accumulation, increased expression of CDKN1A and a reduction in cell viability. Additionally, we could predict survival outcome by classifying primary melanoma tumours using our in vitro derived ‘CITED1-silenced’ gene expression signature. We hypothesize that CITED1 acts a regulator of MITF, functioning to maintain MITF levels in a range compatible with tumourigenesis.
Howlin et al. (2015) Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours. PeerJ 3:e788 https://doi.org/10.7717/peerj.788
Morphology of the jaw, suspensorial, and opercle musculature of Beloniformes and related species (Teleostei: Acanthopterygii), with a special reference to the m. adductor mandibulae complex
The taxon Beloniformes represents a heterogeneous group of teleost fishes that show an extraordinary diversity of jaw morphology. I present new anatomical descriptions of the jaw musculature in six selected beloniforms and four closely related species. A reduction of the external jaw adductor (A1) and a changed morphology of the intramandibular musculature were found in many Beloniformes. This might be correlated with the progressively reduced mobility of the upper and lower jaw bones. The needlefishes and sauries, which are characterised by extremely elongated and stiffened jaws, show several derived characters, which in combination enable the capture of fish at high velocity. The ricefishes are characterised by several derived and many plesiomorphic characters that make broad scale comparisons difficult. Soft tissue characters are highly diverse among hemiramphids and flying fishes reflecting the uncertainty about their phylogenetic position and interrelationship. The morphological findings presented herein may help to interpret future phylogenetic analyses using cranial musculature in Beloniformes.
Werneburg (2015) Morphology of the jaw, suspensorial, and opercle musculature of Beloniformes and related species (Teleostei: Acanthopterygii), with a special reference to the m. adductor mandibulae complex. PeerJ 3:e769 https://doi.org/10.7717/peerj.769
Paleoneuroanatomy of the European lambeosaurine dinosaur Arenysaurus ardevoli
The neuroanatomy of hadrosaurid dinosaurs is well known from North America and Asia. In Europe only a few cranial remains have been recovered that include the braincase. Arenysaurus is the first European endocast for which the paleoneuroanatomy has been studied. The resulting data have enabled us to draw ontogenetic, phylogenetic and functional inferences. Arenysaurus preserves the endocast and the inner ear. This cranial material was CT scanned, and a 3D-model was generated. The endocast morphology supports a general pattern for hadrosaurids with some characters that distinguish it to a subfamily level, such as a brain cavity that is anteroposteriorly shorter or the angle of the major axis of the cerebral hemisphere to the horizontal in lambeosaurines. Both these characters are present in the endocast of Arenysaurus. Osteological features indicate an adult ontogenetic stage, while some paleoneuroanatomical features are indicative of a subadult ontogenetic stage. It is hypothesized that the presence of puzzling mixture of characters that suggest different ontogenetic stages for this specimen may reflect some degree of dwarfism in Arenysaurus. Regarding the inner ear, its structure shows differences from the ornithopod clade with respect to the height of the semicircular canals. These differences could lead to a decrease in the compensatory movements of eyes and head, with important implications for the paleobiology and behavior of hadrosaurid taxa such as Edmontosaurus, Parasaurolophus and Arenysaurus. The endocranial morphology of European hadrosaurids sheds new light on the evolution of this group and may reflect the conditions in the archipelago where these animals lived during the Late Cretaceous.
Cruzado-Caballero et al. (2015) Paleoneuroanatomy of the European lambeosaurine dinosaur Arenysaurus ardevoli. PeerJ 3:e802 https://doi.org/10.7717/peerj.802
Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation
We have previously observed that methane supplied to lake sediment microbial communities as a substrate not only causes a response by bona fide methanotrophic bacteria, but also by non-methane-oxidizing bacteria, especially by members of the family Methylophilaceae. This result suggested that methane oxidation in this environment likely involves communities composed of different functional guilds, rather than a single type of microbe. To obtain further support for this concept and to obtain further insights into the factors that may define such partnerships, we carried out microcosm incubations with sediment samples from Lake Washington at five different oxygen tensions, while methane was supplied at the same concentration in each. Community composition was determined through 16S rRNA gene amplicon sequencing after 10 and 16 weeks of incubation. We demonstrate that, in support of our prior observations, the methane-consuming communities were represented by two major types: the methanotrophs of the family Methylococcaceae and by non-methanotrophic methylotrophs of the family Methylophilaceae. However, different species persisted under different oxygen tensions. At high initial oxygen tensions (150 to 225 µM) the major players were, respectively, species of the genera Methylosarcina and Methylophilus, while at low initial oxygen tensions (15 to 75 µM) the major players were Methylobacter and Methylotenera. These data suggest that oxygen availability is at least one major factor determining specific partnerships in methane oxidation. The data also suggest that speciation within Methylococcaceae and Methylophilaceae may be driven by niche adaptation tailored toward specific placements within the oxygen gradient.
Hernandez et al. (2015) Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation. PeerJ 3:e801 https://doi.org/10.7717/peerj.801
Language workbench user interfaces for data analysis
Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/).
Benson et al. (2015) Language workbench user interfaces for data analysis. PeerJ 3:e800 https://doi.org/10.7717/peerj.800
Interethnic diversity of the CD209 (rs4804803) gene promoter polymorphism in African but not American sickle cell disease
Elucidating the genomic diversity of CD209 gene promoter polymorphism could assist in clarifying disease pathophysiology as well as contribution to co-morbidities. CD209 gene promoter polymorphism has been shown to be associated with susceptibility to infection. We hypothesize that CD209 mutant variants occur at a higher frequency among Africans and in sickle cell disease. We analyzed the frequency of the CD209 gene (rs4804803) in healthy control and sickle cell disease (SCD) populations and determined association with disease. Genomic DNA was extracted from blood samples collected from 145 SCD and 231 control Africans (from Mali), 331 SCD and 379 control African Americans and 159 Caucasians. Comparative analysis among and between groups was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Per ethnic diversification, we found significant disparity in genotypic (23.4% versus 16.9% versus 3.2%) and allelic frequencies (48.7% versus 42.1% versus 19.8%) of the homozygote mutant variant of the CD209 (snp 309A/G) gene promoter between Africans, African Americans and Caucasians respectively. Comparative evaluation between disease and control groups reveal a significant difference in genotypic (10.4% versus 23.4%; p = 0.002) and allelic frequencies (39.7% versus 48.7%; p = 0.02) of the homozygote mutant variant in African SCD and healthy controls respectively, an observation that is completely absent among Americans. Comparing disease groups, we found no difference in the genotypic (p = 0.19) or allelic (p = 0.72) frequencies of CD209 homozygote mutant variant between Africans and Americans with sickle cell disease. The higher frequency of CD209 homozygote mutant variants in the African control group reveals a potential impairment of the capacity to mount an immune response to infectious diseases, and possibly delineate susceptibility to or severity of infectious co-morbidities within and between groups.
Noble et al. (2015) Interethnic diversity of the CD209 (rs4804803) gene promoter polymorphism in African but not American sickle cell disease. PeerJ 3:e799 https://doi.org/10.7717/peerj.799
An assessment of fracture resistance of three composite resin core build-up materials on three prefabricated non-metallic posts, cemented in endodontically treated teeth: an in vitro study
Endodontically treated teeth with excessive loss of tooth structure would require to be restored with post and core to enhance the strength and durability of the tooth and to achieve retention for the restoration. The non-metallic posts have a superior aesthetic quality. Various core build-up materials can be used to build-up cores on the posts placed in endodontically treated teeth. These materials would show variation in their bonding with the non-metallic posts thus affecting the strength and resistance to fracture of the remaining tooth structure. Aims. The aim of the study was to assess the fracture resistance of three composite resin core build-up materials on three prefabricated non-metallic posts, cemented in extracted endodontically treated teeth. Material and Methods. Forty-five freshly extracted maxillary central incisors of approximately of the same size and shape were selected for the study. They were divided randomly into 3 groups of 15 each, depending on the types of non-metallic posts used. Each group was further divided into 3 groups (A, B and C) of 5 samples each depending on three core build-up material used. Student’s unpaired ‘t’ test was also used to analyse and compare each group with the other groups individually, and decide whether their comparisons were statistically significant. Results. Luxacore showed the highest fracture resistance among the three core build-up materials with all the three posts systems. Ti-core had intermediate values of fracture resistance and Lumiglass had the least values of fracture resistance.
