title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1526 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genomic analysis of red-tide water bloomed with Heterosigma akashiwo in Geoje link: https://peerj.com/articles/4854 last-modified: 2018-05-29 description: Microbial community structures of harmful algal bloom (HAB) caused by Heterosigma akashiwo in Geoje were analyzed using the MiSeq platform. To analyze phytoplankton communities without cross-reactivity with predominant bacteria, a new phytoplankton-specific 23S universal primer set was designed by modifying two previously used ones. The new universal primer set turned out to be a useful tool for the analysis of the phytoplankton community; it showed a high specificity for phytoplankton without cross-reactivity to bacterial sequences as well as the wide taxon coverage presenting from prokaryotic cyanobacteria to eukaryotic algae. Next Generation Sequencing (NGS) data generated by two universal primer sets (16S and 23S) provided useful information about the H. akashiwo bloom. According to the 23S universal primer set, proportions of H. akashiwo increased by more than 200-fold as the bloom occurred and its numbers were high enough to detect in control sites. Its operational taxonomic units (OTUs) were detected in the bloom sites at low proportions suggesting that the 16S universal primer set may not be as effective for monitoring harmful algal blooming (HAB) as the 23S universal primer set. In addition, several abundant OTUs in Chlorophyta were not presented by the 16S universal primer set in this study. However, the 16S primer set was useful for detecting decreases in Foraminifera as HAB occurred suggesting that genomic analyses using two universal primer sets would provide more reliable data for understanding microbial community changes by various environmental or ecological events, including HAB. Genomic analyses using two universal primer sets was also useful for determining a correlation between microbial components as HAB occurred. Heterosigma akashiwo was positively correlated with other bloom species, including Karenia mikimotoi, Teleaulax amphioxeia, and bacteria in Verrucomicrobia. creator: Hye-Eun Kang creator: Tae-Ho Yoon creator: Sunyoung Yoon creator: Hak Jun Kim creator: Hyun Park creator: Chang-Keun Kang creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.4854 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kang et al. title: Modeling transcriptional activation changes to Gal4 variants via structure-based computational mutagenesis link: https://peerj.com/articles/4844 last-modified: 2018-05-29 description: As a DNA binding transcriptional activator, Gal4 promotes the expression of genes responsible for galactose metabolism. The Gal4 protein from Saccharomyces cerevisiae (baker’s yeast) has become a model for studying eukaryotic transcriptional activation in general because its regulatory properties mirror those of several eukaryotic organisms, including mammals. Given the availability of a crystallographic structure for Gal4, here we implement an in silico mutagenesis technique that makes use of a four-body knowledge-based energy function, in order to empirically quantify the structural impacts associated with single residue substitutions on the Gal4 protein. These results were used to examine the structure-function relationship in Gal4 based on a recently published experimental mutagenesis study, whereby functional changes to a uniformly distributed set of 1,068 single residue Gal4 variants were obtained by measuring their transcriptional activation levels relative to wild-type. A significant correlation was observed between computed (scalar) structural effect data and measured activity values for this collection of single residue Gal4 variants. Additionally, attribute vectors quantifying position-specific environmental impacts were generated for each of the Gal4 variants via computational mutagenesis, and we implemented supervised classification and regression statistical machine learning algorithms to train predictive models of variant Gal4 activity based on these structural changes. All models performed well under cross-validation testing, with balanced accuracy reaching 91% among the classification models, and with the actual and predicted activity values displaying a correlation as high as r = 0.80 for the regression models. Reliable predictions of transcriptional activation levels for Gal4 variants that have yet to be studied can be instantly generated by submitting their respective structure-based feature vectors to the trained models for testing. Such a computational pre-screening of Gal4 variants may potentially reduce costs associated with running large-scale mutagenesis experiments. creator: Majid Masso creator: Nitin Rao creator: Purnima Pyarasani uri: https://doi.org/10.7717/peerj.4844 