PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages
items: Effects of Origanum vulgare essential oil and its two main components, carvacrol and thymol, on the plant pathogen Botrytis cinerea
items: Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance
items: Efficacy of a new dietary supplement in dogs with advanced chronic kidney disease
items: Monitoring rhinoceroses in Namibia’s private custodianship properties
items: Identifying disease-associated signaling pathways through a novel effector gene analysis
items: Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
items: Methylene blue inhibits nucleation and elongation of SOD1 amyloid fibrils
items: Correlation between fruit weight and nutritional metabolism during development in CPPU-treated Actinidia chinensis ‘Hongyang’
items: Confidence in the dynamic spread of epidemics under biased sampling conditions

Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages
type: item
type: AcademicArticle
description: Background The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major. Methods We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California. Results The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic con…
format: application/pdf
format: text/html
creator: Elizabeth L. Jockusch
creator: Robert W. Hansen
creator: Robert N. Fisher
creator: David B. Wake
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9599
publisher: PeerJ Inc.
rights: ©
abstract: Background The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major. Methods We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California. Results The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic con…
bibliographic citation: Jockusch et al. (2020) Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages. PeerJ 8:e9599 https://doi.org/10.7717/peerj.9599
date submitted: 2019-11-28
date accepted: 2020-07-02
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Jockusch
  given name: Elizabeth L.
author list: Agent
  family name: Hansen
  given name: Robert W.
author list: Agent
  family name: Fisher
  given name: Robert N.
author list: Agent
  family name: Wake
  given name: David B.
doi: 10.7717/peerj.9599
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14

Effects of Origanum vulgare essential oil and its two main components, carvacrol and thymol, on the plant pathogen Botrytis cinerea
type: item
type: AcademicArticle
description: Background Botrytis cinerea causes serious gray mold disease in many plants. This pathogen has developed resistance to many fungicides. Thus, it has become necessary to look for new safe yet effective compounds against B. cinerea. Methods Essential oils (EOs) from 17 plant species were assayed against B. cinerea, of which Origanum vulgare essential oil (OVEO) showed strong antifungal activity, and accordingly its main components were detected by GC/MS. Further study was conducted on the effects of OVEO, carvacrol and thymol in vitro on mycelium growth and spore germination, mycelium morphology, leakages of cytoplasmic contents, mitochondrial injury and accumulation of reactive oxygen species (ROS) of B. cinerea. The control efficacies of OVEO, carvacrol and thymol on tomato gray mold were evaluated in vivo. Results Of all the 17 plant EOs tested, Cinnamomum cassia, Litsea cubeba var. formosana and O. vulgare EOs had the best inhibitory effect on B. cinerea, with 0.5 mg/mL completely inhibiting the mycelium growth of B. cinerea. Twenty-one different compounds of OVEO were identified by gas chromatography–mass spectrometry, and the main chemical components were carvacrol (89.98%), β-caryophyllene (3.34%), thymol (2.39%), α-humulene (1.38%) and 1-methyl-2-propan-2-ylbenzene isopropyl benzene (1.36%). In vitro experiment showed EC50 values of OVEO, carvacrol and thymol were 140.04, 9.09 and 21.32 μg/mL, respectively. Carvacrol and thymol completely inhibited the spore germination of B. cinerea at the concentration of 300 μg/mL while the inhibition rate of OVEO was 80.03%. EC50 of carvacrol and thymol have significantly (P < 0.05) reduced the fresh and dry weight of mycelia. The collapse and damage on B. cinerea mycelia treated with 40 μg/mL of carvacrol and thymol was examined by scanning electron microscope (SEM). Through extracellular conductivity test and fluorescence microscope observation, it was found that carvacrol and thymol led to increase the permeability of t…
format: application/pdf
format: text/html
creator: Huiyu Hou
creator: Xueying Zhang
creator: Te Zhao
creator: Lin Zhou
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.9626
publisher: PeerJ Inc.