Kumar et al. (2015) An assessment of fracture resistance of three composite resin core build-up materials on three prefabricated non-metallic posts, cemented in endodontically treated teeth: an in vitro study. PeerJ 3:e795 https://doi.org/10.7717/peerj.795
Knowledge of malaria prevention among pregnant women and female caregivers of under-five children in rural southwest Nigeria
Introduction. The morbidity and mortality from malaria are still unacceptably high in the developing countries, especially among the vulnerable groups like pregnant women and under-five children, despite all control efforts. The knowledge about the preventive measures of malaria is an important preceding factor for the acceptance and use of malaria preventive measures like Insecticide Treated Nets (ITN) by community members. Therefore, this study assessed the knowledge of malaria prevention among caregivers of under-five children and pregnant women in a rural community in Southwest Nigeria. Methodology. This is part of a larger malaria prevention study in rural Southwest Nigeria. A descriptive cross-sectional survey was conducted among pregnant women and caregivers of under-five children in Igbo-Ora, a rural town in Southwest Nigeria using a semi-structured, interviewer-administered questionnaire. Information was obtained on knowledge of malaria prevention, and overall composite scores were computed for knowledge of malaria prevention and ITN use. Data were analyzed using SPSS version 16. Associations between variables were tested using a Chi-square with the level of statistical significance set at 5%. Results. Of the 631 respondents, 84.9% were caregivers of under-five children and 67.7% were married. Mean age was 27.7 ± 6.3 years with 53.4% aged between 20 and 29 years. Majority (91.1%) had at least primary school education and 60.2% were traders. Overall, 57.7% had poor knowledge of malaria prevention. A good proportion (83.5%) were aware of the use of ITN for malaria prevention while 30.6% had poor knowledge of its use. Respondents who were younger (<30 years), had at least primary education and earn <10,000/per month had significantly poor knowledge of ITN use in malaria prevention. Majority (60.0%) respondents had poor attitude regarding use of ITNs. Conclusion. This study showed that the knowledge of malaria prevention is still low among under-five caregivers and pregnant women in rural Southwest Nigeria despite current control measures. There is a need for concerted health education intervention to improve the knowledge of rural dwellers regarding malaria prevention, including the use of ITN. This will go a long way to improving the reported low level of ownership and utilization of ITN in the rural areas.
Adebayo et al. (2015) Knowledge of malaria prevention among pregnant women and female caregivers of under-five children in rural southwest Nigeria. PeerJ 3:e792 https://doi.org/10.7717/peerj.792
Quantification of Pseudomonas aeruginosa in multispecies biofilms using PMA-qPCR
Multispecies biofilms are an important healthcare problem and may lead to persistent infections. These infections are difficult to treat, as cells in a biofilm are highly resistant to antimicrobial agents. While increasingly being recognized as important, the properties of multispecies biofilms remain poorly studied. In order to do so, the quantification of the individual species is needed. The current cultivation-based approaches can lead to an underestimation of the actual cell number and are time-consuming. In the present study we set up a culture-independent approach based on propidium monoazide qPCR (PMA-qPCR) to quantify Pseudomonas aeruginosa in a multispecies biofilm. As a proof of concept, we explored the influence of the combined presence of Staphylococcus aureus, Streptococcus anginosus and Burkholderia cenocepacia on the antimicrobial susceptibility of P. aeruginosa using this PMA-qPCR approach.
Tavernier et al. (2015) Quantification of Pseudomonas aeruginosa in multispecies biofilms using PMA-qPCR. PeerJ 3:e787 https://doi.org/10.7717/peerj.787
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
High-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and the entailing genetic load of replacing alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with FST > 0.8 between regions whereas neutral loci show no differentiation. This is evidence of natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. The unfolded site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales vary with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show that times scales are faster than under the Kingman coalescent.
Árnason et al. (2015) Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models. PeerJ 3:e786 https://doi.org/10.7717/peerj.786
Perennial growth of hermatypic corals at Rottnest Island, Western Australia (32°S)
To assess the viability of high latitude environments as coral refugia, we report measurements of seasonal changes in seawater parameters (temperature, light, and carbonate chemistry) together with calcification rates for two coral species, Acropora yongei and Pocillopora damicornis from the southernmost geographical limit of these species at Salmon Bay, Rottnest Island (32°S) in Western Australia. Changes in buoyant weight were normalised to colony surface areas as determined from both X-ray computed tomography and geometric estimation. Extension rates for A. yongei averaged 51 ± 4 mm y−1 and were comparable to rates reported for Acroporid coral at other tropical and high latitude locations. Mean rates of calcification for both A. yongei and P. damicornis in winter were comparable to both the preceding and following summers despite a mean seasonal temperature range of ∼6 °C (18.2°–24.3 °C) and more than two-fold changes in the intensity of downwelling light. Seasonal calcification rates for A. yongei (1.31–2.02 mg CaCO3 cm−2 d−1) and P. damicornis (0.34–0.90 mg CaCO3 cm−2 d−1) at Salmon Bay, Rottnest Island were comparable to rates from similar taxa in more tropical environments; however, they appeared to decline sharply once summer temperatures exceeded 23 °C. A coral bleaching event observed in December 2013 provided further evidence of how coral at Rottnest Island are still vulnerable to the deleterious effects of episodic warming despite its high latitude location. Thus, while corals at Rottnest Island can sustain robust year-round rates of coral growth, even over cool winter temperatures of 18°–19 °C, there may be limits on the extent that such environments can provide refuge against the longer term impacts of anthropogenic climate change.
Ross et al. (2015) Perennial growth of hermatypic corals at Rottnest Island, Western Australia (32°S). PeerJ 3:e781 https://doi.org/10.7717/peerj.781
Maintenance energy requirements of odor detection, explosive detection and human detection working dogs
Despite their important role in security, little is known about the energy requirements of working dogs such as odor, explosive and human detection dogs. Previous researchers have evaluated the energy requirements of individual canine breeds as well as dogs in exercise roles such as sprint racing. This study is the first to evaluate the energy requirements of working dogs trained in odor, explosive and human detection. This retrospective study evaluated twenty adult dogs who maintained consistent body weights over a six month period. During this time, the average energy consumption was $136\pm 38~\mathrm{kcal}\cdot {\mathrm{BW}}_{\mathrm{kg}}^{0.75}$136±38kcal⋅BWkg0.75 or two times the calculated resting energy requirement ($\mathrm{RER}=70~\mathrm{kcal}\cdot {\mathrm{BW}}_{\mathrm{kg}}^{0.75}$RER=70kcal⋅BWkg0.75). No statistical differences were found between breeds, age or sex, but a statistically significant association (p = 0.0033, R-square = 0.0854) was seen between the number of searches a dog performs and their energy requirement. Based on this study’s population, it appears that working dogs have maintenance energy requirements similar to the 1974 National Research Council’s (NRC) maintenance energy requirement of $132~\mathrm{kcal}\cdot {\mathrm{BW}}_{\mathrm{kg}}^{0.75}$132kcal⋅BWkg0.75 (National Research Council (NRC), 1974) and the $139\pm 42~\mathrm{kcal}\cdot {\mathrm{BW}}_{\mathrm{kg}}^{0.75}$139±42kcal⋅BWkg0.75 reported for young laboratory beagles (Rainbird & Kienzle, 1990). Additional research is needed to determine if these data can be applied to all odor, explosive and human detection dogs and to determine if other types of working dogs (tracking, search and rescue etc.) have similar energy requirements.
Mullis et al. (2015) Maintenance energy requirements of odor detection, explosive detection and human detection working dogs. PeerJ 3:e767 https://doi.org/10.7717/peerj.767
Parcellating connectivity in spatial maps
A common goal in biological sciences is to model a complex web of connections using a small number of interacting units. We present a general approach for dividing up elements in a spatial map based on their connectivity properties, allowing for the discovery of local regions underlying large-scale connectivity matrices. Our method is specifically designed to respect spatial layout and identify locally-connected clusters, corresponding to plausible coherent units such as strings of adjacent DNA base pairs, subregions of the brain, animal communities, or geographic ecosystems. Instead of using approximate greedy clustering, our nonparametric Bayesian model infers a precise parcellation using collapsed Gibbs sampling. We utilize an infinite clustering prior that intrinsically incorporates spatial constraints, allowing the model to search directly in the space of spatially-coherent parcellations. After showing results on synthetic datasets, we apply our method to both functional and structural connectivity data from the human brain. We find that our parcellation is substantially more effective than previous approaches at summarizing the brain’s connectivity structure using a small number of clusters, produces better generalization to individual subject data, and reveals functional parcels related to known retinotopic maps in visual cortex. Additionally, we demonstrate the generality of our method by applying the same model to human migration data within the United States. This analysis reveals that migration behavior is generally influenced by state borders, but also identifies regional communities which cut across state lines. Our parcellation approach has a wide range of potential applications in understanding the spatial structure of complex biological networks.
