title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1273 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Cloning of a new HSP70 gene from western flowerthrips, Frankliniella occidentalis, and expression patterns during thermal stress link: https://peerj.com/articles/7687 last-modified: 2019-09-25 description: Frankliniella occidentalis (Pergande) is an invasive pest that endangers a wide variety of horticultural and agronomic crops. HSP70 is the most important member of the heat shock protein (HSP) family and plays an important role in insect thermal tolerance. In this study, a new gene encoding HSP70 from F. occidentalis, Fohsp706, was selected from the F. occidentalis transcriptome exposed to thermal stress (40 °C) and cloned by RT-PCR and RACE. Further characterization indicated that Fohsp706 localizes to the cytoplasm and does not contain introns. Quantitative real-time reverse transcriptase PCR indicated that Fohsp706 expression was significantly up-regulated by thermal stress; furthermore, there were significant differences in Fohsp706 expression in adults and second instar nymphs after heat stress. Our results indicated that Fohsp706 contributes to thermotolerance in F. occidentalis and provides another example of how this pest adapts to unfavorable environmental conditions. creator: Xiao-xiang Zhang creator: Jing Qin creator: Jia-Wen Yuan creator: Ming-Xing Lu creator: Yu-Zhou Du uri: https://doi.org/10.7717/peerj.7687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: The interplay between cognitive tasks and vision for upright posture balance in adolescents link: https://peerj.com/articles/7693 last-modified: 2019-09-25 description: BackgroundThe control of an upright stance in humans is important in medicine, psychology, and physiology. The maintenance of upright stance balance depends not only on sensory information from proprioceptive, vestibular, cutaneous, and visual sources but also on cognitive resources. The present study investigated the effects of cognitive tasks while standing with eyes open on upright stance balance in adolescents. We hypothesized that performing a cognitive task while standing with eyes open would increase body sway among these adolescents and that the upright posture would thus become less stable.MethodsA static balance assessment system comprising a force platform connected to a computer was used to evaluate the stability of the upright stance among 21 healthy adolescents under six conditions: no cognitive task, a relatively easy cognitive task, or the same cognitive task made more difficult, with each task being performed while the eyes were open and again while the eyes were closed. The participants performed mental calculations as fast as possible by subtracting either 3 or 18 from a random three-digit number continuously, for the simple cognitive task or the difficult cognitive task, respectively. Each calculation was completed within 10 s. The evaluation indexes used to measure upright posture stability were the root mean square (RMS) of the total body sway in the mediolateral and anteroposterior directions, the mean velocity (MV) value of the total body sway, and the Romberg quotient (RQ) of these values.ResultsThe RMS (p < 0.01) and MV (p < 0.01) values of the upright posture sway were lower when participants performed no cognitive task and their eyes were open than when their eyes were closed. When their eyes were open, compared with no cognitive task, the values of the measures evaluating upright posture sway were higher, meaning the stance was less stable, while performing either the simple or the more difficult cognitive task (RMS: simple task, p < 0.01; difficult task, p < 0.05; MV: simple task, p < 0.01; difficult task, p < 0.01) although no significant differences were detected for the RMS or MV values between the simple and more difficult cognitive tasks. The RQs for both the RMS and the total MV values of the upright posture sway during performance of the difficult cognitive task were significantly lower than when the participants performed no task.ConclusionPerformance of a cognitive task significantly reduced the upright posture balance in adolescents during eyes open although increased task difficulty did not show a greater effect. The interference between the performance of a cognitive task and the visual control of an upright stance may be attributable in part to cognitive and visual processing streams competing for common central resources, consistent with the Multiple Resource Theory of information processing. creator: Hai-Jiang Meng creator: Shan-Shan Luo creator: Yuan-Gang Wang uri: https://doi.org/10.7717/peerj.7693 