PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica
items: Effects of variation in forest fragment habitat on black howler monkey demography in the unprotected landscape around Palenque National Park, Mexico
items: Anatomy and clinical relevance of sub occipital soft tissue connections with the dura mater in the upper cervical spine
items: The ability of the green peach aphid (Myzus persicae) to penetrate mesh crop covers used to protect potato crops against tomato potato psyllid (Bactericera cockerelli)
items: Of power and despair in cetacean conservation: estimation and detection of trend in abundance with noisy and short time-series
items: The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis
items: Silencing of the ARK5 gene reverses the drug resistance of multidrug-resistant SGC7901/DDP gastric cancer cells
items: A note on the effects of epidemic forecasts on epidemic dynamics
items: High antibody titres induced by protein subunit vaccines using Mycobacterium ulcerans antigens Hsp18 and MUL_3720 with a TLR-2 agonist fail to protect against Buruli ulcer in mice
items: Dissecting molecular network structures using a network subgraph approach

Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica
type: item
type: AcademicArticle
description: Luffa is a kind of melon crop widely cultivated in temperate regions worldwide. Browning is one of the serious factors affecting the quality of Luffa. Therefore, the molecular mechanism of Luffa browning is of great significance to study. However, the molecular diversity of Luffa cultivars with different browning-resistant abilities has not been well elucidated. In our study, we used high-throughput sequencing to determine the transcriptome of two Luffa cylindrica cultivars ‘2D-2’ and ‘35D-7’. A total of 115,099 unigenes were clustered, of which 22,607 were differentially expression genes (DEGs). Of these DEGs, 65 encoding polyphenol oxidase, peroxidase, or ascorbate peroxidase were further analyzed. The quantitative real-time PCR (RT-qPCR) data indicated that the expression levels of the LcPPO gene (Accession No.: Cluster-21832.13892) was significantly higher in ‘35D-7’ compared with that in ‘2D-2’. Several POD genes (Accession No.: Cluster-21832.19847, Cluster-21832.30619 and Cluster-48491.2) were also upregulated. Analysis of the plantTFDB database indicated that some transcription factors such as WRKY gene family may also participate in the regulation of Luffa browning. The results indicated that the divergence of genes expression related to enzymatic reaction may lead to the different browning resistances of Luffa. Our study will provide a theoretical basis for breeding of browning-resistant Luffa.
format: application/pdf
format: text/html
creator: Ya-Hui Wang
creator: Xiao-Hong Liu
creator: Rong-Rong Zhang
creator: Zhi-Ming Yan
creator: Ai-Sheng Xiong
creator: Xiao-Jun Su
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9661
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Luffa is a kind of melon crop widely cultivated in temperate regions worldwide. Browning is one of the serious factors affecting the quality of Luffa. Therefore, the molecular mechanism of Luffa browning is of great significance to study. However, the molecular diversity of Luffa cultivars with different browning-resistant abilities has not been well elucidated. In our study, we used high-throughput sequencing to determine the transcriptome of two Luffa cylindrica cultivars ‘2D-2’ and ‘35D-7’. A total of 115,099 unigenes were clustered, of which 22,607 were differentially expression genes (DEGs). Of these DEGs, 65 encoding polyphenol oxidase, peroxidase, or ascorbate peroxidase were further analyzed. The quantitative real-time PCR (RT-qPCR) data indicated that the expression levels of the LcPPO gene (Accession No.: Cluster-21832.13892) was significantly higher in ‘35D-7’ compared with that in ‘2D-2’. Several POD genes (Accession No.: Cluster-21832.19847, Cluster-21832.30619 and Cluster-48491.2) were also upregulated. Analysis of the plantTFDB database indicated that some transcription factors such as WRKY gene family may also participate in the regulation of Luffa browning. The results indicated that the divergence of genes expression related to enzymatic reaction may lead to the different browning resistances of Luffa. Our study will provide a theoretical basis for breeding of browning-resistant Luffa.
