PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of a highly sensitive magneto-enzyme lateral flow immunoassay for dengue NS1 detection
items: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics
items: 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
items: In situ growth and bioerosion rates of Lophelia pertusa in a Norwegian fjord and open shelf cold-water coral habitat
items: Estimating flowering transition dates from status-based phenological observations: a test of methods
items: ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
items: Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats
items: Characterizing gene tree conflict in plastome-inferred phylogenies
items: Efficacy of Paclitaxel plus TS1 against previously treated EGFR mutated non-small cell lung cancer
items: Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth

Development of a highly sensitive magneto-enzyme lateral flow immunoassay for dengue NS1 detection
type: item
type: AcademicArticle
description: Background Dengue 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. Methods We 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. Results This 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. Conclusions We 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.
format: application/pdf
format: text/html
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
subject: Biotechnology
subject: Infectious Diseases
description: doi:10.7717/peerj.7779
publisher: PeerJ Inc.
rights: © 2019 Tran et al.
abstract: Background Dengue 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. Methods We 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. Results This 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. Conclusions We 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.
bibliographic citation: Tran et al. (2019) Development of a highly sensitive magneto-enzyme lateral flow immunoassay for dengue NS1 detection. PeerJ 7:e7779 https://doi.org/10.7717/peerj.7779
date submitted: 2019-04-12
date accepted: 2019-08-28
issued: 2019-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tran
  given name: Tien V.
author list: Agent
  family name: Nguyen
  given name: Ba V.
author list: Agent
  family name: Nguyen
  given name: Thao T.P.
author list: Agent
  family name: Tran
  given name: Tung T.
author list: Agent
  family name: Pham
  given name: Khanh G.
author list: Agent
  family name: Le
  given name: Quang B.
author list: Agent
  family name: Do
  given name: Binh N.
author list: Agent
  family name: Pham
  given name: Hung N.
author list: Agent
  family name: Nguyen
  given name: Chuyen V.
author list: Agent
  family name: Dinh
  given name: Duong P.H.
author list: Agent
  family name: Ha
  given name: Van T.
author list: Agent
  family name: Doan
  given name: Trang H.T.
author list: Agent
  family name: Le
  given name: Hoa Q.
doi: 10.7717/peerj.7779
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-25
copyright: © 2019 Tran et al.
attribution name: Tran et al.

The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics
type: item
type: AcademicArticle
description: Background Chloroplast 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. Methods Mitochondrial 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. Results The 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 spl…
format: application/pdf
format: text/html
creator: Dyfed Lloyd Evans
creator: Thandekile Thandiwe Hlongwane
creator: Shailesh V. Joshi
creator: Diego M. Riaño Pachón
subject: Agricultural Science
subject: Bioinformatics
description: doi:10.7717/peerj.7558
publisher: PeerJ Inc.
rights: © 2019 Lloyd Evans et al.
abstract: Background Chloroplast 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. Methods Mitochondrial 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. Results The 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 spl…
bibliographic citation: Lloyd Evans et al. (2019) The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PeerJ 7:e7558 https://doi.org/10.7717/peerj.7558
date submitted: 2019-03-12
date accepted: 2019-07-26
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lloyd Evans
  given name: Dyfed
author list: Agent
  family name: Hlongwane
  given name: Thandekile Thandiwe
author list: Agent
  family name: Joshi
  given name: Shailesh V.
author list: Agent
  family name: Riaño Pachón
  given name: Diego M.
doi: 10.7717/peerj.7558
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: © 2019 Lloyd Evans et al.
attribution name: Lloyd Evans et al.

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
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Andrés G. Morales-Núñez
creator: Néstor E. Ardila
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7571
publisher: PeerJ Inc.
rights: © 2019 Morales-Núñez and Ardila
abstract: 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.
bibliographic citation: Morales-Núñez et al. (2019) 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. PeerJ 7:e7571 https://doi.org/10.7717/peerj.7571
date submitted: 2019-03-27
date accepted: 2019-07-29
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morales-Núñez
  given name: Andrés G.
author list: Agent
  family name: Ardila
  given name: Néstor E.
doi: 10.7717/peerj.7571
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: ©2019 Morales-Núñez and Ardila
attribution name: Morales-Núñez and Ardila

In situ growth and bioerosion rates of Lophelia pertusa in a Norwegian fjord and open shelf cold-water coral habitat
type: item
type: AcademicArticle
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…
format: application/pdf
format: text/html
creator: Janina V. Büscher
creator: Max Wisshak
creator: Armin U. Form
creator: Jürgen Titschack
creator: Kerstin Nachtigall
creator: Ulf Riebesell
subject: Marine Biology
subject: Climate Change Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.7586
publisher: PeerJ Inc.
rights: © 2019 Büscher et al.
abstract: 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…
bibliographic citation: Büscher et al. (2019) In situ growth and bioerosion rates of Lophelia pertusa in a Norwegian fjord and open shelf cold-water coral habitat. PeerJ 7:e7586 https://doi.org/10.7717/peerj.7586
date submitted: 2019-02-26
date accepted: 2019-07-30
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Büscher
  given name: Janina V.
author list: Agent
  family name: Wisshak
  given name: Max
author list: Agent
  family name: Form
  given name: Armin U.
author list: Agent
  family name: Titschack
  given name: Jürgen
author list: Agent
  family name: Nachtigall
  given name: Kerstin
author list: Agent
  family name: Riebesell
  given name: Ulf
doi: 10.7717/peerj.7586
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: © 2019 Büscher et al.
attribution name: Büscher et al.

