title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1275 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of radiotherapy on the gut microbiome in pediatric cancer patients: a pilot study link: https://peerj.com/articles/7683 last-modified: 2019-09-23 description: The incidence of pediatric cancer is lower than that of adult cancer worldwide. However, the former has detrimental side effects on the health of individuals, even after the cancer is cured, due to the impact of treatment on development. Recently, correlations have been made between the gut microbiome and cancer in several studies but only on adult participants. There is always a complication of dealing with pediatric cancer treatment protocols because they usually include a combination of chemotherapy, radiotherapy, and intensive prophylactic antibiotics. In the current study, a pilot study was conducted to analyze ten fecal samples from three pediatric cancer patients, suffering from rhabdomyosarcoma near their pelvic region, and two healthy individuals. A correlation between microbial composition and response to treatment was reported, in which the responders had generally a lower microbial diversity compared to non-responders. In addition, nucleotide changes and deletions in the tested 16S rRNA sequences post radiotherapy were detected. Despite the small sample size used in the experiments due to the uncommon rhabdomyosarcoma in children, the results can help in understanding the influence of radiotherapy on the gut microbiome in pediatric cancer patients. More work with larger sample size and different cancer types need to be conducted to understand the influence of radiotherapy on gut microbiome to mitigate the deleterious impact of radiation on treated children. creator: Nourhan Sahly creator: Ahmed Moustafa creator: Mohamed Zaghloul creator: Tamer Z. Salem uri: https://doi.org/10.7717/peerj.7683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sahly et al. title: Chemical profile and pancreatic lipase inhibitory activity of Sinobambusa tootsik (Sieb.) Makino leaves link: https://peerj.com/articles/7765 last-modified: 2019-09-23 description: BackgroundSinobambusa tootsik (Sieb.) Makino (S. tootsik) is one species of bamboo distributed in China, Japan and Vietnam. The chemical profile of its leaves and its potential application was unknown yet.MethodsThe chemical profile of S. tootsik was studied by HPLC and UPLC-DAD-QTOF-MS. The S. tootsik extract was prepared by extraction with 50% aqueous ethanol, followed by H103 macroporous resins adsorption and desorption processes. Pancreatic lipase inhibitory activity was determined using p-nitrophenyl palmitate as the substance, which was hydrolyzed by lipase to form coloured p-nitrophenol.ResultsEighteen compounds were identified in S. tootsik. Most of them were the C-glycosylated derivatives of luteolin and apigenin, such as isoorientin, isoorientin-2″-O-rhamnoside and isovitexin. Isoorientin-2″-O-rhamnoside was the most dominant flavonoid in the sample. S. tootsik extract was prepared through resin adsorption/desorption with yield of 1.12 ± 015% and total flavonoids content of 82 ± 2 mg/g (in term of isoorientin). The extract exhibited pancreatic lipase inhibitory activity with IC50 value of 0.93 mg/mL.ConclusionThe chemical profile of S. tootsik leaves was uncovered for the first time. C-glycosyl flavonoids were the main constituents in the plant. The extract exhibited pancreatic lipase inhibitory activity and may have potential for use as a food supplement for controlling obesity. creator: Xiao-Lin Qiu creator: Qing-Feng Zhang uri: https://doi.org/10.7717/peerj.7765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qiu and Zhang title: A comparison of inducible, ontogenetic, and interspecific sources of variation in the foliar metabolome in tropical trees link: https://peerj.com/articles/7536 last-modified: 2019-09-20 description: Plant interactions with other organisms are mediated by chemistry, yet chemistry varies among conspecific and within individual plants. The foliar metabolome—the suite of small-molecule metabolites found in the leaf—changes during leaf ontogeny and is influenced by the signaling molecule jasmonic acid. Species differences in secondary metabolites are thought to play an important ecological role by limiting the host ranges of herbivores and pathogens, and hence facilitating competitive coexistence among plant species in species-rich plant communities such as tropical forests. Yet it remains unclear how inducible