bibliographic citation: Wang et al. (2020) Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica. PeerJ 8:e9661 https://doi.org/10.7717/peerj.9661
date submitted: 2020-05-06
date accepted: 2020-07-15
issued: 2020-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ya-Hui
author list: Agent
  family name: Liu
  given name: Xiao-Hong
author list: Agent
  family name: Zhang
  given name: Rong-Rong
author list: Agent
  family name: Yan
  given name: Zhi-Ming
author list: Agent
  family name: Xiong
  given name: Ai-Sheng
author list: Agent
  family name: Su
  given name: Xiao-Jun
doi: 10.7717/peerj.9661
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-10
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Effects of variation in forest fragment habitat on black howler monkey demography in the unprotected landscape around Palenque National Park, Mexico
type: item
type: AcademicArticle
description: Habitat loss and fragmentation are leading threats to biodiversity today, and primates are particularly vulnerable to anthropogenic habitat disturbance. However, few studies have examined how differential effects of variation in forest fragment characteristics on males and females in a primate population may affect demography and population persistence. We quantified the effects of variation in forest fragment characteristics on the within-fragment demography of black howler monkeys (Alouatta pigra) in forest fragments around Palenque National Park, Mexico, and how these effects differed between adult males and females. We quantified forest loss in the landscape between 2000 and 2017, and used a redundancy analysis to examine the effects of 15 variables quantifying fragment dimensions, forest composition and physical structure, and isolation on fragment population size and density, the proportion of adult males and females in the fragment population, and the mean number of adult males and females per group in 34 fragments (N = 393 monkeys). We hypothesized that (i) population size is positively correlated with fragment area, while population density is negatively correlated, and (ii) the composition of fragment populations results from differential effects of fragment variables on adult males and females. Forest cover decreased by 23.3% from 2000 to 2017. Our results showed a significant effect of fragment variables on population demography in fragments, accounting for 0.69 of the variance in the demographic response variables. Population size increased with fragment area and connectivity, while density decreased. Larger, less isolated fragments with better connectivity, characteristics indicative of abundant secondary growth, and those with more diverse vegetation but lower Simpson’s evenness indices tended to have more adult females per group and a higher proportion of adult females in the population. In contrast, fragments that were largely similar in characteris…
format: application/pdf
format: text/html
creator: Keren Klass
creator: Sarie Van Belle
creator: Alvaro Campos-Villanueva
creator: Fernando Mercado Malabet
creator: Alejandro Estrada
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Environmental Impacts
subject: Population Biology
description: doi:10.7717/peerj.9694
publisher: PeerJ Inc.
rights: © 2020 Klass et al.
abstract: Habitat loss and fragmentation are leading threats to biodiversity today, and primates are particularly vulnerable to anthropogenic habitat disturbance. However, few studies have examined how differential effects of variation in forest fragment characteristics on males and females in a primate population may affect demography and population persistence. We quantified the effects of variation in forest fragment characteristics on the within-fragment demography of black howler monkeys (Alouatta pigra) in forest fragments around Palenque National Park, Mexico, and how these effects differed between adult males and females. We quantified forest loss in the landscape between 2000 and 2017, and used a redundancy analysis to examine the effects of 15 variables quantifying fragment dimensions, forest composition and physical structure, and isolation on fragment population size and density, the proportion of adult males and females in the fragment population, and the mean number of adult males and females per group in 34 fragments (N = 393 monkeys). We hypothesized that (i) population size is positively correlated with fragment area, while population density is negatively correlated, and (ii) the composition of fragment populations results from differential effects of fragment variables on adult males and females. Forest cover decreased by 23.3% from 2000 to 2017. Our results showed a significant effect of fragment variables on population demography in fragments, accounting for 0.69 of the variance in the demographic response variables. Population size increased with fragment area and connectivity, while density decreased. Larger, less isolated fragments with better connectivity, characteristics indicative of abundant secondary growth, and those with more diverse vegetation but lower Simpson’s evenness indices tended to have more adult females per group and a higher proportion of adult females in the population. In contrast, fragments that were largely similar in characteris…
bibliographic citation: Klass et al. (2020) Effects of variation in forest fragment habitat on black howler monkey demography in the unprotected landscape around Palenque National Park, Mexico. PeerJ 8:e9694 https://doi.org/10.7717/peerj.9694
date submitted: 2019-11-06
date accepted: 2020-07-20
issued: 2020-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klass
  given name: Keren
author list: Agent
  family name: Van Belle
  given name: Sarie
author list: Agent
  family name: Campos-Villanueva
  given name: Alvaro
author list: Agent
  family name: Mercado Malabet
  given name: Fernando
author list: Agent
  family name: Estrada
  given name: Alejandro
doi: 10.7717/peerj.9694
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-10
copyright: © 2020 Klass et al.
attribution name: Klass et al.