Estimating flowering transition dates from status-based phenological observations: a test of methods
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Shawn D. Taylor
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.7720
publisher: PeerJ Inc.
rights: © 2019 Taylor
abstract: 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.
bibliographic citation: Taylor (2019) Estimating flowering transition dates from status-based phenological observations: a test of methods. PeerJ 7:e7720 https://doi.org/10.7717/peerj.7720
date submitted: 2019-04-02
date accepted: 2019-08-21
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Taylor
  given name: Shawn D.
doi: 10.7717/peerj.7720
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: ©2019 Taylor
attribution name: Taylor

ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Marco Cacciabue
creator: Anabella Currá
creator: Maria I. Gismondi
subject: Bioinformatics
subject: Virology
description: doi:10.7717/peerj.7729
publisher: PeerJ Inc.
rights: © 2019 Cacciabue et al.
abstract: 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.
bibliographic citation: Cacciabue et al. (2019) ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 7:e7729 https://doi.org/10.7717/peerj.7729
date submitted: 2019-06-24
date accepted: 2019-08-22
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cacciabue
  given name: Marco
author list: Agent
  family name: Currá
  given name: Anabella
author list: Agent
  family name: Gismondi
  given name: Maria I.
doi: 10.7717/peerj.7729
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: ©2019 Cacciabue et al.
attribution name: Cacciabue et al.

Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Shuying Fu
creator: Yuhuan Meng
creator: Shudai Lin
creator: Wenlu Zhang
creator: Yuting He
creator: Lizhen Huang
creator: Hongli Du
subject: Genomics
subject: Diabetes and Endocrinology
subject: Kinesiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.7743
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: 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.
bibliographic citation: Fu et al. (2019) Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats. PeerJ 7:e7743 https://doi.org/10.7717/peerj.7743
date submitted: 2019-05-09
date accepted: 2019-08-25
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Shuying
author list: Agent
  family name: Meng
  given name: Yuhuan
author list: Agent
  family name: Lin
  given name: Shudai
author list: Agent
  family name: Zhang
  given name: Wenlu
author list: Agent
  family name: He
  given name: Yuting
author list: Agent
  family name: Huang
  given name: Lizhen
author list: Agent
  family name: Du
  given name: Hongli
doi: 10.7717/peerj.7743
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: ©2019 Fu et al.
attribution name: Fu et al.

Characterizing gene tree conflict in plastome-inferred phylogenies
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Joseph F. Walker
creator: Nathanael Walker-Hale
creator: Oscar M. Vargas
creator: Drew A. Larson
creator: Gregory W. Stull
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.7747
publisher: PeerJ Inc.
rights: © 2019 Walker et al.
abstract: 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.
bibliographic citation: Walker et al. (2019) Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ 7:e7747 https://doi.org/10.7717/peerj.7747
date submitted: 2019-05-20
date accepted: 2019-08-25
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Walker
  given name: Joseph F.
author list: Agent
  family name: Walker-Hale
  given name: Nathanael
author list: Agent
  family name: Vargas
  given name: Oscar M.
author list: Agent
  family name: Larson
  given name: Drew A.
author list: Agent
  family name: Stull
  given name: Gregory W.
doi: 10.7717/peerj.7747
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: ©2019 Walker et al.
attribution name: Walker et al.

Efficacy of Paclitaxel plus TS1 against previously treated EGFR mutated non-small cell lung cancer
type: item
type: AcademicArticle
description: Background Later 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. Methods We 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. Results Twenty 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. Conclusions TTS1 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.
format: application/pdf
format: text/html
creator: Yen-Han Tseng
creator: Jen-Fu Shih
creator: Heng-Sheng Chao
creator: Yuh-Min Chen
subject: Drugs and Devices
subject: Internal Medicine
subject: Oncology
description: doi:10.7717/peerj.7767
publisher: PeerJ Inc.
rights: © 2019 Tseng et al.
abstract: Background Later 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. Methods We 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. Results Twenty 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. Conclusions TTS1 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.
bibliographic citation: Tseng et al. (2019) Efficacy of Paclitaxel plus TS1 against previously treated EGFR mutated non-small cell lung cancer. PeerJ 7:e7767 https://doi.org/10.7717/peerj.7767
date submitted: 2019-04-18
date accepted: 2019-08-27
issued: 2019-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tseng
  given name: Yen-Han
author list: Agent
  family name: Shih
  given name: Jen-Fu
author list: Agent
  family name: Chao
  given name: Heng-Sheng
author list: Agent
  family name: Chen
  given name: Yuh-Min
doi: 10.7717/peerj.7767
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-24
copyright: ©2019 Tseng et al.
attribution name: Tseng et al.

Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth
type: item
type: AcademicArticle
description: Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N2-fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N2-fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N2-fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis, Fusarium graminearum, Gibberella zeae, Fusarium solani, Colletotrichum gossypii and Alternaria longipes. 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture.
format: application/pdf
format: text/html
creator: Xiaomeng Liu
creator: Qin Li
creator: Yongbin Li
creator: Guohua Guan
creator: Sanfeng Chen
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.7445
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N2-fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N2-fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N2-fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis, Fusarium graminearum, Gibberella zeae, Fusarium solani, Colletotrichum gossypii and Alternaria longipes. 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture.
bibliographic citation: Liu et al. (2019) Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth. PeerJ 7:e7445 https://doi.org/10.7717/peerj.7445
date submitted: 2019-03-21
date accepted: 2019-07-09
issued: 2019-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaomeng
author list: Agent
  family name: Li
  given name: Qin
author list: Agent
  family name: Li
  given name: Yongbin
author list: Agent
  family name: Guan
  given name: Guohua
author list: Agent
  family name: Chen
  given name: Sanfeng
doi: 10.7717/peerj.7445
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-23
copyright: ©2019 Liu et al.
attribution name: Liu et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359