and ontogenetic variation compare with interspecific variation, particularly in tropical trees. Here, we take advantage of novel methods to assemble mass spectra of all compounds in leaf extracts into molecular networks that quantify their chemical structural similarity in order to compare inducible and ontogenetic chemical variation to among-species variation in species-rich tropical tree genera. We ask (i) whether young and mature leaves differ chemically, (ii) whether jasmonic acid-inducible chemical variation differs between young and mature leaves, and (iii) whether interspecific exceeds intraspecific chemical variation for four species from four hyperdiverse tropical tree genera. We observed significant effects of the jasmonic acid treatment for three of eight combinations of species and ontogenetic stage evaluated. Three of the four species also exhibited large metabolomic differences with leaf ontogenetic stage. The profound effect of leaf ontogenetic stage on the foliar metabolome suggests a qualitative turnover in secondary chemistry with leaf ontogeny. We also quantified foliar metabolomes for 45 congeners of the four focal species. Chemical similarity was much greater within than between species for all four genera, even when within-species comparisons included leaves that differed in age and jasmonic acid treatment. Despite ontogenetic and inducible variation within species, chemical differences among congeneric species may be sufficient to partition niche space with respect to chemical defense. creator: Brian E. Sedio creator: Armando Durant Archibold creator: Juan Camilo Rojas Echeverri creator: Chloé Debyser creator: Cristopher A. Boya P creator: S. Joseph Wright uri: https://doi.org/10.7717/peerj.7536 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Effects of Trichophyton mentagrophytes infection on the immune response of rabbits link: https://peerj.com/articles/7632 last-modified: 2019-09-20 description: BackgroundRabbit breeding has developed into a large-scale industry, and as such, the incidence of dermatophytosis in rabbits has become increasingly common. A rabbit model with Trichophyton mentagrophytes infection was established to study the changes within the immune responses after fungal infection.MethodsAfter the T. mentagrophytes challenge on skin, pathogens on the skin were isolated from the rabbits in the fungal infection (FI) groups 20 days. Fungal observation under microscope were carried out. Identification of strains was achieved by polymerase chain reaction (PCR) using the CDR1 gene. The collected anticoagulant blood samples were analyzed for various blood cell parameters. The levels of antibodies, including IgM and IgA, cytokines, including IL-2, IL-6, and macrophage colony-stimulating factor (M-CSF), and soluble CD4 and CD8 in the serum of the FI group vs. the control group were determined independently. RNA isolation from blood samples and fluorescence-based quantitative PCR were carried out for the mRNA level of M-csf 20 days after fungal challenge.ResultsOur model resulted in typical symptoms of dermatophytosis on rabbit skin after challenged with fungus. Pathogens isolated from the infected rabbit skin were confirmed to be T. mentagrophytes by microscopic examination and PCR. The number of lymphocytes in the blood of the FI group was significantly decreased in comparison to the control group 2 days after the fungal challenge, but was significantly increased in comparison the control group 10 days after the fungal challenge (P < 0.01). Platelet counts of the FI group were significantly higher than in the control group at 2 (P < 0.05), 10 (P < 0.05), and 20 (P < 0.01) days after fungal challenge. The red blood cell distribution width of the FI group was significantly increased in comparison to that of the control group at 2, 10, and 20 days after fungal challenge (P < 0.01 for all days). The levels of antibodies (immunoglobulin (Ig) M and IgA (P < 0.01)), cytokines (interleukin (IL)-6 (P < 0.01), macrophage colony-stimulating factor (M-CSF) (P < 0.05)), and soluble CD4 (P < 0.01) and CD8 (P < 0.01) in the serum were significantly different between the FI and control groups. Serum M-csf mRNA level of the FI group was significantly higher than the control group 20 days after fungal challenge (P < 0.01).ConclusionsThis study demonstrates how the immune system responds to infection with T. mentagrophytes and provides potential targets for the prevention and treatment of dermatophytosis. creator: Chenwen Xiao creator: Guolian Bao