title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1739 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The impact of human development on individual health: a causal mediation analysis examining pathways through education and body mass index link: https://peerj.com/articles/3053 last-modified: 2017-03-01 description: BackgroundThe macro environment we live in projects what we can achieve and how we behave, and in turn, shapes our health in complex ways. Policymaking will benefit from insights into the mechanisms underlying how national socioeconomic context affects health. This study examined the impact of human development on individual health and the possible mediating roles of education and body mass index (BMI).MethodsWe analyzed World Health Survey data on 109,448 participants aged 25 or older from 42 low- and middle-income countries with augmented human development index (HDI) in 1990. We used principal components method to create a health score based on measures from eight health state domains, used years of schooling as education indicator and calculated BMI from self-reported height and weight. We used causal mediation analysis technique with random intercepts to account for the multilevel structure.ResultsBelow a reference HDI level of 0.48, HDI was negatively associated with good health (total effect at HDI of 0.23: b =  − 3.44, 95% CI [−6.39–−0.49] for males and b =  − 5.16, 95% CI [−9.24,–−1.08] for females) but was positively associated with good health above this reference level (total effect at HDI of 0.75: b = 4.16, 95% CI [−0.33–8.66] for males and b = 6.62, 95% CI [0.85–12.38] for females). We found a small positive effect of HDI on health via education across reference HDI levels (b ranging from 0.24 to 0.29 for males and 0.40 to 0.49 for females) but not via pathways involving BMI only.ConclusionHuman development has a non-linear effect on individual health, but the impact appears to be mainly through pathways other than education and BMI. creator: Aolin Wang creator: Onyebuchi A. Arah uri: https://doi.org/10.7717/peerj.3053 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang and Arah title: Effects of root exudates of woody species on the soil anti-erodibility in the rhizosphere in a karst region, China link: https://peerj.com/articles/3029 last-modified: 2017-03-01 description: IntroductionRhizospheres, the most active interfaces between plants and soils, play a central role in the long-term maintenance of the biosphere. The anti-erodibility of soils (AES) regulated by the root exudates is crucial to the soil stability in the rhizospheres. However, scientists still debate (1) the key organic matter of the root exudates affecting the AES and (2) the interspecific variation of these root exudates.MethodsWe used an incubation of soils to test the effects of the root exudates from eight woody plant species on the change in soil aggregation and identified the organic matter in these root exudates with gas chromatography-mass spectrometry (GC-MS) and biochemical methods. Furthermore, the relationships between the organic matter in the exudates and the AES in the rhizospheres of 34 additional tree species were analyzed.ResultsThe water-stable aggregates of the soils incubated with the root exudates increased by 15%–50% on average compared with control samples. The interspecific differences were significant. The root exudates included hundreds of specific organic matter types; hydrocarbon, total sugar, total amino acids, and phenolic compounds were crucial to the AES. These organic matter types could explain approximately 20–75% of the variation in the total effect of the root exudates on the AES, which was quantified based on the aggregate status, degree of aggregation, dispersion ratio, and dispersion coefficient.DiscussionThe effects of the root exudates on the AES and the interspecific variation are as important as that of root density, litters, and vegetation covers. Many studies explored the effects of root density, litters, vegetation covers, and vegetation types on the AES, but little attention has been paid to the effects of the root exudates on the AES. Different plants secrete different relative contents of organic matter resulting in the variation of the effect of the root exudates on the AES. Our study quantified the causal relationships between the root exudates and the AES using modeling experiments in laboratory and field observations and indicated the interspecific variation of the AES and organic matter of the root exudates.ConclusionsMore organic compounds of the exudates related to the AES were recognized in this study. These results enhance the understanding of the soil stability at a slope and can be applied to ecosystem restoration. creator: Zhen Hong Wang creator: Hong Fang creator: Mouhui Chen uri: https://doi.org/10.7717/peerj.3029 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) link: https://peerj.com/articles/2982 last-modified: 2017-03-01 description: BackgroundWhole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.MethodsSequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.ResultsWe present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.DiscussionOur findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages. creator: Mun Hua Tan creator: Han Ming Gan creator: Yin Peng Lee creator: Gary C.B. Poore creator: Christopher