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: 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. title: Tanaella quintanai, a new deep-water tanaellid (Crustacea: Peracarida: Tanaidacea) from the Colombian Caribbean Coast, with a key to the species of the genus Tanaella Norman & Stebbing, 1886 link: https://peerj.com/articles/7571 last-modified: 2019-09-24 description: A new tanaidacean, Tanaella quintanai sp. nov., is described based on specimens collected from depths of 1,598 to 2,853 m during 2014–2015. The new species appears to be most closely related to the western Atlantic species, T. kroyeri and T. mclellandi. Tanaella quintanai can be separated from the two former, as well as from the other members of the genus by a combination of characters, including (1) a labium with apical lobe bearing one blunt seta (2) a cheliped with the inner margin of the dactylus bearing a sub-proximal bipinnate seta, (3) pereopods 1−3 with basis having sub-dorsoproximal and sub-ventroproximal margins setulose, (4) pereopods 4−6 with basis having ventroproximal margin setulose, (5) pereopods 4−6 with unguis bearing two parallel rows of small setules, and (6) a pleotelson as long as pleonites 1–5 combined. A key separating the currently recognized species of Tanaella is presented. creator: Andrés G. Morales-Núñez creator: Néstor E. Ardila uri: https://doi.org/10.7717/peerj.7571 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Morales-Núñez and Ardila title: In situ growth and bioerosion rates of Lophelia pertusa in a Norwegian fjord and open shelf cold-water coral habitat link: https://peerj.com/articles/7586 last-modified: 2019-09-24 description: Coral reef resilience depends on the balance between carbonate precipitation, leading to reef growth, and carbonate degradation, for example, through bioerosion. Changes in environmental conditions are likely to affect the two processes differently, thereby shifting the balance between reef growth and degradation. In cold-water corals estimates of accretion-erosion processes in their natural habitat are scarce and solely live coral growth rates were studied with regard to future environmental changes in the laboratory so far, limiting our ability to assess the potential of cold-water coral reef ecosystems to cope with environmental changes. In the present study, growth rates of the two predominant colour morphotypes of live Lophelia pertusa as well as bioerosion rates of dead coral framework were assessed in different environmental settings in Norwegian cold-water coral reefs in a 1-year in situ experiment. Net growth (in weight gain and linear extension) of live L. pertusa was in the lower range of previous estimates and did not significantly differ between inshore (fjord) and offshore (open shelf) habitats. However, slightly higher net growth rates were obtained inshore. Bioerosion rates were significantly higher on-reef in the fjord compared to off-reef deployments in- and offshore. Besides, on-reef coral fragments yielded a broader range of individual growth and bioerosion rates, indicating higher turnover in live reef structures than off-reef with regard to accretion–bioerosion processes. Moreover, if the higher variation in growth rates represents a greater variance in (genetic) adaptations to natural environmental variability in the fjord, inshore reefs could possibly benefit under future ocean change compared to offshore reefs. Although not significantly different due to high variances between replicates, growth rates of orange branches were consistently higher at all sites, while mortality was statistically significantly lower, potentially indicating higher stress-resistance than the less pigmented white phenotype. Comparing the here measured rates of net accretion of live corals (regardless of colour morphotype) with net erosion of dead coral framework gives a first estimate of the dimensions of both processes in natural cold-water coral habitats, indicating that calcium carbonate loss through bioerosion amounts to one fifth to one sixth of the production rates by coral calcification (disregarding accretion processes of other organisms and proportion of live and dead coral framework in a reef). With regard to likely accelerating bioerosion and diminishing growth rates of corals under ocean acidification, the balance of reef accretion and degradation may be shifted towards higher biogenic dissolution in the future. creator: Janina V. Büscher creator: Max Wisshak creator: Armin U. Form creator: Jürgen Titschack creator: Kerstin Nachtigall creator: Ulf Riebesell uri: https://doi.org/10.7717/peerj.7586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Büscher et al. title: Estimating flowering transition dates from status-based phenological observations: a test of methods link: https://peerj.com/articles/7720 last-modified: 2019-09-24 description: The scale of phenological research has expanded due to the digitization of herbarium specimens and volunteer based contributions. These data are status-based, representing the presence or absence of a specific phenophase. Modelling the progress of plant dormancy to growth and reproduction and back to dormancy requires estimating the transition dates from these status-based observations. There are several methods available for this ranging from statistical moments using the day of year to newly introduced methods using concepts from other fields. Comparing the proficiency of different estimators is difficult since true transition dates are rarely known. Here I use a recently released dataset of in-situ flowering observations of the perennial forb Echinacea angustifolia. In this dataset, due to high sampling