Baldassano et al. (2015) Parcellating connectivity in spatial maps. PeerJ 3:e784 https://doi.org/10.7717/peerj.784
Spatial patterning and floral synchrony among trillium populations with contrasting histories of herbivory
We investigated the spatial patterning and floral synchrony within and among populations of a non-clonal, forest understory herb, Trillium catesbaei. Two populations of T. catesbaei within Great Smoky Mountains National Park were monitored for five years: Cades Cove (high deer abundance) and Whiteoak Sink (low deer abundance). All individuals within each population were mapped during year one and five. Only flowering and single-leaf juveniles were mapped during intervening years. Greater distances between flowering plants (plants currently in flower) and substantially lower population densities and smaller patch sizes were observed at Cades Cove versus Whiteoak Sink. However, with the exception of flowering plants, contrasting histories of herbivory did not appear to fundamentally alter the spatial patterning of the T. catesbaei population at Cades Cove, an area with a long and well-documented history of deer overabundance. Regardless of browse history, non-flowering life stages were significantly clustered at all spatial scales examined. Flowering plants were clustered in all years at Whiteoak Sink, but more often randomly distributed at Cades Cove, possibly as a result of their lower abundance. Between years, however, there was a positive spatial association between the locations of flowering plants at both sites. Flowering rate was synchronous between sites, but lagged a year behind favorable spring growing conditions, which likely allowed plants to allocate photosynthate from a favorable year towards flowering the subsequent year. Collectively, our results suggest that chronically high levels of herbivory may be associated with spatial patterning of flowering within populations of a non-clonal plant. They also highlight the persistence of underlying spatial patterns, as evidenced by high levels of spatial clustering among non-flowering individuals, and the pervasive, although muted in a population subjected to chronic herbivory, influence of precipitation and temperature on flowering in long-lived forest herbs.
Webster et al. (2015) Spatial patterning and floral synchrony among trillium populations with contrasting histories of herbivory. PeerJ 3:e782 https://doi.org/10.7717/peerj.782
Bird conservation would complement landslide prevention in the Central Andes of Colombia
Conservation and restoration priorities often focus on separate ecosystem problems. Inspired by the November 11th (2011) landslide event near Manizales, and the current poor results of Colombia’s Article 111 of Law 99 of 1993 as a conservation measure in this country, we set out to prioritize conservation and restoration areas where landslide prevention would complement bird conservation in the Central Andes. This area is one of the most biodiverse places on Earth, but also one of the most threatened. Using the case of the Rio Blanco Reserve, near Manizales, we identified areas for conservation where endemic and small-range bird diversity was high, and where landslide risk was also high. We further prioritized restoration areas by overlapping these conservation priorities with a forest cover map. Restoring forests in bare areas of high landslide risk and important bird diversity yields benefits for both biodiversity and people. We developed a simple landslide susceptibility model using slope, forest cover, aspect, and stream proximity. Using publicly available bird range maps, refined by elevation, we mapped concentrations of endemic and small-range bird species. We identified 1.54 km2 of potential restoration areas in the Rio Blanco Reserve, and 886 km2 in the Central Andes region. By prioritizing these areas, we facilitate the application of Article 111 which requires local and regional governments to invest in land purchases for the conservation of watersheds.
Ocampo-Peñuela et al. (2015) Bird conservation would complement landslide prevention in the Central Andes of Colombia. PeerJ 3:e779 https://doi.org/10.7717/peerj.779
Computational analysis of the LRRK2 interactome
LRRK2 was identified in 2004 as the causative protein product of the Parkinson’s disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson’s disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson’s. Genome-wide association studies (GWAs) have, more recently, reported single nucleotide polymorphisms (SNPs) around the LRRK2 locus to be associated with risk of developing sporadic Parkinson’s disease and inflammatory bowel disorder. The functional research that has followed these genetic breakthroughs has generated an extensive literature regarding LRRK2 pathophysiology; however, there is still no consensus as to the biological function of LRRK2. To provide insight into the aspects of cell biology that are consistently related to LRRK2 activity, we analysed the plethora of candidate LRRK2 interactors available through the BioGRID and IntAct data repositories. We then performed GO terms enrichment for the LRRK2 interactome. We found that, in two different enrichment portals, the LRRK2 interactome was associated with terms referring to transport, cellular organization, vesicles and the cytoskeleton. We also verified that 21 of the LRRK2 interactors are genetically linked to risk for Parkinson’s disease or inflammatory bowel disorder. The implications of these findings are discussed, with particular regard to potential novel areas of investigation.
Manzoni et al. (2015) Computational analysis of the LRRK2 interactome. PeerJ 3:e778 https://doi.org/10.7717/peerj.778
Early archosauromorph remains from the Permo-Triassic Buena Vista Formation of north-eastern Uruguay
The Permo-Triassic archosauromorph record is crucial to understand the impact of the Permo-Triassic mass extinction on the early evolution of the group and its subsequent dominance in Mesozoic terrestrial ecosystems. However, the Permo-Triassic archosauromorph record is still very poor in most continents and hampers the identification of global macroevolutionary patterns. Here we describe cranial and postcranial bones from the Permo-Triassic Buena Vista Formation of northeastern Uruguay that contribute to increase the meagre early archosauromorph record from South America. A basioccipital fused to both partial exoccipitals and three cervical vertebrae are assigned to Archosauromorpha based on apomorphies or a unique combination of characters. The archosauromorph remains of the Buena Vista Formation probably represent a multi-taxonomic assemblage composed of non-archosauriform archosauromorphs and a ‘proterosuchid-grade’ animal. This assemblage does not contribute in the discussion of a Late Permian or Early Triassic age for the Buena Vista Formation, but reinforces the broad palaeobiogeographic distribution of ‘proterosuchid grade’ diapsids in Permo-Triassic beds worldwide.
Ezcurra et al. (2015) Early archosauromorph remains from the Permo-Triassic Buena Vista Formation of north-eastern Uruguay. PeerJ 3:e776 https://doi.org/10.7717/peerj.776
Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method
Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6–99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis.
Machado et al. (2015) Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method. PeerJ 3:e780 https://doi.org/10.7717/peerj.780
First record of multi-species synchronous coral spawning from Malaysia
Knowledge about the timing and synchrony of coral spawning has important implications for both the ecology and management of coral reef ecosystems. Data on the timing of spawning and extent of synchrony, however, are still lacking for many coral reefs, particularly from equatorial regions and from locations within the coral triangle. Here we present the first documentation of a multi-species coral spawning event from reefs around Pulau Tioman, Peninsular Malaysia, a popular diving and tourist destination located on the edge of the coral triangle. At least 8 coral species from 3 genera (Acropora, Montipora and Porites) participated in multi-species spawning over five nights in April 2014, between two nights before and two nights after the full moon. In addition, two Acropora species were witnessed spawning one night prior to the full moon in October 2014. While two of the Acropora species that reproduced in April (A. millepora and A. nasuta) exhibited highly synchronous spawning (100% of sampled colonies), two other common species (A. hyacinthus and A. digitifera) did not contain visible eggs in the majority of colonies sampled (i.e., <15% of colonies) in either April or October, suggesting that these species spawn at other times of the year. To the best of our knowledge, this is the first detailed documented observation of multi-species coral spawning from reefs in Malaysia. These data provide further support for the contention that this phenomenon is a feature of all speciose coral assemblages, including equatorial reefs. More research is needed, however, to determine the seasonal cycles and extent of spawning synchrony on these reefs and elsewhere in Malaysia.
Chelliah et al. (2015) First record of multi-species synchronous coral spawning from Malaysia. PeerJ 3:e777 https://doi.org/10.7717/peerj.777
Body image, visual working memory and visual mental imagery
Body dissatisfaction (BD) is a highly prevalent feature amongst females in society, with the majority of individuals regarding themselves to be overweight compared to their personal ideal, and very few self-describing as underweight. To date, explanations of this dramatic pattern have centred on extrinsic social and media factors, or intrinsic factors connected to individuals’ knowledge and belief structures regarding eating and body shape, with little research examining links between BD and basic cognitive mechanisms. This paper reports a correlational study in which visual and executive cognitive processes that could potentially impact on BD were assessed. Visual memory span and self-rated visual imagery were found to be predictive of BD, alongside a measure of inhibition derived from the Stroop task. In contrast, spatial memory and global precedence were not related to BD. Results are interpreted with reference to the influential multi-component model of working memory.
Darling et al. (2015) Body image, visual working memory and visual mental imagery. PeerJ 3:e775 https://doi.org/10.7717/peerj.775
Your wish is my command! The influence of symbolic modelling on preschool children’s delay of gratification
The ability of children to delay gratification is correlated with a range of positive outcomes in adulthood, showing the potential impact of helping young children increase their competence in this area. This study investigated the influence of symbolic models on the self-control of 3-year old children. Eighty-three children were randomly assigned to one of three modelling conditions: personal storytelling, impersonal storytelling, and control. Children were tested on the delay-of-gratification maintenance paradigm both before and after being exposed to a symbolic model or control condition. Repeated measures ANOVA revealed no significant differences between the two storytelling groups and the control group, indicating that the symbolic models did not influence children’s ability to delay gratification. A serendipitous finding showed a positive relationship between the ability of children to wait and their production and accurate use of temporal terms, which was more pronounced in girls than boys. This finding may be an indication that a higher temporal vocabulary is linked to a continuous representation of the self in time, facilitating a child’s representation of the future-self receiving a larger reward than what the present-self could receive.