creator: Qiang Wei creator: Yan Liu creator: Jiaoyu Wang creator: Quanan Ji creator: Yee Huang uri: https://doi.org/10.7717/peerj.7632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xiao et al. title: A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae link: https://peerj.com/articles/7649 last-modified: 2019-09-20 description: Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family. creator: Kevin Weitemier creator: Shannon C.K. Straub creator: Mark Fishbein creator: C. Donovan Bailey creator: Richard C. Cronn creator: Aaron Liston uri: https://doi.org/10.7717/peerj.7649 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Transposon mutagenesis reveals Pseudomonas cannabina pv. alisalensis optimizes its virulence factors for pathogenicity on different hosts link: https://peerj.com/articles/7698 last-modified: 2019-09-20 description: Pseudomonas cannabina pv. alisalensis (Pcal), which causes bacterial blight disease of Brassicaceae, is an economically important pathogen worldwide. To identify Pcal genes involved in pathogenesis, we conducted a screen for 1,040 individual Pcal KB211 Tn5 mutants with reduced virulence on cabbage plants using a dip-inoculation method. We isolated 53 reduced virulence mutants and identified several potential virulence factors involved in Pcal virulence mechanisms such as the type III secretion system, membrane transporters, transcription factors, and amino acid metabolism. Importantly, Pcal is pathogenic on a range of monocotyledonous and dicotyledonous plants. Therefore, we also carried out the inoculation test on oat plants, which are cultivated after cabbage cultivation as green manure crops. Interestingly among the 53 mutants, 31 mutants also exhibited reduced virulence on oat seedlings, indicating that Pcal optimizes its virulence factors for pathogenicity on different host plants. Our results highlight the importance of revealing the virulence factors for each plant host-bacterial interaction, and will provide new insights into Pcal virulence mechanisms. creator: Nanami Sakata creator: Takako Ishiga creator: Haruka Saito creator: Viet Tru Nguyen creator: Yasuhiro Ishiga uri: https://doi.org/10.7717/peerj.7698 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sakata et al. title: Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species link: https://peerj.com/articles/7713 last-modified: 2019-09-20 description: As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees. creator: Yong Yang creator: Ying Zhang creator: Yukai Chen creator: Juma Gul creator: Jingwen Zhang creator: Qiang Liu creator: Qing Chen uri: https://doi.org/10.7717/peerj.7713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: Role of miR-10b-5p in the prognosis of breast cancer link: https://peerj.com/articles/7728 last-modified: 2019-09-20 description: Breast cancer is the leading cause of cancer-related death in women worldwide. Aberrant expression levels of miR-10b-5p in breast cancer has been reported while the molecular mechanism of miR-10b-5p in tumorigenesis remains elusive. Therefore, this study was aimed to investigate the role of miR-10b-5p in breast cancer and the network of its target genes using bioinformatics analysis. In this study, the expression profiles and prognostic value of miR-10b-5p in breast cancer were analyzed from public databases. Association between miR-10b-5p and clinicopathological parameters were analyzed by non-parametric test. Moreover, the optimal target genes of miR-10b-5p were obtained and their expression patterns were examined using starBase and HPA database. Additionally, the role of these target genes in cancer development were explored via Cancer Hallmarks Analytics Tool (CHAT). The protein–protein interaction (PPI) networks were constructed to further investigate the interactive relationships among these genes. Furthermore, GO, KEGG pathway and Reactome pathway analyses were carried out to decipher functions of these target genes. Results demonstrated that miR-10b-5p was down-regulated in breast cancer and low expression of miR-10b-5p was significantly correlated to worse outcome. Five genes, BIRC5, E2F2, KIF2C, FOXM1, and MCM5, were considered as potential key target genes of miR-10b-5p. As expected, higher expression levels of these genes were observed in breast cancer tissues than in normal tissues. Moreover, analysis from CHAT revealed that these genes were mainly involved in sustaining proliferative signaling in cancer development. In addition, PPI networks analysis revealed strong interactions