Anatomy and clinical relevance of sub occipital soft tissue connections with the dura mater in the upper cervical spine
type: item
type: AcademicArticle
description: Background The upper cervical region is a complex anatomical structure. Myodural bridges between posterior suboccipital muscles and the dura might be important explaining conditions associated with the upper cervical spine dysfunction such as cervicogenic headache. This cadaver study explored the upper cervical spine and evaluated the myodural bridges along with position of spinal cord in response to passive motion of upper cervical spine. Methods A total of seven adult cadavers were used in this exploratory study. The suboccipital muscles and nuchal ligament were exposed. Connections between the Rectus Capitis Posterior major/minor and the Obliquus Capitis minor, the nuchal ligament, posterior aspect of the cervical spine, flavum ligament and the dura were explored and confirmed with histology. The position of the spinal cord was evaluated with passive motions of the upper cervical spine. Outcomes In all cadavers connective tissues attaching the Rectus Capitis Posterior Major to the posterior atlanto-occipital membrane were identified. In the sagittal dissection we observed connection between the nuchal ligament and the dura. Histology revealed that the connection is collagenous in nature. The spinal cord moves within the spinal canal during passive movement. Discussion The presence of tissue connections between ligament, bone and muscles in the suboccipital region was confirmed. The nuchal ligament was continuous with the menigiovertebral ligament and the dura. Passive upper cervical motion results in spinal cord motion within the canal and possible tensioning of nerve and ligamentous connections.
format: application/pdf
format: text/html
creator: Rob Sillevis
creator: Russell Hogg
subject: Neuroscience
subject: Anatomy and Physiology
subject: Orthopedics
description: doi:10.7717/peerj.9716
publisher: PeerJ Inc.
rights: © 2020 Sillevis and Hogg
abstract: Background The upper cervical region is a complex anatomical structure. Myodural bridges between posterior suboccipital muscles and the dura might be important explaining conditions associated with the upper cervical spine dysfunction such as cervicogenic headache. This cadaver study explored the upper cervical spine and evaluated the myodural bridges along with position of spinal cord in response to passive motion of upper cervical spine. Methods A total of seven adult cadavers were used in this exploratory study. The suboccipital muscles and nuchal ligament were exposed. Connections between the Rectus Capitis Posterior major/minor and the Obliquus Capitis minor, the nuchal ligament, posterior aspect of the cervical spine, flavum ligament and the dura were explored and confirmed with histology. The position of the spinal cord was evaluated with passive motions of the upper cervical spine. Outcomes In all cadavers connective tissues attaching the Rectus Capitis Posterior Major to the posterior atlanto-occipital membrane were identified. In the sagittal dissection we observed connection between the nuchal ligament and the dura. Histology revealed that the connection is collagenous in nature. The spinal cord moves within the spinal canal during passive movement. Discussion The presence of tissue connections between ligament, bone and muscles in the suboccipital region was confirmed. The nuchal ligament was continuous with the menigiovertebral ligament and the dura. Passive upper cervical motion results in spinal cord motion within the canal and possible tensioning of nerve and ligamentous connections.