Kumst et al. (2015) Your wish is my command! The influence of symbolic modelling on preschool children’s delay of gratification. PeerJ 3:e774 https://doi.org/10.7717/peerj.774
Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors
Biogenic amine receptors play critical roles in regulating behavior and physiology in both vertebrates and invertebrates, particularly within the central nervous system. Members of the G-protein coupled receptor (GPCR) family, these receptors interact with endogenous bioamine ligands such as dopamine, serotonin, and epinephrine, and are targeted by a wide array of pharmaceuticals. Despite the clear clinical and biological importance of these receptors, their evolutionary history remains poorly characterized. In particular, the relationships among biogenic amine receptors and any specific evolutionary constraints acting within distinct receptor subtypes are largely unknown. To advance and facilitate studies in this receptor family, we have constructed a comprehensive, high-quality sequence alignment of vertebrate biogenic amine receptors. In particular, we have integrated a traditional multiple sequence approach with robust structural domain predictions to ensure that alignment columns accurately capture the highly-conserved GPCR structural domains, and we demonstrate how ignoring structural information produces spurious inferences of homology. Using this alignment, we have constructed a structurally-partitioned maximum-likelihood phylogeny from which we deduce novel biogenic amine receptor relationships and uncover previously unrecognized lineage-specific receptor clades. Moreover, we find that roughly 1% of the 3039 sequences in our final alignment are either misannotated or unclassified, and we propose updated classifications for these receptors. We release our comprehensive alignment and its corresponding phylogeny as a resource for future research into the evolution and diversification of biogenic amine receptors.
Spielman et al. (2015) Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors. PeerJ 3:e773 https://doi.org/10.7717/peerj.773
Initial evaluation of nighttime restlessness in a naturally occurring canine model of osteoarthritis pain
Chronic pain due to osteoarthritis (OA) can lead to significant disruption of sleep and increased restlessness. Our objective was to assess whether naturally occurring canine OA is associated with nighttime restlessness and so has potential as a model of OA-associated sleep disturbance. The study was designed as a two-part prospective masked, placebo-controlled study using client-owned dogs (Part A n = 60; Part B n = 19). Inclusion criteria consisted of OA-associated joint pain and mobility impairment. The primary outcome measure for both parts was nighttime accelerometry. In Part B, quality of sleep was assessed using a clinical metrology instrument (Sleep and Night Time Restlessness Evaluation Score, SNoRE). Part A included dogs receiving two weeks of non-steroidal anti-inflammatory drug (NSAID) preceded with two weeks of no treatment. Part B was a crossover study, with NSAID/placebo administered for two weeks followed by a washout period of one week and another two weeks of NSAID/placebo. Repeated measures analysis of variance was used to assess differences between baseline and treatment. There were no significant changes in accelerometry-measured nighttime activity as a result of NSAID administration. SNoRE measures indicated significant improvements in aspects of the quality of nighttime sleep that did not involve obvious movement. These results reflect the few similar studies in human OA patients. Although accelerometry does not appear to be useful, this model has potential to model the human pain-related nighttime sleep disturbance, and other outcome measures should be explored in this model.
Knazovicky et al. (2015) Initial evaluation of nighttime restlessness in a naturally occurring canine model of osteoarthritis pain. PeerJ 3:e772 https://doi.org/10.7717/peerj.772
X-to-autosome expression and msl-2 transcript abundance correlate among Drosophila melanogaster somatic tissues
In Drosophila melanogaster, the male-specific lethal (MSL) complex has been studied extensively for its role in upregulating male X-linked genes. Recent advances in high-throughput technologies have improved our understanding of how the MSL complex mediates dosage compensation through chromosome-wide chromatin modifications. Most studies, however, have focused on cell line models that cannot reflect any potential heterogeneity of in vivo dosage compensation. Comparisons between cell line and organismal gene-level dosage compensation upregulation suggest the possibility of variation in MSL complex activity among somatic tissues. We hypothesize the degree, up to but not exceeding 2-fold, to which the MSL complex upregulates male X-linked genes varies quantitatively by tissue type. In this model, MSL complex abundance acts as a rheostat to control the extent of upregulation. Using publicly available expression data, we provide evidence for our model in Drosophila somatic tissues. Specifically, we find X-to-autosome expression correlates with the tissue-specific expression of msl-2 which encodes an essential male-specific component of the MSL complex. This result suggests MSL complex mediated dosage compensation varies quantitatively by tissue type. Furthermore, this result has consequences for models explaining the organismal-scale molecular and evolutionary consequences of MSL-mediated dosage compensation.
Vensko II et al. (2015) X-to-autosome expression and msl-2 transcript abundance correlate among Drosophila melanogaster somatic tissues. PeerJ 3:e771 https://doi.org/10.7717/peerj.771
Significance and value of non-traded ecosystem services on farmland
Background. Ecosystem services (ES) generated within agricultural landscapes, including field boundaries, are vital for the sustainable supply of food and fibre. However, the value of ES in agriculture has not been quantified experimentally and then extrapolated globally. Methods. We quantified the economic value of two key but contrasting ES (biological control of pests and nitrogen mineralisation) provided by non-traded non-crop species in ten organic and ten conventional arable fields in New Zealand using field experiments. The arable crops grown, same for each organic and conventional pair, were peas (Pisum sativum), beans (Phaseolus vulgaris), barley (Hordeum vulgare), and wheat (Triticum aestivum). Organic systems were chosen as comparators not because they are the only forms of sustainable agriculture, but because they are subject to easily understood standards. Results. We found that organic farming systems depended on fewer external inputs and produced outputs of energy and crop dry matter generally less than but sometimes similar to those of their conventional counterparts. The economic values of the two selected ES were greater for the organic systems in all four crops, ranging from US$ 68–200 ha−1 yr−1 for biological control of pests and from US$ 110–425 ha−1yr−1 for N mineralisation in the organic systems versus US$ 0 ha−1yr−1 for biological control of pests and from US$ 60–244 ha−1yr−1 for N mineralisation in the conventional systems. The total economic value (including market and non-market components) was significantly greater in organic systems, ranging from US$ 1750–4536 ha−1yr−1, with US$ 1585–2560 ha−1yr−1 in the conventional systems. The non-market component of the economic value in organic fields was also significantly higher than those in conventional fields. Discussion. To illustrate the potential magnitude of these two ES to temperate farming systems and agricultural landscapes elsewhere, we then extrapolate these experimentally derived figures to the global temperate cropping area of the same arable crops. We found that the extrapolated net value of the these two services provided by non-traded species could exceed the combined current global costs of pesticide and fertiliser inputs, even if utilised on only 10% of the global arable area. This approach strengthens the case for ES–rich agricultural systems, provided by non-traded species to global agriculture.
Sandhu et al. (2015) Significance and value of non-traded ecosystem services on farmland. PeerJ 3:e762 https://doi.org/10.7717/peerj.762
Concordance and discordance of sequence survey methods for molecular epidemiology
The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.
Castro-Nallar et al. (2015) Concordance and discordance of sequence survey methods for molecular epidemiology. PeerJ 3:e761 https://doi.org/10.7717/peerj.761
The effects of venting and decompression on Yellow Tang (Zebrasoma flavescens) in the marine ornamental aquarium fish trade
Each year, over 45 countries export 30 million fish from coral reefs as part of the global marine ornamental aquarium trade. This catch volume is partly influenced by collection methods that cause mortality. Barotrauma in fish resulting from forced ascent from depth can contribute to post-collection mortality. However, implementing decompression stops during ascent can prevent barotrauma. Conversely, venting (puncturing the swim bladder to release expanded internal gas) following ascent can mitigate some signs of barotrauma like positive buoyancy. Here, we evaluate how decompression and venting affect stress and mortality in the Yellow Tang (Zebrasoma flavescens). We examined the effects of three ascent treatments, each with decompression stops of varying frequency and duration, coupled with or without venting, on sublethal effects and mortality using histology and serum cortisol measurements. In fish subjected to ascent without decompression stops or venting, a mean post-collection mortality of 6.2% occurred within 24 h of capture. Common collection methods in the fishery, ascent without decompression stops coupled with venting, or one long decompression stop coupled with venting, resulted in no mortality. Histopathologic examination of heart, liver, head kidney, and swim bladder tissues in fish 0d and 21d post-collection revealed no significant barotrauma- or venting-related lesions in any treatment group. Ascent without decompression stops resulted in significantly higher serum cortisol than ascent with many stops, while venting alone did not affect cortisol. Future work should examine links in the supply chain following collection to determine if further handling and transport stressors affect survivorship and sublethal effects.