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Meng et al. title: Soil warming increases soil temperature sensitivity in subtropical Forests of SW China link: https://peerj.com/articles/7721 last-modified: 2019-09-25 description: BackgroundSoil respiration (RS) plays an important role in the concentration of atmospheric CO2 and thus in global climate patterns. Due to the feedback between RS and climate, it is important to investigate RS responses to climate warming.MethodsA soil warming experiment was conducted to explore RS responses and temperature sensitivity (Q10) to climate warming in subtropical forests in Southwestern China, and infrared radiators were used to simulate climate warming.ResultsWarming treatment increased the soil temperature and RS value by 1.4 °C and 7.3%, respectively, and decreased the soil water level by 4.2% (%/%). Both one- and two-factor regressions showed that warming increased the Q10 values by 89.1% and 67.4%, respectively. The effects of water on Q10show a parabolic relationship to the soil water sensitivity coefficient. Both RS and Q10 show no acclimation to climate warming, suggesting that global warming will accelerate soil carbon release. creator: Chaoxiang Yuan creator: Guiqing Zhu creator: Shuangna Yang creator: Gang Xu creator: Yingyun Li creator: Hede Gong creator: Chuansheng Wu uri: https://doi.org/10.7717/peerj.7721 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yuan et al. title: Brodifacoum does not modulate human cannabinoid receptor-mediated hyperpolarization of AtT20 cells or inhibition of adenylyl cyclase in HEK 293 cells link: https://peerj.com/articles/7733 last-modified: 2019-09-25 description: BackgroundSynthetic cannabinoids are a commonly used class of recreational drugs that can have significant adverse effects. There have been sporadic reports of co-consumption of illicit drugs with rodenticides such as warfarin and brodifacoum (BFC) over the past 20 years but recently, hundreds of people have been reported to have been poisoned with a mixture of synthetic cannabinoids and BFC. We have sought to establish whether BFC directly affects cannabinoid receptors, or their activation by the synthetic cannabinoid CP55940 or the phytocannabinoid Δ9-tetrahydrocannabinol (Δ9-THC).MethodsThe effects of BFC on the hyperpolarization of wild type AtT20 cells, or AtT20 cells stably expressing human CB1- or CB2- receptors, were studied using a fluorescent assay of membrane potential. The effect of BFC on CB1- and CB2-mediated inhibition of forskolin-stimulated adenylyl cyclase (AC) activation was measured using a BRET assay of cAMP levels in HEK 293 cells stably expressing human CB1 or CB2.ResultsBFC did not activate CB1 or CB2 receptors, or affect the hyperpolarization of wild type AtT20 cells produced by somatostatin. BFC (1 µM) did not affect the hyperpolarization of AtT20-CB1 or AtT20-CB2 cells produced by CP55940 or Δ9-THC. BFC (1 µM) did not affect the inhibition of forskolin-stimulated AC activity by CP55940 in HEK 293 cells expressing CB1 or CB2. BFC (1 µM) also failed to affect the desensitization of CB1 and CB2 signaling produced by prolonged (30 min) application of CP55940 or Δ9-THC to AtT20 cells.DiscussionBFC is not a cannabinoid receptor agonist, and appeared not to affect cannabinoid receptor activation. Our data suggests there is no pharmacodynamic rationale for mixing BFC with synthetic cannabinoids; however, it does not speak to whether BFC may affect synthetic cannabinoid metabolism or biodistribution. The reasons underlying the mixing of BFC with synthetic cannabinoids are unknown, and it remains to be established whether the “contamination” was deliberate or accidental. However, the consequences for people who ingested the mixture were often serious, and sometimes fatal, but this seems unlikely to be due to BFC action at cannabinoid receptors. creator: Shivani Sachdev creator: Rochelle Boyd creator: Natasha L. Grimsey creator: Marina Santiago creator: Mark Connor uri: https://doi.org/10.7717/peerj.7733 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sachdev et al. title: Identification of genes encoding ALMT and MATE transporters as candidate aluminum tolerance genes from a typical acid soil plant, Psychotria rubra (Rubiaceae) link: https://peerj.com/articles/7739 last-modified: 2019-09-25 description: To understand how tropical plants have adapted to acid soils, we analyzed the transcriptome of seedlings of Psychotria rubra, a typical species found on acid soils. Using RNA-seq, we identified 22,798 genes, including several encoding proteins of the Al3+-activated malate transporter (ALMT) and multidrug and toxic compound extrusion (MATE) families. Molecular