bibliographic citation: Sillevis et al. (2020) Anatomy and clinical relevance of sub occipital soft tissue connections with the dura mater in the upper cervical spine. PeerJ 8:e9716 https://doi.org/10.7717/peerj.9716
date submitted: 2020-04-29
date accepted: 2020-07-23
issued: 2020-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sillevis
  given name: Rob
author list: Agent
  family name: Hogg
  given name: Russell
doi: 10.7717/peerj.9716
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-10
copyright: © 2020 Sillevis and Hogg
attribution name: Sillevis and Hogg

The ability of the green peach aphid (Myzus persicae) to penetrate mesh crop covers used to protect potato crops against tomato potato psyllid (Bactericera cockerelli)
type: item
type: AcademicArticle
description: In Central and North America, Australia and New Zealand, potato (Solanum tuberosum) crops are attacked by Bactericera cockerelli, the tomato potato psyllid (TPP). ‘Mesh crop covers’ which are used in Europe and Israel to protect crops from insect pests, have been used experimentally in New Zealand for TPP control. While the covers have been effective for TPP management, the green peach aphid (GPA, Myzus persicae) has been found in large numbers under the mesh crop covers. This study investigated the ability of the GPA to penetrate different mesh hole sizes. Experiments using four sizes (0.15 × 0.15, 0.15 × 0.35, 0.3 × 0.3 and 0.6 × 0.6 mm) were carried out under laboratory conditions to investigate: (i) which mesh hole size provided the most effective barrier to GPA; (ii) which morph of adult aphids (apterous or alate) and/or their progeny could breach the mesh crop cover; (iii) would leaves touching the underside of the cover, as opposed to having a gap between leaf and the mesh, increase the number of aphids breaching the mesh; and (iv) could adults feed on leaves touching the cover by putting only their heads and/or stylets through it? No adult aphids, either alate or apterous, penetrated the mesh crop cover; only nymphs did this, the majority being the progeny of alate adults. Nymphs of the smaller alatae aphids penetrated the three coarsest mesh sizes; nymphs of the larger apterae penetrated the two coarsest sizes, but no nymphs penetrated the smallest mesh size. There was no statistical difference in the number of aphids breaching the mesh crop cover when the leaflets touched its underside compared to when there was a gap between leaf and mesh crop cover. Adults did not feed through the mesh crop cover, though they may have been able to sense the potato leaflet using visual and/or olfactory cues and produce nymphs as a result. As these covers are highly effective for managing TPP on field potatoes, modifications of this protocol are required to make it effecti…
format: application/pdf
format: text/html
creator: Howard London
creator: David J. Saville
creator: Charles N. Merfield
creator: Oluwashola Olaniyan
creator: Stephen D. Wratten
subject: Agricultural Science
description: doi:10.7717/peerj.9317
publisher: PeerJ Inc.
rights: © 2020 London et al.
abstract: In Central and North America, Australia and New Zealand, potato (Solanum tuberosum) crops are attacked by Bactericera cockerelli, the tomato potato psyllid (TPP). ‘Mesh crop covers’ which are used in Europe and Israel to protect crops from insect pests, have been used experimentally in New Zealand for TPP control. While the covers have been effective for TPP management, the green peach aphid (GPA, Myzus persicae) has been found in large numbers under the mesh crop covers. This study investigated the ability of the GPA to penetrate different mesh hole sizes. Experiments using four sizes (0.15 × 0.15, 0.15 × 0.35, 0.3 × 0.3 and 0.6 × 0.6 mm) were carried out under laboratory conditions to investigate: (i) which mesh hole size provided the most effective barrier to GPA; (ii) which morph of adult aphids (apterous or alate) and/or their progeny could breach the mesh crop cover; (iii) would leaves touching the underside of the cover, as opposed to having a gap between leaf and the mesh, increase the number of aphids breaching the mesh; and (iv) could adults feed on leaves touching the cover by putting only their heads and/or stylets through it? No adult aphids, either alate or apterous, penetrated the mesh crop cover; only nymphs did this, the majority being the progeny of alate adults. Nymphs of the smaller alatae aphids penetrated the three coarsest mesh sizes; nymphs of the larger apterae penetrated the two coarsest sizes, but no nymphs penetrated the smallest mesh size. There was no statistical difference in the number of aphids breaching the mesh crop cover when the leaflets touched its underside compared to when there was a gap between leaf and mesh crop cover. Adults did not feed through the mesh crop cover, though they may have been able to sense the potato leaflet using visual and/or olfactory cues and produce nymphs as a result. As these covers are highly effective for managing TPP on field potatoes, modifications of this protocol are required to make it effecti…
bibliographic citation: London et al. (2020) The ability of the green peach aphid (Myzus persicae) to penetrate mesh crop covers used to protect potato crops against tomato potato psyllid (Bactericera cockerelli). PeerJ 8:e9317 https://doi.org/10.7717/peerj.9317
date submitted: 2018-05-15
date accepted: 2020-05-17
issued: 2020-08-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: London
  given name: Howard
author list: Agent
  family name: Saville
  given name: David J.
author list: Agent
  family name: Merfield
  given name: Charles N.
author list: Agent
  family name: Olaniyan
  given name: Oluwashola
author list: Agent
  family name: Wratten
  given name: Stephen D.
doi: 10.7717/peerj.9317
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-07
copyright: ©2020 London et al.
attribution name: London et al.