M. Austin uri: https://doi.org/10.7717/peerj.2982 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Tan et al. title: Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae link: https://peerj.com/articles/2979 last-modified: 2017-03-01 description: Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian–dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol’s iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10–25 μM after 7 days. Strobilation under optimal conditions reached 80–100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae. creator: Patricia Cabrales-Arellano creator: Tania Islas-Flores creator: Patricia E. Thomé creator: Marco A. Villanueva uri: https://doi.org/10.7717/peerj.2979 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Cabrales-Arellano et al. title: LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks link: https://peerj.com/articles/3052 last-modified: 2017-02-28 description: One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto. creator: Alberto J. Martin creator: Sebastián Contreras-Riquelme creator: Calixto Dominguez creator: Tomas Perez-Acle uri: https://doi.org/10.7717/peerj.3052 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Martin et al. title: Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana link: https://peerj.com/articles/3047 last-modified: 2017-02-28 description: BackgroundThe emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.MethodsWe first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages.ResultsWe show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol.DiscussionThis study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone. creator: Grace Kpeli creator: Andrew H. Buultjens creator: Stefano Giulieri creator: Evelyn Owusu-Mireku creator: Samuel Y. Aboagye creator: Sarah L. Baines creator: Torsten Seemann creator: Dieter Bulach creator: Anders Gonçalves da Silva creator: Ian R. Monk creator: Benjamin P. Howden creator: Gerd Pluschke creator: Dorothy Yeboah-Manu creator: Timothy Stinear uri: https://doi.org/10.7717/peerj.3047 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Kpeli et al. title: An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples link: https://peerj.com/articles/3045 last-modified: 2017-02-28 description: BackgroundSalmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings.MethodsHere we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples.ResultsThe method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain).DiscussionThis new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms. creator: Laura Clusa creator: Alba Ardura creator: Sara Fernández creator: Agustín A. Roca creator: Eva García-Vázquez uri: https://doi.org/10.7717/peerj.3045 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Clusa et al. title: Spatial distribution of environmental DNA in a nearshore marine habitat link: https://peerj.com/articles/3044 last-modified: 2017-02-28 description: In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments. creator: James L. O’Donnell creator: Ryan P. Kelly creator: Andrew Olaf Shelton creator: Jameal F. Samhouri creator: Natalie C. Lowell creator: Gregory D. Williams uri: https://doi.org/10.7717/peerj.3044 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Predatory blue crabs induce stronger nonconsumptive effects in eastern oysters Crassostrea virginica than scavenging blue crabs link: https://peerj.com/articles/3042 last-modified: 2017-02-28 description: By influencing critical prey traits such as foraging or habitat selection, predators can affect entire ecosystems, but the nature of cues that trigger prey reactions to predators are not well understood. Predators may scavenge to supplement their energetic needs and scavenging frequency may vary among individuals within a species due to preferences and prey availability. Yet prey reactions to consumers that are primarily scavengers versus those that are active foragers have not been investigated, even though variation in prey reactions to scavengers or predators might influence cascading nonconsumptive effects in food webs. Oysters Crassostrea virginica react to crab predators by growing stronger shells. We exposed oysters to exudates from crabs fed live oysters or fed aged oyster tissue to simulate scavenging, and to controls without crab cues. Oysters grew stronger shells when exposed to either crab exudate, but their shells were significantly stronger when crabs were fed live oysters. The stronger response to predators than scavengers could be due to inherent differences in diet cues representative of reduced risk in the presence of scavengers or to degradation of conspecific alarm cues in aged treatments, which may mask risk from potential predators subsisting by scavenging. creator: Avery E. Scherer creator: Miranda M. Garcia creator: Delbert L. Smee uri: https://doi.org/10.7717/peerj.3042 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Scherer et al. title: How conserved are the conserved 16S-rRNA regions? link: https://peerj.com/articles/3036 last-modified: 2017-02-28 description: The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker. creator: Marcel Martinez-Porchas creator: Enrique Villalpando-Canchola creator: Luis Enrique Ortiz Suarez creator: Francisco Vargas-Albores uri: https://doi.org/10.7717/peerj.3036 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Martinez-Porchas et al.