rights: © 2020 Hou et al.
abstract: Background Botrytis cinerea causes serious gray mold disease in many plants. This pathogen has developed resistance to many fungicides. Thus, it has become necessary to look for new safe yet effective compounds against B. cinerea. Methods Essential oils (EOs) from 17 plant species were assayed against B. cinerea, of which Origanum vulgare essential oil (OVEO) showed strong antifungal activity, and accordingly its main components were detected by GC/MS. Further study was conducted on the effects of OVEO, carvacrol and thymol in vitro on mycelium growth and spore germination, mycelium morphology, leakages of cytoplasmic contents, mitochondrial injury and accumulation of reactive oxygen species (ROS) of B. cinerea. The control efficacies of OVEO, carvacrol and thymol on tomato gray mold were evaluated in vivo. Results Of all the 17 plant EOs tested, Cinnamomum cassia, Litsea cubeba var. formosana and O. vulgare EOs had the best inhibitory effect on B. cinerea, with 0.5 mg/mL completely inhibiting the mycelium growth of B. cinerea. Twenty-one different compounds of OVEO were identified by gas chromatography–mass spectrometry, and the main chemical components were carvacrol (89.98%), β-caryophyllene (3.34%), thymol (2.39%), α-humulene (1.38%) and 1-methyl-2-propan-2-ylbenzene isopropyl benzene (1.36%). In vitro experiment showed EC50 values of OVEO, carvacrol and thymol were 140.04, 9.09 and 21.32 μg/mL, respectively. Carvacrol and thymol completely inhibited the spore germination of B. cinerea at the concentration of 300 μg/mL while the inhibition rate of OVEO was 80.03%. EC50 of carvacrol and thymol have significantly (P < 0.05) reduced the fresh and dry weight of mycelia. The collapse and damage on B. cinerea mycelia treated with 40 μg/mL of carvacrol and thymol was examined by scanning electron microscope (SEM). Through extracellular conductivity test and fluorescence microscope observation, it was found that carvacrol and thymol led to increase the permeability of t…
bibliographic citation: Hou et al. (2020) Effects of Origanum vulgare essential oil and its two main components, carvacrol and thymol, on the plant pathogen Botrytis cinerea. PeerJ 8:e9626 https://doi.org/10.7717/peerj.9626
date submitted: 2020-02-05
date accepted: 2020-07-08
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Huiyu
author list: Agent
  family name: Zhang
  given name: Xueying
author list: Agent
  family name: Zhao
  given name: Te
author list: Agent
  family name: Zhou
  given name: Lin
doi: 10.7717/peerj.9626
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: © 2020 Hou et al.
attribution name: Hou et al.

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance
type: item
type: AcademicArticle
description: Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal’s growth performance. Here, we compared the bacterial profiles along with the shrimp’s gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp (Penaeus monodon) were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes (Brevibacillus and Fusibacter) and Bacteroidetes (Spongiimonas), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might cont…
format: application/pdf
format: text/html
creator: Tanaporn Uengwetwanit
creator: Umaporn Uawisetwathana
creator: Sopacha Arayamethakorn
creator: Juthatip Khudet
creator: Sage Chaiyapechara
creator: Nitsara Karoonuthaisiri
creator: Wanilada Rungrassamee
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9646
publisher: PeerJ Inc.
rights: © 2020 Uengwetwanit et al.
abstract: Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal’s growth performance. Here, we compared the bacterial profiles along with the shrimp’s gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp (Penaeus monodon) were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes (Brevibacillus and Fusibacter) and Bacteroidetes (Spongiimonas), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might cont…
bibliographic citation: Uengwetwanit et al. (2020) Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance. PeerJ 8:e9646 https://doi.org/10.7717/peerj.9646
date submitted: 2020-04-21
date accepted: 2020-07-12
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uengwetwanit
  given name: Tanaporn
author list: Agent
  family name: Uawisetwathana
  given name: Umaporn
author list: Agent
  family name: Arayamethakorn
  given name: Sopacha
author list: Agent
  family name: Khudet
  given name: Juthatip
author list: Agent
  family name: Chaiyapechara
  given name: Sage
author list: Agent
  family name: Karoonuthaisiri
  given name: Nitsara
author list: Agent
  family name: Rungrassamee
  given name: Wanilada
doi: 10.7717/peerj.9646
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: ©2020 Uengwetwanit et al.
attribution name: Uengwetwanit et al.