Munday et al. (2015) The effects of venting and decompression on Yellow Tang (Zebrasoma flavescens) in the marine ornamental aquarium fish trade. PeerJ 3:e756 https://doi.org/10.7717/peerj.756
Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing
The ability of Shiga toxin-producing Escherichia coli (STEC) to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx) subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS) of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains were overcome by using two complementary bioinformatics methods: mapping and de novo assembly. We compared the WGS analysis with the results obtained using a PCR approach and investigated the diversity within and between the subtypes. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444) concordance between PCR and WGS. When common source strains were excluded, 236/349 strains of STEC O157 had multiple copies of different Stx subtypes and 54 had multiple copies of the same Stx subtype. Of those strains harbouring multiple copies of the same Stx subtype, 33 had variants between the alleles while 21 had identical copies. Strains harbouring Stx2a only were most commonly found to have multiple alleles of the same subtype (42%). Both the PCR and WGS approach to stx subtyping provided a good level of sensitivity and specificity. In addition, the WGS data also showed there were a significant proportion of strains harbouring multiple alleles of the same Stx subtype associated with clinical disease in England.
Ashton et al. (2015) Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing. PeerJ 3:e739 https://doi.org/10.7717/peerj.739
The impact of stress on financial decision-making varies as a function of depression and anxiety symptoms
Stress can precipitate the onset of mood and anxiety disorders. This may occur, at least in part, via a modulatory effect of stress on decision-making. Some individuals are, however, more resilient to the effects of stress than others. The mechanisms underlying such vulnerability differences are nevertheless unknown. In this study we attempted to begin quantifying individual differences in vulnerability by exploring the effect of experimentally induced stress on decision-making. The threat of unpredictable shock was used to induce stress in healthy volunteers (N = 47) using a within-subjects, within-session design, and its impact on a financial decision-making task (the Iowa Gambling Task) was assessed alongside anxious and depressive symptomatology. As expected, participants learned to select advantageous decks and avoid disadvantageous decks. Importantly, we found that stress provoked a pattern of harm-avoidant behaviour (decreased selection of disadvantageous decks) in individuals with low levels of trait anxiety. By contrast, individuals with high trait anxiety demonstrated the opposite pattern: stress-induced risk-seeking (increased selection of disadvantageous decks). These contrasting influences of stress depending on mood and anxiety symptoms might provide insight into vulnerability to common mental illness. In particular, we speculate that those who adopt a more harm-avoidant strategy may be better able to regulate their exposure to further environmental stress, reducing their susceptibility to mood and anxiety disorders.
Robinson et al. (2015) The impact of stress on financial decision-making varies as a function of depression and anxiety symptoms. PeerJ 3:e770 https://doi.org/10.7717/peerj.770
A meta-analysis of plant facilitation in coastal dune systems: responses, regions, and research gaps
Empirical studies in salt marshes, arid, and alpine systems support the hypothesis that facilitation between plants is an important ecological process in severe or ‘stressful’ environments. Coastal dunes are both abiotically stressful and frequently disturbed systems. Facilitation has been documented, but the evidence to date has not been synthesized. We did a systematic review with meta-analysis to highlight general research gaps in the study of plant interactions in coastal dunes and examine if regional and local factors influence the magnitude of facilitation in these systems. The 32 studies included in the systematic review were done in coastal dunes located in 13 countries around the world but the majority was in the temperate zone (63%). Most of the studies adopt only an observational approach to make inferences about facilitative interactions, whereas only 28% of the studies used both observational and experimental approaches. Among the factors we tested, only geographic region mediates the occurrence of facilitation more broadly in coastal dune systems. The presence of a neighbor positively influenced growth and survival in the tropics, whereas in temperate and subartic regions the effect was neutral for both response variables. We found no evidence that climatic and local factors, such as life-form and life stage of interacting plants, affect the magnitude of facilitation in coastal dunes. Overall, conclusions about plant facilitation in coastal dunes depend on the response variable measured and, more broadly, on the geographic region examined. However, the high variability and the limited number of studies, especially in tropical region, indicate we need to be cautious in the generalization of the conclusions. Anyway, coastal dunes provide an important means to explore topical issues in facilitation research including context dependency, local versus regional drivers of community structure, and the importance of gradients in shaping the outcome of net interactions.
Castanho et al. (2015) A meta-analysis of plant facilitation in coastal dune systems: responses, regions, and research gaps. PeerJ 3:e768 https://doi.org/10.7717/peerj.768
Mineral derivatives in alleviating oral mucositis during cancer therapy: a systematic review
Objectives. Oral mucositis (mouth ulcers) is a cancer therapy side effect. Costly treatment interventions are often neglected in favor of cost-effective agents. This review assessed the general efficacy of mineral derivatives (a cost-effective agent) in alleviating oral mucositis (OM) during cancer therapy compared to the standard care, or placebo—including a decision tree to aide healthcare workers. Data Sources. Electronic searches of MEDLINE via OVID, EMBASE, CENTRAL, CANCERLIT via PubMed, and CINAHL via EBSCO (year 2000 to 11 September 2014) were undertaken for randomised controlled trials. A meta-search strategy extracted content from aggregate online databases. Review Methods. Randomized controlled trials were assessed (participants, intervention, outcome, results, and risk of bias) for inclusion. The author abstracted binary and continuous data synthesised to Hedges’ g in a random effects model. The primary outcome measures were severity (incidence of peak oral mucositis, duration of oral mucositis, and time to onset); secondary outcome measures were the incidence of pain, and analgesic use. Serum mineral levels, total parenteral nutrition, and adverse events were discussed. The decision tree was mapped using sensitivity, specificity, pre-test and post-test Bayesian probability. Results. 1027 citations were identified and 16 studies were included (n = 1120; mean age 49 years). Cancer therapies consisted of chemotherapy, radiotherapy, chemo-radiotherapy, or hematopoietic stem cell transplantation. Outcome mineral derivatives were zinc (n = 549), calcium phosphate (n = 227), povidone-iodine (n = 228), or selenium (n = 116). Severity was measured across variable OM grading systems: In 13 studies, individuals in treatment groups (n = 958) experienced peak OM less than controls (g = −0.47, 95% CI −0.7 to −0.2, p = 0.0006); time to OM onset was significantly delayed in treatment than controls (g = −0.51, 95% CI−0.8 to −0.2, p = 0.0002; five studies); OM mean duration, pain incidences, or analgesics use was not significant. The decision analysis favored selenium. Conclusion. The general positive effect trend suggests individuals taking mineral derivatives during cancer therapies are less likely to experience peak OM than those without. However, significant bias and heterogeneity indicates the need for developing further methods in account of diverse protocols and include novel recordings (serum mineral levels and cell signals) in estimating a uniform true effect.
Lee (2015) Mineral derivatives in alleviating oral mucositis during cancer therapy: a systematic review. PeerJ 3:e765 https://doi.org/10.7717/peerj.765
Testing the influence of environmental heterogeneity on fish species richness in two biogeographic provinces
Environmental homogenization in coastal ecosystems impacted by human activities may be an important factor explaining the observed decline in fish species richness. We used fish community data (>200 species) from extensive surveys conducted in two biogeographic provinces (extent >1,000 km) in North America to quantify the relationship between fish species richness and local (grain <10 km2) environmental heterogeneity. Our analyses are based on samples collected at nearly 800 stations over a period of five years. We demonstrate that fish species richness in coastal ecosystems is associated locally with the spatial heterogeneity of environmental variables but not with their magnitude. The observed effect of heterogeneity on species richness was substantially greater than that generated by simulations from a random placement model of community assembly, indicating that the observed relationship is unlikely to arise from veil or sampling effects. Our results suggest that restoring or actively protecting areas of high habitat heterogeneity may be of great importance for slowing current trends of decreasing biodiversity in coastal ecosystems.
Massicotte et al. (2015) Testing the influence of environmental heterogeneity on fish species richness in two biogeographic provinces. PeerJ 3:e760 https://doi.org/10.7717/peerj.760
The monophyly of Susisuchidae (Crocodyliformes) and its phylogenetic placement in Neosuchia
Eusuchian crocodyliforms, which include all living crocodylians, have historically been characterized by two anatomical specializations: a ball-in-socket vertebral joint and an extensive secondary hard palate with a pterygoid-bound internal choana. The Early Cretaceous neosuchian clade Susisuchidae is typically regarded as phylogenetically near Eusuchia. The putative susisuchid Isisfordia duncani was initially described as a transitional form exhibiting incipient versions of these eusuchian traits. Here we examine aspects of the morphology of Isisfordia and comment on the morphology of its putative sister taxon Susisuchus. Our reexamination supports the notion of Isisfordia possessing transitional vertebral morphology but we present a new interpretation of its palate construction that shows it to be more plesiomorphic than previously thought. The secondary choana of Isisfordia is not pterygoid bound. Instead, long palatines expand distally lapping under the pterygoid to form the anterior border of the choana as is common among many advanced neosuchians. Incorporation of these observations into an expanded phylogenetic dataset of neosuchian crocodyliforms results in a new phylogenetic hypothesis for Susisuchidae. Isisfordia and Susisuchus form a monophyletic Susisuchidae that sits near the base of Neosuchia, and is not the sister taxon of Eusuchia.