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Masso et al. title: Changes in species abundance after seven years of elevated atmospheric CO2 and warming in a Subarctic birch forest understorey, as modified by rodent and moth outbreaks link: https://peerj.com/articles/4843 last-modified: 2018-05-29 description: A seven-year long, two-factorial experiment using elevated temperatures (5 °C) and CO2 (concentration doubled compared to ambient conditions) designed to test the effects of global climate change on plant community composition was set up in a Subarctic ecosystem in northernmost Sweden. Using point-frequency analyses in permanent plots, an increased abundance of the deciduous Vaccinium myrtillus, the evergreens V. vitis-idaea and Empetrum nigrum ssp. hermaphroditum and the grass Avenella flexuosa was found in plots with elevated temperatures. We also observed a possibly transient community shift in the warmed plots, from the vegetation being dominated by the deciduous V. myrtillus to the evergreen V. vitis-idaea. This happened as a combined effect of V. myrtillus being heavily grazed during two events of herbivore attack—one vole outbreak (Clethrionomys rufocanus) followed by a more severe moth (Epirrita autumnata) outbreak that lasted for two growing seasons—producing a window of opportunity for V. vitis-idaea to utilize the extra light available as the abundance of V. myrtillus decreased, while at the same time benefitting from the increased growth in the warmed plots. Even though the effect of the herbivore attacks did not differ between treatments they may have obscured any additional treatment effects. This long-term study highlights that also the effects of stochastic herbivory events need to be accounted for when predicting future plant community changes. creator: Brita M. Svensson creator: Bengt Å. Carlsson creator: Jerry M. Melillo uri: https://doi.org/10.7717/peerj.4843 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Svensson et al. title: Sorting nexin-1 is a candidate tumor suppressor and potential prognostic marker in gastric cancer link: https://peerj.com/articles/4829 last-modified: 2018-05-29 description: Sorting nexin-1 (SNX1) is an important functional protein in cell endocytosis, efflux, protein sorting, cell signal transduction, etc; however, the expression, the role and clinical relevance of SNX1 have not been investigated in gastric cancer (GC). In this study, we first performed a bioinformatics investigation using the data obtained from The Cancer Genome Atlas (TCGA) database. The result showed that SNX1 mRNA levels were significantly lower in GC tissues than in paracancerous tissues. In a study of 150 cases of GC, including 60 cases with paired paracancerous and cancer tissues and 90 cases with detailed follow-up information, SNX1 expression was analyzed by immunohistochemistry. Our study on paired paracancerous and cancer tissues showed that SNX1 protein expression remarkably decreased in GC tissues (50/60, 83.33%). A study on 90 patients with detailed follow-up information showed that tumors with higher SNX1 protein level were correlated with better clinicopathologic stages (p = 0.0285), nodal status (p = 0.0286), smaller tumor sizes (p = 0.0294) and a better survival rate in patients with GC (p = 0.0245). Univariate analysis of the 90 patients with GC showed that low-level SNX1 was significantly correlated with decreased overall survival of GC patients (p = 0.008), and associated with a relatively higher cumulative hazard of death. Exogenous expression of SNX1 inhibited the growth, migration, invasion and promoted the apoptosis and enhanced the sensitivity of GC cells to the chemotherapeutic drug 5-Fluorouracil (5-Fu) in vitro, while knockdown of SNX1 by short hairpin RNA (shRNA) significantly promoted the growth, migration, invasion and reduced the apoptosis and the sensitivity of GC cells to 5-Fu. SNX1 also showed to influence the levels of epithelial-mesenchymal transition markers including Vimentin, Snail, and E-cadherin in GC cells in vitro. Taken together, we propose here that SNX1 serves as a tumor suppressor and prognostic marker that reduces tumor cell malignancy for GC. creator: Xiao-Yong Zhan creator: Yaqiong Zhang creator: Ertao Zhai creator: Qing-Yi Zhu creator: Yulong He uri: https://doi.org/10.7717/peerj.4829 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhan et al. title: Genome-wide characterization and expression analysis of GRAS gene family in pepper (Capsicum annuum L.) link: https://peerj.com/articles/4796 last-modified: 2018-05-29 description: Plant-specific GRAS transcription factors regulate various biological processes in plant growth, development and stress responses. However, this important gene family was not fully characterized in pepper (Capsicum annuum L.), an economically important