Efficacy of a new dietary supplement in dogs with advanced chronic kidney disease
type: item
type: AcademicArticle
description: Chronic kidney disease (CKD) is a common disease in elderly dogs. The present study aims to evaluate the efficacy of a dietary supplement containing calcium carbonate, calcium-lactate gluconate, chitosan and sodium bicarbonate in dogs with IRIS stage 3 of CKD. Twenty dogs were enrolled in the study, ten were administered the new dietary supplementation for 180 days (T group) while the others were used as control group (C group). Haematologic, biochemical and urinalysis were performed every 30 days. A significant reduction in the T group compared to the C group in serum phosphorus level and increase in serum bicarbonate and ionized calcium values were recorded. The urine protein-to-creatinine ratio (UPC) was significantly lower in the T group at the end of the study compared to the C group. The tested supplement could be considered as a supportive treatment for dogs with advanced CKD.
format: application/pdf
format: text/html
creator: Elisa Martello
creator: Francesca Perondi
creator: Maria Teresa Capucchio
creator: Ilaria Biasato
creator: Elena Biasibetti
creator: Tiziana Cocca
creator: Natascia Bruni
creator: Ilaria Lippi
subject: Food Science and Technology
subject: Veterinary Medicine
description: doi:10.7717/peerj.9663
publisher: PeerJ Inc.
rights: © 2020 Martello et al.
abstract: Chronic kidney disease (CKD) is a common disease in elderly dogs. The present study aims to evaluate the efficacy of a dietary supplement containing calcium carbonate, calcium-lactate gluconate, chitosan and sodium bicarbonate in dogs with IRIS stage 3 of CKD. Twenty dogs were enrolled in the study, ten were administered the new dietary supplementation for 180 days (T group) while the others were used as control group (C group). Haematologic, biochemical and urinalysis were performed every 30 days. A significant reduction in the T group compared to the C group in serum phosphorus level and increase in serum bicarbonate and ionized calcium values were recorded. The urine protein-to-creatinine ratio (UPC) was significantly lower in the T group at the end of the study compared to the C group. The tested supplement could be considered as a supportive treatment for dogs with advanced CKD.
bibliographic citation: Martello et al. (2020) Efficacy of a new dietary supplement in dogs with advanced chronic kidney disease. PeerJ 8:e9663 https://doi.org/10.7717/peerj.9663
date submitted: 2020-01-03
date accepted: 2020-07-15
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martello
  given name: Elisa
author list: Agent
  family name: Perondi
  given name: Francesca
author list: Agent
  family name: Capucchio
  given name: Maria Teresa
author list: Agent
  family name: Biasato
  given name: Ilaria
author list: Agent
  family name: Biasibetti
  given name: Elena
author list: Agent
  family name: Cocca
  given name: Tiziana
author list: Agent
  family name: Bruni
  given name: Natascia
author list: Agent
  family name: Lippi
  given name: Ilaria
doi: 10.7717/peerj.9663
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: ©2020 Martello et al.
attribution name: Martello et al.