frequency and unique physiology, the transition dates of onset, peak, and end of flowering are known to within 3 days. I used a Monte Carlo analysis to test eight different estimators across two scales using a range of sample sizes and proportion of flowering presence observations. I evaluated the estimators accuracy in predicting the onset, peak, and end of flowering at the population level, and predicting onset and end of flowering for individual plants. Overall, a method using a Weibull distribution performed the best for population level onset and end estimates, but other estimators may be more appropriate when there is a large amount of absence observations relative to presence observations. For individual estimates a method using the midway point between the first flower presence and most prior flower absence, within 7 days, is the best option as long as the restriction does not limit the final sample size. Otherwise, the Weibull method is adequate for individual estimates as well. These methods allow practitioners to effectively utilize the large amount of status-based phenological observations currently available. creator: Shawn D. Taylor uri: https://doi.org/10.7717/peerj.7720 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Taylor title: ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics link: https://peerj.com/articles/7729 last-modified: 2019-09-24 description: Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed. creator: Marco Cacciabue creator: Anabella Currá creator: Maria I. Gismondi uri: https://doi.org/10.7717/peerj.7729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cacciabue et al. title: Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats link: https://peerj.com/articles/7743 last-modified: 2019-09-24 description: The hypothalamus has an integral role in energy homeostasis regulation, and its dysfunctions lead to the development of type 2 diabetes (T2D). Physical activity positively affects the prevention and treatment of T2D. However, there is not much information on the adaptive mechanisms of the hypothalamus. In this study, RNA sequencing was used to determine how acute exercise affects hypothalamic transcriptome from both type 2 diabetic Goto-Kakizaki (GK) and control Wistar rats with or without a single session of running (15 m/min for 60 min). Through pairwise comparisons, we identified 957 differentially expressed genes (DEGs), of which 726, 197, and 98 genes were found between GK and Wistar, exercised GK and GK, and exercised Wistar and Wistar, respectively. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that lipid metabolism-related terms and pathways were enriched in GK and exercised GK rats, and nervous system related terms and pathways were enriched in exercised GK and Wistar rats. Furthermore, 45 DEGs were associated with T2D and related phenotypes according to the annotations in the Rat Genome Database. Among these 45 DEGs, several genes (Plin2, Cd36, Lpl, Wfs1, Cck) related to lipid metabolism or the nervous system are associated with the exercise-induced benefits in the hypothalamus of GK rats. Our findings might assist in identifying potential therapeutic targets for T2D prevention and treatment. creator: Shuying Fu creator: Yuhuan Meng creator: Shudai Lin creator: Wenlu Zhang creator: Yuting He creator: Lizhen Huang creator: Hongli Du uri: https://doi.org/10.7717/peerj.7743 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fu et al. title: Characterizing gene tree conflict in plastome-inferred phylogenies link: https://peerj.com/articles/7747 last-modified: 2019-09-24 description: Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes. creator: Joseph F. Walker creator: Nathanael Walker-Hale creator: Oscar M. Vargas creator: Drew A. Larson creator: Gregory W. Stull uri: https://doi.org/10.7717/peerj.7747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Walker et al. title: Efficacy of Paclitaxel plus TS1 against previously treated EGFR mutated non-small cell lung cancer link: https://peerj.com/articles/7767 last-modified: 2019-09-24 description: BackgroundLater line chemotherapy (≥2nd lines) such as Docetaxel or immunotherapy is frequently used. As the life expectancy of lung cancer patients is getting longer, we need to provide more treatment options. Other treatment options are not well documented except for Doxetaxel and immunotherapy. Therefore, the efficacy of paclitaxel plus TS1 (TTS1) is warranted.MethodsWe retrospectively reviewed the chart records of our non-small cell lung cancer patients who were treated between 2010 and 2013. Clinical characteristics, type of tumor, EGFR mutation status, and treatment response to first-line EGFR-TKI therapy and efficacy of TTS1, were collected.ResultsTwenty eight patients were enrolled in this study. No patients archived complete response and seven patients had partial response (ORR: 25%). The disease control rate was 60.7% (17/28). The progression free survival (PFS) was 4.0 months and overall survival (OS) was 15.8 months. Of them, 17 had EGFR mutations, eight EGFR wild type, and three were unknown EGFR status. After TTS1 treatment, patients with EGFR mutations had better PFS (4.9 months vs. 1.8 months) and OS (15.5 months vs. 7.2 months) compared with those of EGFR wild type.ConclusionsTTS1 are effective later line chemotherapy, especially in tumor EGFR mutated patients. Paclitaxel plus TS1 is another treatment of choice for NSCLC patients before a more effective treatment strategy is found. creator: Yen-Han Tseng creator: Jen-Fu Shih creator: Heng-Sheng Chao creator: Yuh-Min Chen uri: https://doi.org/10.7717/peerj.7767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tseng et al.