Turner et al. (2015) The monophyly of Susisuchidae (Crocodyliformes) and its phylogenetic placement in Neosuchia. PeerJ 3:e759 https://doi.org/10.7717/peerj.759
Weight–length relationships and Fulton’s condition factors of skipjack tuna (Katsuwonus pelamis) in the western and central Pacific Ocean
This paper describes the weight–length relationships (WLRs) and Fulton’s condition factors (K) of skipjack tuna (Katsuwonus pelamis) in purse seine fisheries from three cruises in the western and central Pacific Ocean (WCPO): August–September 2009 (AS09), November–December 2012 (ND12), and June–July 2013 (JJ13). The fork length and weight of a total of 1678 specimens were measured. The results showed that the fork length of more than 70% of specimens was below 60 cm (76% in AS09, 87% in ND12, and 73% in JJ13). The coefficient b in the combined sex group was 3.367, 3.300 and 3.234 in JJ13, AS09 and ND12, respectively. The b values of WLRs when fork length was >60 cm were significantly less than 3 (P = 0.062), but when fork length was <60 cm they were significantly greater than 3 (P = 0.028). The K value ranges of JJ13, AS09 and ND12 in different fork length groups were 1.3–1.84 (1.62 ± 0.18), 1.57–2.02 (1.86 ± 0.15), and 1.44–1.78 (0.65 ± 0.13), respectively. Moreover, K values in different fork length classes for each cruise had one turning point: 60–65 cm for JJ13; 60–65 cm for ND12; and 55–60 cm for AS09. The results of this study provide basic information on the WLRs and K values of skipjack tuna in different seasons and growth phases in the WCPO, which are useful for fishery biologists and fishery managers.
Jin et al. (2015) Weight–length relationships and Fulton’s condition factors of skipjack tuna (Katsuwonus pelamis) in the western and central Pacific Ocean. PeerJ 3:e758 https://doi.org/10.7717/peerj.758
Ultrastructural study of sperm cells in Acanthocolpidae: the case of Stephanostomum murielae and Stephanostomoides tenuis (Digenea)
The mature spermatozoa of Stephanostomum murielae and Stephanostomoides tenuis are described by transmission electron microscopy. They present several ultrastructural features previously reported in other digeneans. Their spermatozoa possess two axonemes of different length showing the 9 + ‘1’ trepaxonematan pattern, four attachment zones, two mitochondria (with an anterior moniliform one in S. murielae), a nucleus, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies and granules of glycogen. The main differences between the mature spermatozoon of S. murielae and S. tenuis are the maximum number of cortical microtubules, the morphology of the anterior spermatozoon extremity and the anterior mitochondrion. This study is the first concerning members of the family Acanthocolpidae. The main ultrastructural characteristics discussed are the morphology of the anterior and posterior spermatozoon extremities, antero-lateral electron dense material, external ornamentations, spine-like bodies and number and morphology of mitochondria. In addition, the phylogenetic significance of all these ultrastructural features is discussed and compared to molecular results in order to highlight the complex relationships in the Digenea.
Bakhoum et al. (2015) Ultrastructural study of sperm cells in Acanthocolpidae: the case of Stephanostomum murielae and Stephanostomoides tenuis (Digenea). PeerJ 3:e744 https://doi.org/10.7717/peerj.744
Nurturing 21st century physician knowledge, skills and attitudes with medical home innovations: the Wright Center for Graduate Medical Education teaching health center curriculum experience
Purpose. The effect of patient centered medical home (PCMH) curriculum interventions on residents’ self-reported and demonstrated knowledge, skills and attitudes in PCMH competency arenas (KSA) is lacking in the literature. This study aimed to assess the impact of PCMH curricular innovations on the KSA of Internal Medicine residents. Methods. Twenty four (24) Internal Medicine residents—12 Traditional (TR) track residents and 12 Teaching Health Center (THC) track residents—began training in Academic Year (AY) 2011 at the Wright Center for Graduate Medical Education (WCGME). They were followed through AY2013, covering three years of training. PCMH curricular innovations were focally applied July 2011 until May 2012 to THC residents. These curricular innovations were spread program-wide in May 2012. Semi-annual, validated PCMH Clinician Assessments assessing KSA were started in AY2011 and were completed by all residents. Results. Mean KSA scores of TR residents were similar to those of THC residents at baseline for all PCMH competencies. In May 2012, mean scores of THC residents were significantly higher than TR residents for most KSA. After program-wide implementation of PCMH innovations, mean scores of TR residents for all KSA improved and most became equalized to those of THC residents. Globally improved KSA scores of THC and TR residents were maintained through May 2014, with the majority of improvements above baseline and reaching statistical significance. Conclusions. PCMH curricular innovations inspired by Health Resources and Services Administration (HRSA’s) Teaching Health Center funded residency program expansion quickly and consistently improved the KSA of Internal Medicine residents.
Thomas-Hemak et al. (2015) Nurturing 21st century physician knowledge, skills and attitudes with medical home innovations: the Wright Center for Graduate Medical Education teaching health center curriculum experience. PeerJ 3:e766 https://doi.org/10.7717/peerj.766
Pronounced and prevalent intersexuality does not impede the ‘Demon Shrimp’ invasion
Crustacean intersexuality is widespread and often linked to infection by sex-distorting parasites. However, unlike vertebrate intersexuality, its association with sexual dysfunction is unclear and remains a matter of debate. The ‘Demon Shrimp,’ Dikerogammarus haemobaphes, an amphipod that has invaded continental waterways, has recently become widespread in Britain. Intersexuality has been noted in D. haemobaphes but not investigated further. We hypothesise that a successful invasive population should not display a high prevalence of intersexuality if this condition represents a truly dysfunctional phenotype. In addition, experiments have indicated that particular parasite burdens in amphipods may facilitate invasions. The rapid and ongoing invasion of British waterways represents an opportunity to determine whether these hypotheses are consistent with field observations. This study investigates the parasites and sexual phenotypes of D. haemobaphes in British waterways, characterising parasite burdens using molecular screening, and makes comparisons with the threatened Gammarus pulex natives. We reveal that invasive and native populations have distinct parasitic profiles, suggesting the loss of G. pulex may have parasite-mediated eco-system impacts. Furthermore, the parasite burdens are consistent with those previously proposed to facilitate biological invasions. Our study also indicates that while no intersexuality occurs in the native G. pulex, approximately 50% of D. haemobaphes males present pronounced intersexuality associated with infection by the microsporidian Dictyocoela berillonum. This unambiguously successful invasive population presents, to our knowledge, the highest reported prevalence of male intersexuality. This is the clearest evidence to date that such intersexuality does not represent a form of debilitating sexual dysfunction that negatively impacts amphipod populations.
Green Etxabe et al. (2015) Pronounced and prevalent intersexuality does not impede the ‘Demon Shrimp’ invasion. PeerJ 3:e757 https://doi.org/10.7717/peerj.757
The association between fluid balance and mortality in patients with ARDS was modified by serum potassium levels: a retrospective study
Background and Objective. Acute respiratory distress syndrome (ARDS) is characterized by pulmonary edema and may benefit from conservative fluid management. However, conflicting results exist in the literature. The study aimed to investigate the association between mean fluid balance and mortality outcome in ARDS patients who required invasive mechanical ventilation. Methods. The study was a secondary analysis of a prospectively collected dataset obtained from the NHLBI Biologic Specimen and Data Repository Information Coordinating Center. ARDS patients with invasive mechanical ventilation were eligible. Demographic and laboratory data were extracted from the dataset. Multivariable regression model was built by stepwise selection of covariates. A fractional polynomial approach was used to test the linearity of mean fluid balance in the model. The potential interactions of mean fluid balance with other variables were tested. Main Results. A total of 282 patients were eligible for the analysis, including 61 non-survivors with a mortality rate of 21.6%. After stepwise regression analysis, mean fluid balance remained to be an independent predictor of death (OR: 1.00057; 95% CI [1.00034–1.00080]). The two-term model obtained using fractional polynomial analysis was not superior to the linear model. There was significant interaction between mean fluid balance and serum potassium levels (p = 0.011). While the risk of death increased with increasing mean fluid balance at potassium levels of 1.9, 2.9 , 3.9 and 4.9 mmol/l, the risk decreased at potassium level of 5.9 mmol/l. Conclusion. The present study demonstrates that more positive fluid balance in the first 8 days is significantly associated with increased risk of death. However, the relationship between mean fluid balance and mortality can be modified by serum potassium levels. With hyperkalemia, more positive fluid balance is associated with reduced risk of death.