Of power and despair in cetacean conservation: estimation and detection of trend in abundance with noisy and short time-series
type: item
type: AcademicArticle
description: Many conservation instruments rely on detecting and estimating a population decline in a target species to take action. Trend estimation is difficult because of small sample size and relatively large uncertainty in abundance/density estimates of many wild populations of animals. Focusing on cetaceans, we performed a prospective analysis to estimate power, type-I, sign (type-S) and magnitude (type-M) error rates of detecting a decline in short time-series of abundance estimates with different signal-to-noise ratio. We contrasted results from both unregularized (classical) and regularized approaches. The latter allows to incorporate prior information when estimating a trend. Power to detect a statistically significant estimates was in general lower than 80%, except for large declines. The unregularized approach (status quo) had inflated type-I error rates and gave biased (either over- or under-) estimates of a trend. The regularized approach with a weakly-informative prior offered the best trade-off in terms of bias, statistical power, type-I, type-S and type-M error rates and confidence interval coverage. To facilitate timely conservation decisions, we recommend to use the regularized approach with a weakly-informative prior in the detection and estimation of trend with short and noisy time-series of abundance estimates.
format: application/pdf
format: text/html
creator: Matthieu Authier
creator: Anders Galatius
creator: Anita Gilles
creator: Jérôme Spitz
subject: Conservation Biology
subject: Marine Biology
subject: Statistics
subject: Population Biology
description: doi:10.7717/peerj.9436
publisher: PeerJ Inc.
rights: © 2020 Authier et al.
abstract: Many conservation instruments rely on detecting and estimating a population decline in a target species to take action. Trend estimation is difficult because of small sample size and relatively large uncertainty in abundance/density estimates of many wild populations of animals. Focusing on cetaceans, we performed a prospective analysis to estimate power, type-I, sign (type-S) and magnitude (type-M) error rates of detecting a decline in short time-series of abundance estimates with different signal-to-noise ratio. We contrasted results from both unregularized (classical) and regularized approaches. The latter allows to incorporate prior information when estimating a trend. Power to detect a statistically significant estimates was in general lower than 80%, except for large declines. The unregularized approach (status quo) had inflated type-I error rates and gave biased (either over- or under-) estimates of a trend. The regularized approach with a weakly-informative prior offered the best trade-off in terms of bias, statistical power, type-I, type-S and type-M error rates and confidence interval coverage. To facilitate timely conservation decisions, we recommend to use the regularized approach with a weakly-informative prior in the detection and estimation of trend with short and noisy time-series of abundance estimates.
bibliographic citation: Authier et al. (2020) Of power and despair in cetacean conservation: estimation and detection of trend in abundance with noisy and short time-series. PeerJ 8:e9436 https://doi.org/10.7717/peerj.9436
date submitted: 2020-01-14
date accepted: 2020-06-08
issued: 2020-08-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Authier
  given name: Matthieu
author list: Agent
  family name: Galatius
  given name: Anders
author list: Agent
  family name: Gilles
  given name: Anita
author list: Agent
  family name: Spitz
  given name: Jérôme
doi: 10.7717/peerj.9436
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-07
copyright: © 2020 Authier et al.
attribution name: Authier et al.