phylogenetic analysis of ALMTs and MATEs revealed the grouping of those from P. rubra, which may be useful to select targets for elucidating the molecular basis of P. rubra adaptation to acid soils in the future. The transcriptome datasets obtained in this study would help us to further understand the physiological and ecological aspects of soil adaptation of Psychotria species. creator: Akira Iguchi creator: Kazutsuka Sanmiya creator: Kenta Watanabe uri: https://doi.org/10.7717/peerj.7739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Iguchi et al. title: Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.) link: https://peerj.com/articles/7750 last-modified: 2019-09-25 description: BackgroundStarch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism, determining amylopectin structure.MethodsFull length coding sequences (CDS) of SBE genes were cloned using reverse transcription PCR (RT-PCR) technology, and neighbor-joining (NJ) tree was used for phylogenetic analysis. Single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyze the spatial and temporal expression of NnSBE genes. The effect of NnSBE genes on amylopectin’s fine structures was explored using affinity and the enzyme activity analysis of two isoforms in amylopectin and amylose.ResultsIn this study, two SBE family genes, NnSBEI and NnSBEIII, were identified in lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis sorted NnSBEI into SBE family B and NnSBEIII into SBE family A. UPGMA phylogenetic tree divided 45 individuals of lotus into three classes. The homozygous haplotype (A G G A G) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in the middle of the development stage, while NnSBEI increased in the mid-late developmental stage. The different affinity activity of the two isozymes binding amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity.DiscussionGenetic diversity showed that NnSBE genes received artificial selection during the process of cultivation and domestication in lotus seeds. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes were related to the chain length of amylopectin. creator: Fenglin Zhu creator: Han Sun creator: Ying Diao creator: Xingwen Zheng creator: Keqiang Xie creator: Zhongli Hu uri: https://doi.org/10.7717/peerj.7750 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhu et al. title: Cloning expression and immunogenicity analysis of inhibin gene in Ye Mule Aries sheep link: https://peerj.com/articles/7761 last-modified: 2019-09-25 description: BackgroundYe Mule Aries sheep is one of the most important sheep breeds in Xinjiang, China. This breed is well adapted to harsh environmental conditions and displays strong disease resistance, fast growth, and high cold tolerance. To analyze the clonal expression and immunogenicity of the Ye Mule Aries sheep inhibin gene, total RNA was extracted from sheep ovarian tissue and used as a template to generate a eukaryotic expression vector and study inhibin immunogenicity.MethodsPrimers were designed to amplify the inhibin A gene via polymerase chain reaction and the amplified product was cloned between the ScalI and EcoRI restriction sites of the expression vector pEGFP-N1 to construct a recombinant plasmid, pEGFP-INHα. Following the validation of successful cloning, the pEGFP-INHα plasmid was transfected into BHK cells to verify expression in eukaryotes and subsequently utilized as an antigen in rabbits. Rabbits were tested for anti-inhibin antibodies and serum follicle-stimulating hormone (FSH) concentrations.ResultsThe analysis of the INHα gene sequence revealed that INHα is 1109 bp long and is translated to an approximately 40 KDa protein. Bioinformatics approach indicated that the INHα gene is highly conserved between organisms. Immunization with the eukaryotic expression vector, pEGFP-INHα, which expresses the INHα gene elicited immune response and generatigeneration on of anti-INHα antibody. The antibody had a significant regulatory effect on the serum concentration of FSH in rabbits and led to higher levels of FSH, indicating increased ovary function.ConclusionsThe present work resulted in a successful construction of eukaryotic expression plasmid pEGFP-INHα and verified the immunogenicity of this highly conserved protein. Further, the expression of pEGFP-INHα was shown to have a significant impact on the secretion of FSH, indicating a potential regulatory role in ovarian function. In conclusion, our current findings can serve as a working model for studying the effect of INHα on the breeding performance of Ye Mule Aries sheep, providing a novel strategy to improve their reproduction rates. creator: Zengwen Huang creator: Juan Zhang creator: WuReliHazi