Zhang et al. (2015) The association between fluid balance and mortality in patients with ARDS was modified by serum potassium levels: a retrospective study. PeerJ 3:e752 https://doi.org/10.7717/peerj.752
Diversity and ecological structure of vibrios in benthic and pelagic habitats along a latitudinal gradient in the Southwest Atlantic Ocean
We analyzed the diversity and population structure of the 775 Vibrio isolates from different locations of the southwestern Atlantic Ocean (SAO), including St. Peter and St. Paul Archipelago (SPSPA), Abrolhos Bank (AB) and the St. Sebastian region (SS), between 2005 and 2010. In this study, 195 novel isolates, obtained from seawater and major benthic organisms (rhodoliths and corals), were compared with a collection of 580 isolates previously characterized (available at www.taxvibrio.lncc.br). The isolates were distributed in 8 major habitat spectra according to AdaptML analysis on the basis of pyrH phylogenetic reconstruction and ecological information, such as isolation source (i.e., corals: Madracis decactis, Mussismilia braziliensis, M. hispida, Phyllogorgia dilatata, Scolymia wellsi; zoanthids: Palythoa caribaeorum, P. variabilis and Zoanthus solanderi; fireworm: Hermodice carunculata; rhodolith; water and sediment) and sampling site regions (SPSPA, AB and SS). Ecologically distinct groups were discerned through AdaptML, which finds phylogenetic groups that are significantly different in their spectra of habitat preferences. Some habitat spectra suggested ecological specialization, with habitat spectra 2, 3, and 4 corresponding to specialization on SPSPA, AB, and SS, respectively. This match between habitat and location may reflect a minor exchange of Vibrio populations between geographically isolated benthic systems. Moreover, we found several widespread Vibrio species predominantly from water column, and different populations of a single Vibrio species from H. carunculata in ecologically distinct groups (H-1 and H-8 respectively). On the other hand, AdaptML detected phylogenetic groups that are found in both the benthos and in open water. The ecological grouping observed suggests dispersal and connectivity between the benthic and pelagic systems in AB. This study is a first attempt to characterize the biogeographic distribution of vibrios in both seawater and several benthic hosts in the SAO. The benthopelagic coupling observed here stands out the importance of vibrios in the global ocean health.
Chimetto Tonon et al. (2015) Diversity and ecological structure of vibrios in benthic and pelagic habitats along a latitudinal gradient in the Southwest Atlantic Ocean. PeerJ 3:e741 https://doi.org/10.7717/peerj.741
Effects of statins on TH1 modulating cytokines in human subjects
Background. Activation of the innate immune system by cholesterol accelerates atherosclerosis. High levels or modified forms of cholesterol stimulate release of the inflammatory cytokines IL-12 and IL-18 that synergistically stimulate T lymphocytes to produce the atherogenic cytokine interferon-γ. While activation of the innate immune system by cholesterol is well-described in animal models and human subjects with high cholesterol levels or known atherosclerotic disease, the interaction of cholesterol and lipoproteins with the innate immune system in human subjects without known atherosclerosis is less well-described. The goal of our study was to assess the TH1 modulating cytokines IL-12 p40 and IL-18, and their counter regulatory cytokines IL-18 binding protein and IL-27, to determine if their levels are linked to cholesterol levels or other factors. Methods. We performed a blinded, randomized hypothesis-generating study in human subjects without known atherosclerotic disease. We measured serum lipids, lipoprotein levels, and collected plasma samples at baseline. Subjects were randomized to two weeks of therapy with atorvastatin, pravastatin, or rosuvastatin. Lipids and cytokine levels were measured after two weeks of statin treatment. Subjects were given a four-week statin-free period. At the end of the four-week statin-free period, venous blood was sampled again to determine if serum lipids returned to within 5% of their pre-statin levels. When lipid levels returned to baseline, subjects were again treated with the next statin in the randomization scheme. IL-12, IL-18, IL-18 binding protein, and IL-27 were measured at baseline and after each statin treatment to determine effects of statin treatment on their blood levels, and identify correlations with lipids and lipoproteins. Results. Therapy with statins revealed no significant change in the levels of IL-12, IL-18, IL-18 binding protein or IL-27 levels. We found that IL-18 levels positively correlate with total cholesterol levels (r2 = 0.15, p < 0.03), but not HDL or LDL cholesterol. In contrast, IL-12 p40 levels inversely correlated with total cholesterol (r2 = −0.17, p < 0.008), HDL cholesterol (r2 = −0.22, p < 0.002), and apolipoprotein A1 (r2 = −0.21, p < 0.002). Similarly, IL-18 binding protein levels inversely correlated with apolipoprotein A1 levels (r2 = −0.13, p < 0.02). Conclusions. Our findings suggest that total cholesterol levels positively regulate IL-18, while HDL cholesterol and apolipoprotein A1 may reduce IL-12 p40 and IL-18 binding protein levels. Additional studies in a larger patient population are needed to confirm these findings, and verify mechanistically whether HDL cholesterol can directly suppress IL-12 p40 and IL-18 binding protein levels in human subjects.
Cimato et al. (2015) Effects of statins on TH1 modulating cytokines in human subjects. PeerJ 3:e764 https://doi.org/10.7717/peerj.764
Nephila clavata L Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)
Nephila clavata L Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest that the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.
Hoebeke et al. (2015) Nephila clavata L Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae). PeerJ 3:e763 https://doi.org/10.7717/peerj.763
Requirements for data integration platforms in biomedical research networks: a reference model
Biomedical research networks need to integrate research data among their members and with external partners. To support such data sharing activities, an adequate information technology infrastructure is necessary. To facilitate the establishment of such an infrastructure, we developed a reference model for the requirements. The reference model consists of five reference goals and 15 reference requirements. Using the Unified Modeling Language, the goals and requirements are set into relation to each other. In addition, all goals and requirements are described textually in tables. This reference model can be used by research networks as a basis for a resource efficient acquisition of their project specific requirements. Furthermore, a concrete instance of the reference model is described for a research network on liver cancer. The reference model is transferred into a requirements model of the specific network. Based on this concrete requirements model, a service-oriented information technology architecture is derived and also described in this paper.
Ganzinger et al. (2015) Requirements for data integration platforms in biomedical research networks: a reference model. PeerJ 3:e755 https://doi.org/10.7717/peerj.755
Amyloid domains in the cell nucleus controlled by nucleoskeletal protein lamin B1 reveal a new pathway of mercury neurotoxicity
Mercury (Hg) is a bioaccumulating trace metal that globally circulates the atmosphere and waters in its elemental, inorganic and organic chemical forms. While Hg represents a notorious neurotoxicant, the underlying cellular pathways are insufficiently understood. We identify amyloid protein aggregation in the cell nucleus as a novel pathway of Hg-bio-interactions. By mass spectrometry of purified protein aggregates, a subset of spliceosomal components and nucleoskeletal protein lamin B1 were detected as constituent parts of an Hg-induced nuclear aggregome network. The aggregome network was located by confocal imaging of amyloid-specific antibodies and dyes to amyloid cores within splicing-speckles that additionally recruit components of the ubiquitin-proteasome system. Hg significantly enhances global proteasomal activity in the nucleus, suggesting that formation of amyloid speckles plays a role in maintenance of protein homeostasis. RNAi knock down showed that lamin B1 for its part regulates amyloid speckle formation and thus likewise participates in nuclear protein homeostasis. As the Hg-induced cascade of interactions between the nucleoskeleton and protein homeostasis reduces neuronal signalling, amyloid fibrillation in the cell nucleus is introduced as a feature of Hg-neurotoxicity that opens new avenues of future research. Similar to protein aggregation events in the cytoplasm that are controlled by the cytoskeleton, amyloid fibrillation of nuclear proteins may be driven by the nucleoskeleton.
Arnhold et al. (2015) Amyloid domains in the cell nucleus controlled by nucleoskeletal protein lamin B1 reveal a new pathway of mercury neurotoxicity. PeerJ 3:e754 https://doi.org/10.7717/peerj.754
Evidence from studies in rodents and in isolated adipocytes that agonists of the chemerin receptor CMKLR1 may be beneficial in the treatment of type 2 diabetes
The literature is unclear on whether the adipokine chemerin has pro- or anti-inflammatory properties or plays any role in the aetiology of type 2 diabetes or obesity. To address these questions, and in particular the potential of agonists or antagonists of the chemerin receptor CMKLR1 in the treatment of type 2 diabetes and obesity, we studied the metabolic phenotypes of both male and female, CMKLR1 knockout and heterozygote mice. We also investigated changes in plasma chemerin levels and chemerin gene mRNA content in adipose tissue in models of obesity and diabetes, and in response to fasting or administration of the insulin sensitizing drug rosiglitazone, which also has anti-inflammatory properties. The effects of murine chemerin and specific C-terminal peptides on glucose uptake in wild-type and CMKLR1 knockout adipocytes were investigated as a possible mechanism by which chemerin affects the blood glucose concentration. Both male and female CMKLR1 knockout and heterozygote mice displayed a mild tendency to obesity and impaired glucose homeostasis, but only when they were fed on a high-fat died, rather than a standard low-fat diet. Obesity and impaired glucose homeostasis did not occur concurrently, suggesting that obesity was not the sole cause of impaired glucose homeostasis. Picomolar concentrations of chemerin and its C15- and C19-terminal peptides stimulated glucose uptake in the presence of insulin by rat and mouse wild-type epididymal adipocytes, but not by murine CMKLR1 knockout adipocytes. The insulin concentration-response curve was shifted to the left in the presence of 40 pM chemerin or its C-15 terminal peptide. The plasma chemerin level was raised in diet-induced obesity and ob/ob but not db/db mice, and was reduced by fasting and, in ob/ob mice, by treatment with rosiglitazone. These findings suggest that an agonist of CMKLR1 is more likely than an antagonist to be of value in the treatment of type 2 diabetes and to have associated anti-obesity and anti-inflammatory activities. One mechanism by which an agonist of CMKLR1 might improve glucose homeostasis is by increasing insulin-stimulated glucose uptake by adipocytes.
