title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1630 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Complex versus simple models: ion-channel cardiac toxicity prediction link: https://peerj.com/articles/4352 last-modified: 2018-02-05 description: There is growing interest in applying detailed mathematical models of the heart for ion-channel related cardiac toxicity prediction. However, a debate as to whether such complex models are required exists. Here an assessment in the predictive performance between two established large-scale biophysical cardiac models and a simple linear model Bnet was conducted. Three ion-channel data-sets were extracted from literature. Each compound was designated a cardiac risk category using two different classification schemes based on information within CredibleMeds. The predictive performance of each model within each data-set for each classification scheme was assessed via a leave-one-out cross validation. Overall the Bnet model performed equally as well as the leading cardiac models in two of the data-sets and outperformed both cardiac models on the latest. These results highlight the importance of benchmarking complex versus simple models but also encourage the development of simple models. creator: Hitesh B. Mistry uri: https://doi.org/10.7717/peerj.4352 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mistry title: Sea cucumbers reduce chromophoric dissolved organic matter in aquaculture tanks link: https://peerj.com/articles/4344 last-modified: 2018-02-05 description: BackgroundMono-specific aquaculture effluents contain high concentrations of nutrients and organic matter, which affect negatively the water quality of the recipient ecosystems. A fundamental feature of water quality is its transparency. The fraction of dissolved organic matter that absorbs light is named chromophoric dissolved organic matter (CDOM). A sustainable alternative to mono-specific aquaculture is the multitrophic aquaculture that includes species trophically complementary named “extractive” species that uptake the waste byproducts. Sea cucumbers are recognized as efficient extractive species due to the consumption of particulate organic matter (POM). However, the effects of sea cucumbers on CDOM are still unknown.MethodsDuring more than one year, we monitored CDOM in two big-volume tanks with different trophic structure. One of the tanks (−holothurian) only contained around 810 individuals of Anemonia sulcata, whereas the other tank (+holothurian) also included 90 individuals of Holothuria tubulosa and Holothuria forskali. We routinely analyzed CDOM absorption spectra and determined quantitative (absorption coefficients at 325 nm) and qualitative (spectral slopes) optical parameters in the inlet waters, within the tanks, and in their corresponding effluents. To confirm the time-series results, we also performed three experiments. Each experiment consisted of two treatments: +holothurians (+H) and –holothurians (−H). We set up three +H tanks with 80 individuals of A. sulcata and 10 individuals of H. tubulosa in each tank and four –H tanks that contained only 80 individuals of A. sulcata.ResultsIn the time-series, absorption coefficients at 325 nm (a325) and spectral slopes from 275 to 295 nm (S275−295) were significantly lower in the effluent of the +holothurian tank (average: 0.33 m−1 and 16 µm−1, respectively) than in the effluent of the −holothurian tank (average: 0.69 m−1 and 34 µm−1, respectively), the former being similar to those found in the inlet waters (average: 0.32 m−1 and 22 µm−1, respectively). This reduction in the absorption of the dissolved organic matter appears to be mediated by the POM consumption by holothurians. The experiments confirmed the results observed in the time-series. The a325 and S275−295 values were significantly lower in the treatment with holothurians than in the treatment without holothurians indicating a reduction in the concentration of chromophoric organic compounds, particularly of low molecular weight.DiscussionConsequently, sea cucumbers appear to improve water transparency in aquaculture tanks. The underlying mechanism of this improvement might be related to the POM consumption by holothurians, which reduces the concentration of CDOM derived from POM disaggregation or to the direct assimilation of dissolved compounds of low molecular weight as chromophoric amino acids. creator: Seyed Mohammad Sadeghi-Nassaj creator: Teresa S. Catalá creator: Pedro A. Álvarez creator: Isabel Reche uri: https://doi.org/10.7717/peerj.4344 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sadeghi-Nassaj et al. title: Deficient mismatch repair and RAS mutation in colorectal carcinoma patients: a retrospective study in Eastern China link: https://peerj.com/articles/4341 last-modified: 2018-02-05 description: ObjectivesTo investigate the frequency and prognostic role of deficient mismatch repair (dMMR) and RAS mutation in Chinese patients with colorectal carcinoma.MethodsClinical and pathological information from 813 patients were reviewed and recorded. Expression of mismatch repair proteins was tested by immunohistochemistry. Mutation analyses for RAS gene were performed by real-time polymerase chain reaction. Correlations of mismatch repair status and RAS mutation status with clinicopathological characteristics and disease survival were determined.ResultsThe overall percentage of dMMR was 15.18% (121/797). The proportion of dMMR was higher in patients <50 years old (p < 0.001) and in the right side of the colon (p < 