between target genes. GO, KEGG, and Reactome pathway analysis suggested that these target genes of miR-10b-5p in breast cancer were significantly involved in cell cycle. Predicted target genes were further validated by qRT-PCR analysis in human breast cancer cell line MDA-MB-231 transfected with miR-10b mimic or antisense inhibitors. Taken together, our data suggest that miR-10b-5p functions to impede breast carcinoma progression via regulation of its key target genes and hopefully serves as a potential diagnostic and prognostic marker for breast cancer. creator: Junmin Wang creator: Yanyun Yan creator: Zhiqi Zhang creator: Yali Li uri: https://doi.org/10.7717/peerj.7728 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Sleep apnea detection from a single-lead ECG signal with automatic feature-extraction through a modified LeNet-5 convolutional neural network link: https://peerj.com/articles/7731 last-modified: 2019-09-20 description: Sleep apnea (SA) is the most common respiratory sleep disorder, leading to some serious neurological and cardiovascular diseases if left untreated. The diagnosis of SA is traditionally made using Polysomnography (PSG). However, this method requires many electrodes and wires, as well as an expert to monitor the test. Several researchers have proposed instead using a single channel signal for SA diagnosis. Among these options, the ECG signal is one of the most physiologically relevant signals of SA occurrence, and one that can be easily recorded using a wearable device. However, existing ECG signal-based methods mainly use features (i.e. frequency domain, time domain, and other nonlinear features) acquired from ECG and its derived signals in order to construct the model. This requires researchers to have rich experience in ECG, which is not common. A convolutional neural network (CNN) is a kind of deep neural network that can automatically learn effective feature representation from training data and has been successfully applied in many fields. Meanwhile, most studies have not considered the impact of adjacent segments on SA detection. Therefore, in this study, we propose a modified LeNet-5 convolutional neural network with adjacent segments for SA detection. Our experimental results show that our proposed method is useful for SA detection, and achieves better or comparable results when compared with traditional machine learning methods. creator: Tao Wang creator: Changhua Lu creator: Guohao Shen creator: Feng Hong uri: https://doi.org/10.7717/peerj.7731 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers link: https://peerj.com/articles/7742 last-modified: 2019-09-20 description: Annual ryegrass (Lolium multiflorum) is a widely used cool-season turf and forage grass with high productivity and ornamental characteristics. However, the abundant intra-cultivar genetic variability usually hampers the application of conventional techniques for cultivar identification. The objectives of this study were to: (1) describe an efficient strategy for identification of six tetraploid annual ryegrass cultivars and (2) investigate the genetic diversity based on SSR markers. A total of 242 reliable bands were obtained from 29 SSR primer pairs with an average of 8.3 bands for each primer pair and the average value of polymorphic information content (PIC) was 0.304. The result of analysis of molecular variance (AMOVA) revealed that 81.99% of the genetic variation occurred in within-cultivars and 18.01% among-cultivars. The principal coordinate analysis (PCoA) showed that the first two principal axes explain 8.57% (PC1) and 6.05% (PC2) of total variation, respectively. By using multi-bulk strategy based on different filtering thresholds, the results suggested that bands frequency of 40% could be used as a reliable standard for cultivar identification in annual ryegrass. Under this threshold, 12 SSR primer pairs (00-04A, 02-06G, 02-08C, 03-05A, 04-05B, 10-09E, 12-01A, 13-02H, 13-12D, 14-06F, 15-01C and 17-10D) were detected for direct identification of six tetraploid annual ryegrass cultivars, which could be incorporated into conservation schemes to protect the intellectual property of breeders, ensure purity for consumers, as well as guarantee effective use of cultivars in future. creator: Gang Nie creator: Ting Huang creator: Xiao Ma creator: Linkai Huang creator: Yan Peng creator: Yanhong Yan creator: Zhou Li creator: Xia Wang creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.7742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nie et al.