Wargent et al. (2015) Evidence from studies in rodents and in isolated adipocytes that agonists of the chemerin receptor CMKLR1 may be beneficial in the treatment of type 2 diabetes. PeerJ 3:e753 https://doi.org/10.7717/peerj.753
The effects of island forest restoration on open habitat specialists: the endangered weevil Hadramphus spinipennis Broun and its host-plant Aciphylla dieffenbachii Kirk
Human alteration of islands has made restoration a key part of conservation management. As islands are restored to their original state, species interactions change and some populations may be impacted. In this study we examine the coxella weevil, (Hadramphus spinipennis Broun) and its host-plant Dieffenbach’s speargrass (Aciphylla dieffenbachii Kirk), which are both open habitat specialists with populations on Mangere and Rangatira Islands, Chathams, New Zealand. Both of these islands were heavily impacted by the introduction of livestock; the majority of the forest was removed and the weevil populations declined due to the palatability of their host-plant to livestock. An intensive reforestation program was established on both islands over 50 years ago but the potential impacts of this restoration project on the already endangered H. spinipennis are poorly understood. We combined genetic and population data from 1995 and 2010–2011 to determine the health and status of these species on both islands. There was some genetic variation between the weevil populations on each island but little variation within the species as a whole. The interactions between the weevil and its host-plant populations appear to remain intact on Mangere, despite forest regeneration. A decline in weevils and host-plant on Rangatira does not appear to be caused by canopy regrowth. We recommend that (1) these populations be monitored for ongoing effects of long-term reforestation, (2) the cause of the decline on Rangatira be investigated, and (3) the two populations of weevils be conserved as separate evolutionarily significant units.
Fountain et al. (2015) The effects of island forest restoration on open habitat specialists: the endangered weevil Hadramphus spinipennis Broun and its host-plant Aciphylla dieffenbachii Kirk. PeerJ 3:e749 https://doi.org/10.7717/peerj.749
Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits
Morphological variation in the geographically widespread coral Porites lobata can make it difficult to distinguish from other massive congeneric species. This morphological variation could be attributed to geographic variability, phenotypic plasticity, or a combination of such factors. We examined genetic and microscopic morphological variability in P. lobata samples from the Galápagos, Easter Island, Tahiti, Fiji, Rarotonga, and Australia. Panamanian P. evermanni specimens were used as a previously established distinct outgroup against which to test genetic and morphological methods of discrimination. We employed a molecular analysis of variance (AMOVA) based on ribosomal internal transcribed spacer region (ITS) sequence, principal component analysis (PCA) of skeletal landmarks, and Mantel tests to compare genetic and morphological variation. Both genetic and morphometric methods clearly distinguished P. lobata and P. evermanni, while significant genetic and morphological variance was attributed to differences among geographic regions for P. lobata. Mantel tests indicate a correlation between genetic and morphological variation for P. lobata across the Pacific. Here we highlight landmark morphometric measures that correlate well with genetic differences, showing promise for resolving species of Porites, one of the most ubiquitous yet challenging to identify architects of coral reefs.
Forsman et al. (2015) Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. PeerJ 3:e751 https://doi.org/10.7717/peerj.751
Effectiveness of telenutrition in a women’s weight loss program
Objective. The objective of this study is to evaluate the effectiveness of telenutrition versus traditional nutritional consultations for female obese patients in need of nutritional treatment. Methods. A comparative clinical study was conducted among 233 obese or overweight women (including 20 who dropped out and 60 who failed) who consulted a nutrition clinic in Barranquilla (Colombia) for nutritional assessment and chose either telenutrition or a traditional consultation that included a weekly follow-up consultation over 16 weeks, food consumption patterns, Body Mass Index (BMI, kg/m2) registeration and waist and hip circumference registeration. Treatment responses and differences between telenutrition and the traditional consultations were made according to BMI, waist, hip and initial-waist/height ratio (iWaist), calculating for the relative risk. Results. In 68 (29.2%) women who chose traditional attention, 9 (37.5%) dropped out, 24 (40%) failed and 35 (23.5%) were successful, showing 1.4% (1.0 SD) BMI loss, 5.8% (3.4 SD) in waist circumference, 4.5% (2.8 SD) in hip circumference and 0.04% (0.02 SD) in iWaist/height ratio. In 165 (70.8%) women who chose telenutrition, 15 (62.5%) dropped out, 36 (60%) failed and 114 (76.5%) were successful, showing 1.1% (1.0 SD) BMI loss, 5.0% (3.2 SD) in waist circumference, 3.5% (3.1 SD) in hip circumference and 0.03% (0.02 SD) in iWaist/height ratio. A significance level of p < 0.05 is considered. Conclusion. Telenutrition has a failure or dropout risk factor of about half of the value of traditional consultation, and showed slight, statistically significant differences. This study concludes that telenutrition can support or sometimes replace traditional consultations when developing weight loss programs for obese women.
Kuzmar et al. (2015) Effectiveness of telenutrition in a women’s weight loss program. PeerJ 3:e748 https://doi.org/10.7717/peerj.748
The Hsp70-like StkA functions between T4P and Dif signaling proteins as a negative regulator of exopolysaccharide in Myxococcus xanthus
Myxococcus xanthus displays a form of surface motility known as social (S) gliding. It is mediated by the type IV pilus (T4P) and requires the exopolysaccharide (EPS) to function. It is clear that T4P retraction powers S motility. EPS on a neighboring cell or deposited on a gliding surface is proposed to anchor the distal end of a pilus and trigger T4P retraction at its proximal end. Inversely, T4P has been shown to regulate EPS production upstream of the Dif signaling pathway. Here we describe the isolation of two Tn insertions at the stk locus which had been known to play roles in cellular cohesion and formation of cell groups. An insertion in stkA (MXAN_3474) was identified based on its ability to restore EPS to a pilA deletion mutant. The stkA encodes a DnaK or Hsp70 homolog and it is upstream of stkB (MXAN_3475) and stkC (MXAN_3476). A stkB insertion was identified in a separate genetic screen because it eliminated EPS production of an EPS+ parental strain. Our results with in-frame deletions of these three stk genes indicated that the stkA mutant produced increased level of EPS while stkB and stkC mutants produced less EPS relative to the wild type. S motility and developmental aggregation were affected by deletions of stkA and stkB but only minimally by the deletion of stkC. Genetic epistasis indicated that StkA functions downstream of T4P but upstream of the Dif proteins as a negative regulator of EPS production in M. xanthus.
Moak et al. (2015) The Hsp70-like StkA functions between T4P and Dif signaling proteins as a negative regulator of exopolysaccharide in Myxococcus xanthus. PeerJ 3:e747 https://doi.org/10.7717/peerj.747
Analytical and experimental FWHM of a gamma camera: theoretical and practical issues
Introduction. It is well known that resolution on a gamma camera varies as a function of distance, scatter and the camera’s characteristics (collimator type, crystal thickness, intrinsic resolution etc). Manufacturers frequently provide only a few pre-calculated resolution values (using a line source in air, 10–15 cm from the collimator surface and without scattering). However, these are typically not obtained in situations resembling a clinical setting. From a diagnostic point of view, it is useful to know the expected resolution of a gamma camera at a given distance from the collimator surface for a particular setting in order to decide whether it is worth scanning patients with “small lesion” or not. When dealing with absolute quantification it is also mandatory to know precisely the expected resolution and its uncertainty in order to make appropriate corrections. Aim. Our aims are: to test a novel mathematical approach, the cubic spline interpolation, for the extraction of the full width at half maximum (FWHM) from the acquisition of a line source (experimental resolution) also considering measurement uncertainty; to compare it with the usually adopted methods such as the gaussian approach; to compare it with the theoretical resolution (analytical resolution) of a gamma camera at different distances; to create a web-based educational program with which to test these theories. Methods. Three mathematical methods (direct calculation, global interpolation using gaussian and local interpolation using splines) for calculating FWHM from a line source (planar scintigraphy) were tested and compared. A NEMA Triple Line Source Phantom was used to obtain static images both in air and with different scattering levels. An advanced, open-source software (MATLAB/Octave and PHP based) was created “ad hoc” to obtain and compare FWHM values and relative uncertainty. Results and Conclusion. Local interpolation using splines proved faster and more reliable than the usually-adopted Gaussian interpolation. The proposed freely available software proved effective in assessing both FWHM and its uncertainty.
Cecchin et al. (2015) Analytical and experimental FWHM of a gamma camera: theoretical and practical issues. PeerJ 3:e722 https://doi.org/10.7717/peerj.722