title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1527 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Transcranial direct current stimulation over the right DLPFC selectively modulates subprocesses in working memory link: https://peerj.com/articles/4906 last-modified: 2018-05-28 description: BackgroundWorking memory, as a complex system, consists of two independent components: manipulation and maintenance process, which are defined as executive control and storage process. Previous studies mainly focused on the overall effect of transcranial direct current stimulation (tDCS) on working memory. However, little has been known about the segregative effects of tDCS on the sub-processes within working memory.MethodTranscranial direct current stimulation, as one of the non-invasive brain stimulation techniques, is being widely used to modulate the cortical activation of local brain areas. This study modified a spatial n-back experiment with anodal and cathodal tDCS exertion on the right dorsolateral prefrontal cortex (DLPFC), aiming to investigate the effects of tDCS on the two sub-processes of working memory: manipulation (updating) and maintenance. Meanwhile, considering the separability of tDCS effects, we further reconfirmed the causal relationship between the right DLPFC and the sub-processes of working memory with different tDCS conditions.ResultsThe present study showed that cathodal tDCS on the right DLPFC selectively improved the performance of the modified 2-back task in the difficult condition, whereas anodal tDCS significantly reduced the performance of subjects and showed an speeding-up tendency of response time. More precisely, the results of discriminability index and criterion showed that only cathodal tDCS enhanced the performance of maintenance in the difficult condition. Neither of the two tDCS conditions affected the performance of manipulation (updating).ConclusionThese findings provide evidence that cathodal tDCS of the right DLPFC selectively affects maintenance capacity. Besides, cathodal tDCS also serves as an interference suppressor to reduce the irrelevant interference, thereby indirectly improving the working memory capacity. Moreover, the right DLPFC is not the unique brain regions for working memory manipulation (updating). creator: Jiarui Wang creator: Jinhua Tian creator: Renning Hao creator: Lili Tian creator: Qiang Liu uri: https://doi.org/10.7717/peerj.4906 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al. title: Proteomics of Nasonia vitripennis and the effects of native Wolbachia infection on N. vitripennis link: https://peerj.com/articles/4905 last-modified: 2018-05-28 description: BackgroundNasonia vitripennis, a parasitic wasp, is a good model organism to study developmental and evolutionary genetics and to evaluate the interactions between insect hosts and their symbionts. Wolbachia may be the most prevalent endosymbiont among insect species due to their special ability to improve the fitness of the infected hosts. Transinfection of bacteria or fungi could substantially alter the expression of host immune system components. However, few studies have focused on the effects of native Wolbachia infection. Accordingly, in this study, we evaluated the proteomics of N. vitripennis following Wolbachia infection.MethodsWe studied the proteomics of N. vitripennis following native Wolbachia infection and in antibiotic-treated Wolbachia-free samples using isobaric tags for relative and absolute quantification-liquid chromatography tandem mass spectrometry, accompanying with some ecological experiments.ResultsIn total, 3,096 proteins were found to be associated with a wide range of biological processes, molecular functions, and cellular components. Interestingly, there were few significant changes in immune or reproductive proteins between samples with and without Wolbachia infection. Differentially expressed proteins were involved in the binding process, catalytic activity, and the metabolic process, as confirmed by quantitative reverse transcription polymerase chain reaction.DiscussionInvasion of any pathogen or bacterium within a short time can cause an immunoreaction in the host. Our results implied that during the long process of coexistence, the immune system of the host was not as sensitive as when the symbiont initially infected the host, implying that the organisms had gradually adjusted to cohabitation. creator: Jie Li creator: Ningxin Wang creator: Yong Liu creator: Shiqi Qiu uri: https://doi.org/10.7717/peerj.4905 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China link: https://peerj.com/articles/4893 last-modified: 2018-05-28 description: ObjectivesThe prognosis of people with pancreatic cancer is extremely unfavorable. However, the prognostic factors remain largely undefined. We aimed to perform comprehensive analyses of clinicopathologic characteristics, laboratory parameters, and treatment protocols for exploring their role as prognostic factors of pancreatic cancer.MethodsPatients diagnosed with pancreatic cancer and hospitalized at the China National Cancer Center between April 2006 and May 2016 were enrolled in this retrospective cohort study. Clinicopathologic characteristics, laboratory parameters, and treatment protocols were compared among patients at different stages of the disease. The association between these factors and overall survival (OS) was analyzed using the Kaplan–Meier method and Cox proportional hazards model.ResultsThe present study included 1,433 consecutive patients with pancreatic cancer. Median OS was 10.6 months (95% confidence interval [CI] 9.8–11.3 months), with 1-, 3-, and 5-year survival rates of 43.7%, 14.8%, and 8.8%, respectively. Cox multivariate analysis findings identified the following factors as independent predictors of OS: gender (female vs male, hazard ratio 0.72, 95% CI [0.54–0.95]); elevated total bilirubin (TBil; 1.82, 1.34–2.47); elevated carbohydrate antigen 19-9 (CA19-9; 1.72, 1.17–2.54); tumor being located in pancreatic body and tail (1.52, 1.10–2.10); advanced T stage (T3-4 vs T1-2, 1.62, 1.15–2.27); lymph node metastasis (1.57, 1.20–2.07); distant metastasis (1.59, 1.12–2.27); the presence of surgical resection (0.53, 0.34–0.81); and the presence of systemic chemotherapy (0.62, 0.45–0.82).ConclusionsBeing male, elevated TBil and carcinoembryonic antigen, tumor being located in pancreatic body and tail, advanced T stage, lymph node and distant metastasis, the absence of surgical resection, and the absence of systematic chemotherapy were associated with worse OS in patients with pancreatic cancer. creator: Shuisheng Zhang creator: Xiaozhun Huang creator: Yuan Tian creator: Saderbieke Aimaiti creator: Jianwei Zhang creator: Jiuda Zhao creator: Yingtai Chen creator: Chengfeng Wang uri: https://doi.org/10.7717/peerj.4893 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhang et al. title: BLAST-based validation of metagenomic sequence assignments link: https://peerj.com/articles/4892 last-modified: 2018-05-28 description: When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by “first-pass” classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available. creator: Adam L. Bazinet creator: Brian D. Ondov creator: Daniel D. Sommer creator: Shashikala Ratnayake uri: https://doi.org/10.7717/peerj.4892 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bazinet et al.