Monitoring rhinoceroses in Namibia’s private custodianship properties
type: item
type: AcademicArticle
description: Routinely censusing rhinoceros’ populations is central to their conservation and protection from illegal killing. In Namibia, both white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros occur on private land, in the latter case under a custodianship program of the Namibian Ministry of Environment and Tourism (MET). Black rhinoceros custodian landowners are responsible for the protection of the rhinoceroses on their land and are required to report regularly to the MET. Monitoring imposes a financial burden on custodians yet many of the techniques used involve expensive monitoring techniques that include the need for aerial support and/or animal instrumentation. During May and June 2018, WildTrack undertook a pilot study to census black and white rhinoceros on three private custodianship properties in Namibia. We tested three footprint identification methods for obtaining estimates of rhinoceros populations in an effort to provide less costly alternative monitoring options to rhinoceros custodians. The first was a full monitoring protocol with two components: (a) tracking each individual animal and matching them to their footprints, (b) identifying those individuals from the heel lines on the prints. The second method used simple visual heel line identification ex-situ, and the third method used just an objective footprint identification technique. These methods offer different options of fieldwork labour and cost and were designed to offer monitoring options to custodians that provided information about rhinoceros movement and location, with minimal disturbance to the rhinoceros, and best matched their human and economic resources. In this study, we describe the three methods and report the results of the pilot study to compare and evaluate their utility for rhinoceros monitoring. The first method successfully matched each trail photographed to a known rhinoceros at each site. When the other two methods disagreed with the first, they did so by failing to…
format: application/pdf
format: text/html
creator: Zoe C. Jewell
creator: Sky Alibhai
creator: Peter R. Law
creator: Kenneth Uiseb
creator: Stephen Lee
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.9670
publisher: PeerJ Inc.
rights: © 2020 Jewell et al.
abstract: Routinely censusing rhinoceros’ populations is central to their conservation and protection from illegal killing. In Namibia, both white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros occur on private land, in the latter case under a custodianship program of the Namibian Ministry of Environment and Tourism (MET). Black rhinoceros custodian landowners are responsible for the protection of the rhinoceroses on their land and are required to report regularly to the MET. Monitoring imposes a financial burden on custodians yet many of the techniques used involve expensive monitoring techniques that include the need for aerial support and/or animal instrumentation. During May and June 2018, WildTrack undertook a pilot study to census black and white rhinoceros on three private custodianship properties in Namibia. We tested three footprint identification methods for obtaining estimates of rhinoceros populations in an effort to provide less costly alternative monitoring options to rhinoceros custodians. The first was a full monitoring protocol with two components: (a) tracking each individual animal and matching them to their footprints, (b) identifying those individuals from the heel lines on the prints. The second method used simple visual heel line identification ex-situ, and the third method used just an objective footprint identification technique. These methods offer different options of fieldwork labour and cost and were designed to offer monitoring options to custodians that provided information about rhinoceros movement and location, with minimal disturbance to the rhinoceros, and best matched their human and economic resources. In this study, we describe the three methods and report the results of the pilot study to compare and evaluate their utility for rhinoceros monitoring. The first method successfully matched each trail photographed to a known rhinoceros at each site. When the other two methods disagreed with the first, they did so by failing to…
bibliographic citation: Jewell et al. (2020) Monitoring rhinoceroses in Namibia’s private custodianship properties. PeerJ 8:e9670 https://doi.org/10.7717/peerj.9670
date submitted: 2019-12-13
date accepted: 2020-07-16
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jewell
  given name: Zoe C.
author list: Agent
  family name: Alibhai
  given name: Sky
author list: Agent
  family name: Law
  given name: Peter R.
author list: Agent
  family name: Uiseb
  given name: Kenneth
author list: Agent
  family name: Lee
  given name: Stephen
doi: 10.7717/peerj.9670
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: ©2020 Jewell et al.
attribution name: Jewell et al.