vegetable crop. Here, a total of 50 CaGRAS members were identified in pepper genome and renamed by their respective chromosomal distribution. Genomic organization revealed that most CaGRAS genes (84%) have no intron. Phylogenetic analysis divided pepper CaGRAS members into 10 subfamilies, with each having distinct conserved domains and functions. For the expansion of the GRAS genes in pepper, segmental duplication contributed more than tandem duplication did. Gene expression analysis in various tissues demonstrated that most of CaGRAS genes exhibited a tissue- and development stage-specific expression pattern, uncovering their potential functions in pepper growth and development. Moreover, 21 CaGRAS genes were differentially expressed under cold, drought, salt and gibberellin acid (GA) treatments, indicating that they may implicated in plant response to abiotic stress. Notably, GA responsive cis-elements were detected in the promoter regions of the majority of CaGRAS genes, suggesting that CaGRAS may involve in signal cross-talking. The first comprehensive analysis of GRAS gene family in pepper genome by this study provide insights into understanding the GRAS-mediated regulation network, benefiting the genetic improvements in pepper and some other relative plants. creator: Baoling Liu creator: Yan Sun creator: Jinai Xue creator: Xiaoyun Jia creator: Runzhi Li uri: https://doi.org/10.7717/peerj.4796 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liu et al. title: Exosomes in cancer: small vesicular transporters for cancer progression and metastasis, biomarkers in cancer therapeutics link: https://peerj.com/articles/4763 last-modified: 2018-05-29 description: Cancer progression is a polygenic procedure in which the exosomes can function as substantial roles. Exosomes are tiny, phospholipid bilayer membrane nanovesicles of endocytic derivation with a diameter of 40–100 nm. These nanovesicles can transport bioactive molecules containing mRNAs, proteins, DNA fragments, and non-coding RNAs from a donor cell to recipient cells, and cause the alteration in genetic and epigenetic factors and reprogramming of the target cells. Many diverse cell types such as mesenchymal cells, immune cells, and cancer cells can induce the release of exosomes. Increasing evidence illustrated that the exosomes derived from tumor cells might trigger the tumor initiation, tumor cell growth and progression, metastasis, and drug resistance. The secreted nanovesicles of exosomes can play significant roles in cells communicate via shuttling the nucleic acid molecules and proteins to target cells and tissues. In this review, we discussed multiple mechanisms related to biogenesis, load, and shuttle of the exosomes. Also, we illustrated the diverse roles of exosomes in several types of human cancer development, tumor immunology, angiogenesis, and metastasis. The exosomes may act as the promising biomarkers for the prognosis of various types of cancers which suggested a new pathway for anti-tumor therapeutic of these nanovesicles and promoted exosome-based cancer for clinical diagnostic and remedial procedures. creator: Atefe Abak creator: Alireza Abhari creator: Sevda Rahimzadeh uri: https://doi.org/10.7717/peerj.4763 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Abak et al. title: DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes link: https://peerj.com/articles/4742 last-modified: 2018-05-29 description: The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program detection, characterization, and reconstruction of repetitive regions, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases. creator: Alexander Seitz creator: Friederike Hanssen creator: Kay Nieselt uri: https://doi.org/10.7717/peerj.4742 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Seitz et al. title: Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data link: https://peerj.com/articles/4925 last-modified: 2018-05-28 description: High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer (ITS) amplicons, we created two ITS spike-in control mock communities composed of cloned DNA in plasmids: a biological mock community, consisting of ITS sequences from fungal taxa, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that: (1) a non-biological synthetic control (e.g., SynMock) is the best solution for parameterizing bioinformatics pipelines, (2) pre-clustering steps for variable length amplicons are critically important, (3) a major source of bias is attributed to the initial polymerase chain reaction (PCR) and thus HTAS read abundances are typically not representative of starting values. We developed AMPtk, a versatile software solution equipped to deal with variable length amplicons and quality filter HTAS data based on spike-in controls. While we describe herein a non-biological SynMock community for ITS