0.001). Deficient mismatch repair was also associated with mucinous production (p < 0.001), poor differentiation (p < 0.001), early tumor stage (p < 0.05) and bowel wall invasion (p < 0.05). The overall RAS mutation rate was 45.88%, including 42.56% (346/813) KRAS mutation and 3.69% (30/813) NRAS mutation (including three patients with mutations in both). KRAS mutation was significantly associated with mucinous production (p < 0.05), tumor stage (p < 0.05) and was higher in non-smokers (p < 0.05) and patients with a family history of colorectal carcinoma (p < 0.05). Overall, 44.63% (54/121) dMMR tumors harbored KRAS mutation, however, dMMR tumors were less likely to have NRAS mutation. Moreover, dMMR, KRAS and NRAS mutation were not prognostic factors for stage I–III colorectal carcinoma.ConclusionsThis study confirms that the status of molecular markers involving mismatch repair status and RAS mutation reflects the specific clinicopathological characteristics of colorectal carcinoma. creator: Xiangyan Zhang creator: Wenwen Ran creator: Jie Wu creator: Hong Li creator: Huamin Liu creator: Lili Wang creator: Yujing Xiao creator: Xiaonan Wang creator: Yujun Li creator: Xiaoming Xing uri: https://doi.org/10.7717/peerj.4341 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Relative evolutionary rate inference in HyPhy with LEISR link: https://peerj.com/articles/4339 last-modified: 2018-02-05 description: We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced “laser”), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for inferring relative site-wise evolutionary rates, primarily from protein data. We extend the original method for more general use in several key ways: (i) we increase the support for nucleotide data with additional models, (ii) we allow for datasets of arbitrary size, (iii) we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, (iv) we produce rate estimates at all sites rather than at just a subset of sites, and (v) we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8, and it is accessible as an option in the HyPhy analysis menu (“Relative evolutionary rate inference”), which calls the HyPhy batchfile LEISR.bf. creator: Stephanie J. Spielman creator: Sergei L. Kosakovsky Pond uri: https://doi.org/10.7717/peerj.4339 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Spielman and Kosakovsky Pond title: Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss link: https://peerj.com/articles/4350 last-modified: 2018-02-02 description: The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and order as in other known bryophyte chondriomes. The genome contains 66 genes including three rRNAs, 24 tRNAs, and 40 conserved mitochondrial proteins genes. Unlike the majority of previously sequenced bryophyte mitogenomes, it lacks the functional nad7 gene. The phylogenetic reconstruction and scrutiny analysis of the primary structure of nad7 gene carried out in this study suggest its independent pseudogenization in different bryophyte lineages. Evaluation of the microsatellite (simple sequence repeat) content of the M. elongata mitochondrial genome indicates that it could be used as a tool in further studies as a phylogenetic marker. The strongly supported phylogenetic tree presented here, derived from 33 protein coding sequences of 40 bryophyte species, is consistent with other reconstructions based on a number of different data sets. creator: Denis V. Goryunov creator: Svetlana V. Goryunova creator: Oxana I. Kuznetsova creator: Maria D. Logacheva creator: Irina A. Milyutina creator: Alina V. Fedorova creator: Michael S. Ignatov creator: Aleksey V. Troitsky uri: https://doi.org/10.7717/peerj.4350 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Goryunov et al. title: Molecular systematics of the subfamily Limenitidinae (Lepidoptera: Nymphalidae) link: https://peerj.com/articles/4311 last-modified: 2018-02-02 description: We studied the systematics of the subfamily Limenitidinae (Lepidoptera: Nymphalidae) using molecular methods to reconstruct a robust phylogenetic hypothesis. The molecular data matrix comprised 205 Limenitidinae species, four outgroups, and 11,327 aligned nucleotide sites using up to 18 genes per species of which seven genes (CycY, Exp1, Nex9, PolII, ProSup, PSb and UDPG6DH) have not previously been used in phylogenetic studies. We recovered the monophyly of the subfamily Limenitidinae and seven higher clades corresponding to four traditional tribes Parthenini, Adoliadini, Neptini, Limenitidini as well as three additional independent lineages. One contains the genera Harma + Cymothoe and likely a third, Bhagadatta, and the other two independent lineages lead to Pseudoneptis and to Pseudacraea. These independent lineages are circumscribed as new tribes. Parthenini was recovered as sister to rest of Limenitidinae, but the relationships of the remaining six lineages were ambiguous. A number of genera were found to be non-monophyletic, with Pantoporia, Euthalia, Athyma, and Parasarpa being polyphyletic, whereas Limenitis, Neptis, Bebearia, Euryphura, and Adelpha were paraphyletic. creator: Bidur Dhungel creator: Niklas Wahlberg uri: https://doi.org/10.7717/peerj.4311 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dhungel and Wahlberg title: A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions link: https://peerj.com/articles/4299 last-modified: 2018-02-02 description: The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity. creator: Jeffery M. Saarela creator: Sean V. Burke creator: William P. Wysocki creator: Matthew D. Barrett creator: Lynn G. Clark creator: Joseph M. Craine creator: Paul M. Peterson creator: Robert J. Soreng creator: Maria S. Vorontsova creator: Melvin R. Duvall uri: https://doi.org/10.7717/peerj.4299 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Saarela et al. title: Redescription of Calyptosuchus (Stagonolepis) wellesi (Archosauria: Pseudosuchia: Aetosauria) from the Late Triassic of the Southwestern United States with a discussion of genera in vertebrate paleontology link: https://peerj.com/articles/4291 last-modified: 2018-02-02 description: Calyptosuchus wellesi is a medium-sized desmatosuchian aetosaur common in Adamanian (early to middle Norian) age rocks from the Chinle Formation and Dockum Group of the Western United States. Known chiefly from osteoderms, this taxon has never been fully described and non-osteoderm material assigned to Calyptosuchus has been done so based on questionable criteria. Mapping of aetosaurian elements from the Placerias Quarry allows for the recognition of associated material providing support for referrals of non-osteoderm material. Furthermore, another previously undescribed specimen from the Chinle Formation of Arizona provides more details about this taxon. Presently Calyptosuchus lacks discrete autapomorphies, but can be distinguished from other aetosaurs based on a unique combination of characters supported by a phylogenetic analysis. Calyptosuchus is one of the most common aetosaurians in the Western United States and an index taxon of the early Adamanian biozone. The name Calyptosuchus is retained and encouraged as the applicable genus name for the species wellesi rather than the often used Stagonolepis because assignments of taxa to multi-species genus names are problematic and in this case provides a proposed taxonomic relationship that cannot be unambiguously supported, even by phylogenetic analyses. Because of the inherent limitations of the fossil record, referral of specimens and species to species and genera respectively is an epistemological problem in vertebrate paleontology. creator: William G. Parker uri: https://doi.org/10.7717/peerj.4291 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Parker title: Ants of the Monomorium monomorium species-group (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species from southwestern Saudi Arabia link: https://peerj.com/articles/4277 last-modified: 2018-02-01 description: We revise the taxonomy of the myrmicine ants of the Monomorium monomorium species-group for the Arabian Peninsula. Six species are recognized: Monomorium aeyade Collingwood & Agosti, 1996, M. clavicorne André, 1881, M. exiguum Forel, 1894, M. holothir Bolton, 1987, M. mohammedi sp. n., and M. sarawatense Sharaf & Aldawood, 2013. On the basis of the worker caste, we describe Monomorium mohammedi sp. n. from the southwestern region of the Kingdom of Saudi Arabia (KSA). We designate a neotype for Monomorium aeyade Collingwood & Agosti and redescribe and illustrate the worker caste. Furthermore, we provide a worker-based species identification key, distribution maps for the treated species, and ecological and biological notes, if available. Monomorium holothir is recorded for the first time from the KSA. Also, we propose M. clavicorne var. punicaSantschi, 1915a as a junior synonym of M. clavicorne, as well as M. dryhimi Aldawood & Sharaf, 2011 and M. montanum Collingwood & Agosti, 1996 to be treated as junior synonyms of Monomorium exiguum. creator: Mostafa Sharaf creator: Hathal M. Al Dhafer creator: Abdulrahman S. Aldawood creator: Francisco Hita Garcia uri: https://doi.org/10.7717/peerj.4277 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sharaf et al. title: Evolutionary dynamics of GII.17 norovirus link: https://peerj.com/articles/4333 last-modified: 2018-02-01 description: BackgroundDuring the winter of 2014–2015, a rarely reported norovirus (NoV) genotype GII.17 was found to have increased its frequency in norovirus outbreaks in East Asia, surpassing the GII.4 NoV infections. GII.17 genotype has been detected for over three decades in the world. The aim of this study is to examine the evolutionary dynamics of GII.17 over the last four decades.MethodsNoV GII.17 sequences with complete or nearly complete VP1 were downloaded from GenBank and the phylogenetic analyses were then conducted.ResultsThe maximum likelihood analysis showed that GII.17 genotype could be divided into four different clades (Clades A–D). The strains detected after 2012, which could be the cause of the outbreaks, were separated into Clades C–D with their mean amino acid distance being 4.5%. Bayesian Markov chain Monte Carlo analyses indicated that the rate of nucleotide substitution per sites was 1.68 × 10−3 nucleotide substitutions/site/year and the time of the most recent common ancestor was 1840. The P2 subdomain of GII.17 was highly variable with 44% (56/128) amino acids variations including two insertions at positions 295–296 and one deletion at position 385 (Clades C and D) and one insertion at position 375 (Clade D). Variations existed in Epitopes A, B and D corresponding to GII.4 and human histo-blood group antigens binding site I in P2 subdomain.ConclusionThe novel GII.17 strains that caused outbreaks in 2013–2015 may have two new variants. The evolvement of HBGAs binding site and epitopes in P2 subdomain might contribute to the novel GII.17 strains predominance in some regions. creator: Shaowei Sang creator: Xiaoyun Yang uri: https://doi.org/10.7717/peerj.4333 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sang and Yang