Identifying disease-associated signaling pathways through a novel effector gene analysis
type: item
type: AcademicArticle
description: Background Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they received. The signals that the effector genes receive can be quite different in normal vs. disease conditions. However, most of current signaling pathway analysis methods do not take these signal variations into consideration. Methods In this study, we developed a novel signaling pathway analysis method called signaling pathway functional attributes analysis (SPFA) method. This method analyzes the signal variations that effector genes received between two conditions (normal and disease) in different signaling pathways. Results We compared the SPFA method to seven other methods across 33 Gene Expression Omnibus datasets using three measurements: the median rank of target pathways, the median p-value of target pathways, and the percentages of significant pathways. The results confirmed that SPFA was the top-ranking method in terms of median rank of target pathways and the fourth best method in terms of median p-value of target pathways. SPFA’s percentage of significant pathways was modest, indicating a good false positive rate and false negative rate. Overall, SPFA was comparable to the other methods. Our results also suggested that the signal variations calculated by SPFA could help identify abnormal functional attributes and parts of pathways. The SPFA R code and functions can be accessed at https://github.com/ZhenshenBao/SPFA.
format: application/pdf
format: text/html
creator: Zhenshen Bao
creator: Bing Zhang
creator: Li Li
creator: Qinyu Ge
creator: Wanjun Gu
creator: Yunfei Bai
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.9695
publisher: PeerJ Inc.
rights: © 2020 Bao et al.
abstract: Background Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they received. The signals that the effector genes receive can be quite different in normal vs. disease conditions. However, most of current signaling pathway analysis methods do not take these signal variations into consideration. Methods In this study, we developed a novel signaling pathway analysis method called signaling pathway functional attributes analysis (SPFA) method. This method analyzes the signal variations that effector genes received between two conditions (normal and disease) in different signaling pathways. Results We compared the SPFA method to seven other methods across 33 Gene Expression Omnibus datasets using three measurements: the median rank of target pathways, the median p-value of target pathways, and the percentages of significant pathways. The results confirmed that SPFA was the top-ranking method in terms of median rank of target pathways and the fourth best method in terms of median p-value of target pathways. SPFA’s percentage of significant pathways was modest, indicating a good false positive rate and false negative rate. Overall, SPFA was comparable to the other methods. Our results also suggested that the signal variations calculated by SPFA could help identify abnormal functional attributes and parts of pathways. The SPFA R code and functions can be accessed at https://github.com/ZhenshenBao/SPFA.
bibliographic citation: Bao et al. (2020) Identifying disease-associated signaling pathways through a novel effector gene analysis. PeerJ 8:e9695 https://doi.org/10.7717/peerj.9695
date submitted: 2020-02-19
date accepted: 2020-07-20
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bao
  given name: Zhenshen
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Li
  given name: Li
author list: Agent
  family name: Ge
  given name: Qinyu
author list: Agent
  family name: Gu
  given name: Wanjun
author list: Agent
  family name: Bai
  given name: Yunfei
doi: 10.7717/peerj.9695
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: © 2020 Bao et al.
attribution name: Bao et al.

Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
type: item
type: AcademicArticle
description: The kiwifruit bacterial canker (Pseudomonas syringae pv. actinidiae; Psa) causes severe damage to kiwifruit production worldwide. Psa biovar 6 (Psa6), which was isolated in Japan in 2015, produces two types of phytotoxins: coronatine and phaseolotoxin. To elucidate the unique virulence of Psa6, we performed transcriptomic analysis of phytotoxin synthesis genes and type III effector genes in in vitro cultivation using various media. The genes related to phytotoxin synthesis and effectors of Psa6 were strictly regulated in the coronatine-inducing mediums (HS and HSC); 14 of 23 effector genes and a hrpL sigma factor gene were induced at 3 h after transferring to the media (early-inducible genes), and phytotoxin synthesis genes such as argD of phaseolotoxin and cfl of coronatine were induced at 6 and 12 h after transferring to the media (late-inducible genes). In contrast, induction of these genes was not observed in the hrp-inducing medium. Next, to examine whether the changes in gene expression in different media is specific to Psa6, we investigated gene expression in other related bacteria. For Psa biovar 1 (Psa1), biovar 3 (Psa3), and P. s. pv. glycinea (Psg), no clear trends were observed in expression behavior across various culture media and incubation times. Therefore, Psa6 seems to exert its virulence efficiently by using two phytotoxins and effectors according to environmental changes. This is not seen in other biovars and pathovars, so it is thought that Psa6 has acquired its own balance of virulence.