sequences, the concept and AMPtk software can be widely applied to any HTAS dataset to improve data quality. creator: Jonathan M. Palmer creator: Michelle A. Jusino creator: Mark T. Banik creator: Daniel L. Lindner uri: https://doi.org/10.7717/peerj.4925 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: The relationship between body mass index and pain, disease activity, depression and anxiety in women with fibromyalgia link: https://peerj.com/articles/4917 last-modified: 2018-05-28 description: BackgroundObesity is a possible factor which affects severity of symptoms and disease activity in fibromyalgia syndrome (FMS). The aim of our study was to determine the association between body mass index (BMI) and pain, tender point count (TPC), disease activity, anxiety and depression in patients with FMS.MethodsThis was a descriptive study. A total of 124 female FMS patients between 18 and 55 years of age were enrolled. FMS patients were evaluated with visual analog scale (VAS), fibromyalgia impact questionnaire (FIQ), Hamilton anxiety scale (HAM-A) and Hamilton depression scale (HAM-D). Patients were divided into three groups according to BMI levels: normal weight, overweight and obese. Normal weight was defined as BMI 18.5–24.9, overweight as BMI 25.0–29.9 and obesity as BMI ≥ 30. We assessed the BMI status and its association with symptom severity in patients with FMS.ResultsSignificant differences were detected in VAS, TPC, FIQ and HAM-D among the groups (p < 0.05). There were no significant differences between the groups in HAM-A (p = 0.328). The highest scores were found in the obese group. Significant positive correlations were determined between BMI levels and VAS, TPC, FIQ and HAM-D (r = 0.277, p = 0.002; r = 0.384, p < 0.001; r = 0.292, p = 0.001; r = 0.357, p < 0.001).DiscussionObese female FMS patients had higher levels of pain, TPC, disease activity and depression. BMI was significantly and positively correlated with clinical manifestations of FMS. Therefore, FMS treatment programs should include weight loss strategies. creator: Burhan Fatih Koçyiğit creator: Ramazan Azim Okyay uri: https://doi.org/10.7717/peerj.4917 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Koçyiğit and Okyay title: Change of niche in guanaco (Lama guanicoe): the effects of climate change on habitat suitability and lineage conservatism in Chile link: https://peerj.com/articles/4907 last-modified: 2018-05-28 description: BackgroundThe main goal of this contribution was to define the ecological niche of the guanaco (Lama guanicoe), to describe potential distributional changes, and to assess the relative importance of niche conservatism and divergence processes between the two lineages described for the species (L.g. cacsilensis and L.g. guanicoe).MethodsWe used maximum entropy to model lineage’s climate niche from 3,321 locations throughout continental Chile, and developed future niche models under climate change for two extreme greenhouse gas emission scenarios (RCP2.6 and RCP8.5). We evaluated changes of the environmental niche and future distribution of the largest mammal in the Southern Cone of South America. Evaluation of niche conservatism and divergence were based on identity and background similarity tests.ResultsWe show that: (a) the current geographic distribution of lineages is associated with different climatic requirements that are related to the geographic areas where these lineages are located; (b) future distribution models predict a decrease in the distribution surface under both scenarios; (c) a 3% decrease of areal protection is expected if the current distribution of protected areas is maintained, and this is expected to occur at the expense of a large reduction of high quality habitats under the best scenario; (d) current and future distribution ranges of guanaco mostly adhere to phylogenetic niche divergence hypotheses between lineages.DiscussionAssociating environmental variables with species ecological niche seems to be an important aspect of unveiling the particularities of, both evolutionary patterns and ecological features that species face in a changing environment. We report specific descriptions of how these patterns may play out under the most extreme climate change predictions and provide a grim outlook of the future potential distribution of guanaco in Chile. From an ecological perspective, while a slightly smaller distribution area is expected, this may come with an important reduction of available quality habitats. From the evolutionary perspective, we describe the limitations of this taxon as it experiences forces imposed by climate change dynamics. creator: Andrea G. Castillo creator: Dominique Alò creator: Benito A. González creator: Horacio Samaniego uri: https://doi.org/10.7717/peerj.4907 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Castillo et al.