Hazihan creator: Zhengyun Cai creator: Guosheng Xin creator: Xiaofang Feng creator: Yaling Gu uri: https://doi.org/10.7717/peerj.7761 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huang et al. title: Human disturbance caused stronger influences on global vegetation change than climate change link: https://peerj.com/articles/7763 last-modified: 2019-09-25 description: Global vegetation distribution has been influenced by human disturbance and climate change. The past vegetation changes were studied in numerous studies while few studies had addressed the relative contributions of human disturbance and climate change on vegetation change. To separate the influences of human disturbance and climate change on the vegetation changes, we compared the existing vegetation which indicates the vegetation distribution under human influences with the potential vegetation which reflects the vegetation distribution without human influences. The results showed that climate-induced vegetation changes only occurred in a few grid cells from the period 1982–1996 to the period 1997–2013. Human-induced vegetation changes occurred worldwide, except in the polar and desert regions. About 3% of total vegetation distribution was transformed by human activities from the period 1982–1996 to the period 1997–2013. Human disturbances caused stronger damage to global vegetation change than climate change. Our results indicated that the regions where vegetation experienced both human disturbance and climate change are eco-fragile regions. creator: Xianliang Zhang creator: Xuanrui Huang uri: https://doi.org/10.7717/peerj.7763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang and Huang title: Development of a highly sensitive magneto-enzyme lateral flow immunoassay for dengue NS1 detection link: https://peerj.com/articles/7779 last-modified: 2019-09-25 description: BackgroundDengue infection represents a global health issue of growing importance. Dengue non-structural protein 1 (NS1) plays a central role in the early detection of the disease. The most common method for NS1 detection is testing by lateral flow immunoassays (LFIAs) with varying sensitivity. In this study, we present a highly sensitive magneto-enzyme LFIA for prompt diagnosis of dengue.MethodsWe have demonstrated the development of a magneto-enzyme LFIA combining super-paramagnetic nanoparticles as labels and Biotin–Streptavidin signal amplification strategy to detect dengue NS1. Factors affecting the test performance including antibody pair, super-paramagnetic nanoparticle size, nitrocellulose membrane type, amounts of detection and capture antibodies, and amounts of Streptavidin-polyHRP were optimized. Analytical sensitivity and cross-reactivity were determined. Clinical performance of the novel assay was evaluated using a panel of 120 clinical sera.ResultsThis newly developed assay could detect NS1 of all four serotypes of dengue virus (DENV). The limit of detection (LOD) was found to be as low as 0.25 ng ml−1 for DENV-1 and DENV-3, 0.1 ng ml−1 for DENV-2, and 1.0 ng ml−1 for DENV-4. The LOD for DENV-2 was a 50-fold improvement over the best values previously reported. There was an absence of cross-reactivity with Zika NS1, Hepatitis B virus, Hepatitis C virus, and Japanese encephalitis virus. The sensitivity and specificity of the novel assay were 100% when tested on clinical samples.ConclusionsWe have successfully developed a magneto-enzyme LFIA, allowing rapid and highly sensitive detection of dengue NS1, which is essential for proper management of patients infected with DENV. creator: Tien V. Tran creator: Ba V. Nguyen creator: Thao T.P. Nguyen creator: Tung T. Tran creator: Khanh G. Pham creator: Quang B. Le creator: Binh N. Do creator: Hung N. Pham creator: Chuyen V. Nguyen creator: Duong P.H. Dinh creator: Van T. Ha creator: Trang H.T. Doan creator: Hoa Q. Le uri: https://doi.org/10.7717/peerj.7779 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tran et al. title: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics link: https://peerj.com/articles/7558 last-modified: 2019-09-24 description: BackgroundChloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.MethodsMitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.ResultsThe sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane’s female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed.ConclusionTranscript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars. creator: Dyfed Lloyd Evans creator: Thandekile Thandiwe Hlongwane creator: Shailesh V. Joshi creator: Diego M. Riaño Pachón uri: https://doi.org/10.7717/peerj.7558 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lloyd Evans et al.