format: application/pdf
format: text/html
creator: Karin Hirose
creator: Yasuhiro Ishiga
creator: Takashi Fujikawa
subject: Agricultural Science
subject: Biochemistry
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.9697
publisher: PeerJ Inc.
rights: © 2020 Hirose et al.
abstract: The kiwifruit bacterial canker (Pseudomonas syringae pv. actinidiae; Psa) causes severe damage to kiwifruit production worldwide. Psa biovar 6 (Psa6), which was isolated in Japan in 2015, produces two types of phytotoxins: coronatine and phaseolotoxin. To elucidate the unique virulence of Psa6, we performed transcriptomic analysis of phytotoxin synthesis genes and type III effector genes in in vitro cultivation using various media. The genes related to phytotoxin synthesis and effectors of Psa6 were strictly regulated in the coronatine-inducing mediums (HS and HSC); 14 of 23 effector genes and a hrpL sigma factor gene were induced at 3 h after transferring to the media (early-inducible genes), and phytotoxin synthesis genes such as argD of phaseolotoxin and cfl of coronatine were induced at 6 and 12 h after transferring to the media (late-inducible genes). In contrast, induction of these genes was not observed in the hrp-inducing medium. Next, to examine whether the changes in gene expression in different media is specific to Psa6, we investigated gene expression in other related bacteria. For Psa biovar 1 (Psa1), biovar 3 (Psa3), and P. s. pv. glycinea (Psg), no clear trends were observed in expression behavior across various culture media and incubation times. Therefore, Psa6 seems to exert its virulence efficiently by using two phytotoxins and effectors according to environmental changes. This is not seen in other biovars and pathovars, so it is thought that Psa6 has acquired its own balance of virulence.
bibliographic citation: Hirose et al. (2020) Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions. PeerJ 8:e9697 https://doi.org/10.7717/peerj.9697
date submitted: 2020-05-04
date accepted: 2020-07-20
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hirose
  given name: Karin
author list: Agent
  family name: Ishiga
  given name: Yasuhiro
author list: Agent
  family name: Fujikawa
  given name: Takashi
doi: 10.7717/peerj.9697
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: ©2020 Hirose et al.
attribution name: Hirose et al.

Methylene blue inhibits nucleation and elongation of SOD1 amyloid fibrils
type: item
type: AcademicArticle
description: Protein aggregation into highly-structured amyloid fibrils is linked to several neurodegenerative diseases. Such fibril formation by superoxide dismutase I (SOD1) is considered to be related to amyotrophic lateral sclerosis, a late-onset and fatal disorder. Despite much effort and the discovery of numerous anti-amyloid compounds, no effective cure or treatment is currently available. Methylene blue (MB), a phenothiazine dye, has been shown to modulate the aggregation of multiple amyloidogenic proteins. In this work we show its ability to inhibit both the spontaneous amyloid aggregation of SOD1 as well as elongation of preformed fibrils.
format: application/pdf
format: text/html
creator: Greta Musteikyte
creator: Mantas Ziaunys
creator: Vytautas Smirnovas
subject: Biochemistry
subject: Biophysics
subject: Cell Biology
subject: Molecular Biology
subject: Neurology
description: doi:10.7717/peerj.9719
publisher: PeerJ Inc.
rights: © 2020 Musteikyte et al.
abstract: Protein aggregation into highly-structured amyloid fibrils is linked to several neurodegenerative diseases. Such fibril formation by superoxide dismutase I (SOD1) is considered to be related to amyotrophic lateral sclerosis, a late-onset and fatal disorder. Despite much effort and the discovery of numerous anti-amyloid compounds, no effective cure or treatment is currently available. Methylene blue (MB), a phenothiazine dye, has been shown to modulate the aggregation of multiple amyloidogenic proteins. In this work we show its ability to inhibit both the spontaneous amyloid aggregation of SOD1 as well as elongation of preformed fibrils.
bibliographic citation: Musteikyte et al. (2020) Methylene blue inhibits nucleation and elongation of SOD1 amyloid fibrils. PeerJ 8:e9719 https://doi.org/10.7717/peerj.9719
date submitted: 2020-05-05
date accepted: 2020-07-23
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Musteikyte
  given name: Greta
author list: Agent
  family name: Ziaunys
  given name: Mantas
author list: Agent
  family name: Smirnovas
  given name: Vytautas
doi: 10.7717/peerj.9719
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: ©2020 Musteikyte et al.
attribution name: Musteikyte et al.

Correlation between fruit weight and nutritional metabolism during development in CPPU-treated Actinidia chinensis ‘Hongyang’
type: item
type: AcademicArticle
description: Forchlorfenuron, N-(2-chloro-4-pyridyl)-N-phenylurea (CPPU), is often used to promote fruit growth and improve production. The role of CPPU in kiwifruit growth has been established. However, the correlation between fruit weight and nutritional metabolism during development after CPPU treatments remains largely undetermined. Here, we surveyed the variations in weight and nutrient components of the ‘Hongyang’ kiwifruit (Actinidia chinensis) when CPPU was sprayed on fruit 25 days after anthesis. The CPPU application did not significantly influence the dry matter, soluble solids, starch, vitamin C or protein concentrations. However, the fresh weight, length and maximum diameter were significantly increased compared with the control. Moreover, in fruit of the same developmental stage, the fructose, glucose and soluble sugar levels increased after the CPPU treatment, compared with the control. On the contrary, citric, quinic and titratable acid concentrations decreased. However, a correlation analysis between fresh weight and the nutritional contents revealed that CPPU did not affect the concentrations of the most abundant organic acids (quinic and citric) and sugars (glucose, fructose and sucrose), compared with control fruit of the same weight. Therefore, CPPU applications enhance ‘Hongyang’ kiwifruit weight/size. However, there were no significant differences in the nutritional qualities of treated and untreated fruit having the same weights.
format: application/pdf
format: text/html
creator: Guo-liang Qiu
creator: Qi-guo Zhuang
creator: Yu-fei Li
creator: Si-yu Li
creator: Cun Chen
creator: Zheng-hao Li
creator: Yu-yang Zhao
creator: Yi Yang
creator: Zhi-bin Liu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.9724
publisher: PeerJ Inc.
rights: © 2020 Qiu et al.
abstract: Forchlorfenuron, N-(2-chloro-4-pyridyl)-N-phenylurea (CPPU), is often used to promote fruit growth and improve production. The role of CPPU in kiwifruit growth has been established. However, the correlation between fruit weight and nutritional metabolism during development after CPPU treatments remains largely undetermined. Here, we surveyed the variations in weight and nutrient components of the ‘Hongyang’ kiwifruit (Actinidia chinensis) when CPPU was sprayed on fruit 25 days after anthesis. The CPPU application did not significantly influence the dry matter, soluble solids, starch, vitamin C or protein concentrations. However, the fresh weight, length and maximum diameter were significantly increased compared with the control. Moreover, in fruit of the same developmental stage, the fructose, glucose and soluble sugar levels increased after the CPPU treatment, compared with the control. On the contrary, citric, quinic and titratable acid concentrations decreased. However, a correlation analysis between fresh weight and the nutritional contents revealed that CPPU did not affect the concentrations of the most abundant organic acids (quinic and citric) and sugars (glucose, fructose and sucrose), compared with control fruit of the same weight. Therefore, CPPU applications enhance ‘Hongyang’ kiwifruit weight/size. However, there were no significant differences in the nutritional qualities of treated and untreated fruit having the same weights.
bibliographic citation: Qiu et al. (2020) Correlation between fruit weight and nutritional metabolism during development in CPPU-treated Actinidia chinensis ‘Hongyang’. PeerJ 8:e9724 https://doi.org/10.7717/peerj.9724
date submitted: 2020-01-27
date accepted: 2020-07-23
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Guo-liang
author list: Agent
  family name: Zhuang
  given name: Qi-guo
author list: Agent
  family name: Li
  given name: Yu-fei
author list: Agent
  family name: Li
  given name: Si-yu
author list: Agent
  family name: Chen
  given name: Cun
author list: Agent
  family name: Li
  given name: Zheng-hao
author list: Agent
  family name: Zhao
  given name: Yu-yang
author list: Agent
  family name: Yang
  given name: Yi
author list: Agent
  family name: Liu
  given name: Zhi-bin
doi: 10.7717/peerj.9724
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: © 2020 Qiu et al.
attribution name: Qiu et al.

Confidence in the dynamic spread of epidemics under biased sampling conditions
type: item
type: AcademicArticle
description: The interpretation of sampling data plays a crucial role in policy response to the spread of a disease during an epidemic, such as the COVID-19 epidemic of 2020. However, this is a non-trivial endeavor due to the complexity of real world conditions and limits to the availability of diagnostic tests, which necessitate a bias in testing favoring symptomatic individuals. A thorough understanding of sampling confidence and bias is necessary in order make accurate conclusions. In this manuscript, we provide a stochastic model of sampling for assessing confidence in disease metrics such as trend detection, peak detection and disease spread estimation. Our model simulates testing for a disease in an epidemic with known dynamics, allowing us to use Monte-Carlo sampling to assess metric confidence. This model can provide realistic simulated data which can be used in the design and calibration of data analysis and prediction methods. As an example, we use this method to show that trends in the disease may be identified using under 10,000 biased samples each day, and an estimate of disease spread can be made with additional 1,000–2,000 unbiased samples each day. We also demonstrate that the model can be used to assess more advanced metrics by finding the precision and recall of a strategy for finding peaks in the dynamics.
format: application/pdf
format: text/html
creator: James Brunner
creator: Nicholas Chia
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: Statistics
subject: Population Biology
description: doi:10.7717/peerj.9758
publisher: PeerJ Inc.
rights: © 2020 Brunner and Chia
abstract: The interpretation of sampling data plays a crucial role in policy response to the spread of a disease during an epidemic, such as the COVID-19 epidemic of 2020. However, this is a non-trivial endeavor due to the complexity of real world conditions and limits to the availability of diagnostic tests, which necessitate a bias in testing favoring symptomatic individuals. A thorough understanding of sampling confidence and bias is necessary in order make accurate conclusions. In this manuscript, we provide a stochastic model of sampling for assessing confidence in disease metrics such as trend detection, peak detection and disease spread estimation. Our model simulates testing for a disease in an epidemic with known dynamics, allowing us to use Monte-Carlo sampling to assess metric confidence. This model can provide realistic simulated data which can be used in the design and calibration of data analysis and prediction methods. As an example, we use this method to show that trends in the disease may be identified using under 10,000 biased samples each day, and an estimate of disease spread can be made with additional 1,000–2,000 unbiased samples each day. We also demonstrate that the model can be used to assess more advanced metrics by finding the precision and recall of a strategy for finding peaks in the dynamics.
bibliographic citation: Brunner et al. (2020) Confidence in the dynamic spread of epidemics under biased sampling conditions. PeerJ 8:e9758 https://doi.org/10.7717/peerj.9758
date submitted: 2020-06-04
date accepted: 2020-07-28
issued: 2020-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brunner
  given name: James
author list: Agent
  family name: Chia
  given name: Nicholas
doi: 10.7717/peerj.9758
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-14
copyright: © 2020 Brunner and Chia
attribution name: Brunner and Chia

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