The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis
type: item
type: AcademicArticle
description: Background The distribution and use of camphor (Cinnamomum camphora L.) trees are constrained by increasing soil salinity in south-eastern China along the Yangtze River. However, the response mechanism of this species to salinity, especially in team of photosynthesis, are unknown. Methods Here, we analysed themorphological, physiological, ultrastructural, and proteomic traits of camphor seedlings under NaCl (103.45 mM) treatment in pot experiments for 80 days. Results The growth was limited because of photosynthetic inhibition, with the most significant disturbance occurring within 50 days. Salinity caused severe reductions in the leaf photosynthetic rate (An), stomatal conductance (gs), maximal chlorophyll fluorescence (Fm), maximum quantum yield of PSII (Fv/Fm), non-photochemical quenching (NPQ), relative quantum efficiency of PSII photochemistry (ΦPSII), photochemical quenching coefficient (qP) and photo-pigment contents (chlorophyll a (Cha), chlorophyll b (Chb), total chlorophyll (Chl)); weakened the antioxidant effects, including those of malondialdehyde (MDA), superoxide dismutase (SOD) and peroxidase (POD); and injured chloroplasts. The physiologicalresults indicated that the main reason for photo-inhibition was oxidative factors induced by NaCl. The proteomic results based on isobaric tags for relative and absolute quantitation (iTRAQ) further confirmedthat photosynthesis was the most significant disrupted process by salinity (P < 0.01) and there were 30 downregulated differentially expression proteins (DEPs) and one upregulated DEP related to restraint of the photosynthetic system, which affected photosystem I, photosystem II, the Cytochrome b6/f complex, ATP synthase and the light-harvesting chlorophyll protein complex. In addition, 57 DEPs were related to photo-inhibition by redox effect and 6 downregulated DEPs, including O2 evolving complex 33kD family protein (gi—224094610) and five other predicted proteins (gi—743921083, gi—743840443, gi—743885735, gi…
format: application/pdf
format: text/html
creator: Jiammin Yue
creator: Dawei Shi
creator: Liang Zhang
creator: Zihan Zhang
creator: Zhiyuan Fu
creator: Qiong Ren
creator: Jinchi Zhang
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9443
publisher: PeerJ Inc.
rights: © 2020 Yue et al.
abstract: Background The distribution and use of camphor (Cinnamomum camphora L.) trees are constrained by increasing soil salinity in south-eastern China along the Yangtze River. However, the response mechanism of this species to salinity, especially in team of photosynthesis, are unknown. Methods Here, we analysed themorphological, physiological, ultrastructural, and proteomic traits of camphor seedlings under NaCl (103.45 mM) treatment in pot experiments for 80 days. Results The growth was limited because of photosynthetic inhibition, with the most significant disturbance occurring within 50 days. Salinity caused severe reductions in the leaf photosynthetic rate (An), stomatal conductance (gs), maximal chlorophyll fluorescence (Fm), maximum quantum yield of PSII (Fv/Fm), non-photochemical quenching (NPQ), relative quantum efficiency of PSII photochemistry (ΦPSII), photochemical quenching coefficient (qP) and photo-pigment contents (chlorophyll a (Cha), chlorophyll b (Chb), total chlorophyll (Chl)); weakened the antioxidant effects, including those of malondialdehyde (MDA), superoxide dismutase (SOD) and peroxidase (POD); and injured chloroplasts. The physiologicalresults indicated that the main reason for photo-inhibition was oxidative factors induced by NaCl. The proteomic results based on isobaric tags for relative and absolute quantitation (iTRAQ) further confirmedthat photosynthesis was the most significant disrupted process by salinity (P < 0.01) and there were 30 downregulated differentially expression proteins (DEPs) and one upregulated DEP related to restraint of the photosynthetic system, which affected photosystem I, photosystem II, the Cytochrome b6/f complex, ATP synthase and the light-harvesting chlorophyll protein complex. In addition, 57 DEPs were related to photo-inhibition by redox effect and 6 downregulated DEPs, including O2 evolving complex 33kD family protein (gi—224094610) and five other predicted proteins (gi—743921083, gi—743840443, gi—743885735, gi…
bibliographic citation: Yue et al. (2020) The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis. PeerJ 8:e9443 https://doi.org/10.7717/peerj.9443
date submitted: 2019-02-14
date accepted: 2020-06-08
issued: 2020-08-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Jiammin
author list: Agent
  family name: Shi
  given name: Dawei
author list: Agent
  family name: Zhang
  given name: Liang
author list: Agent
  family name: Zhang
  given name: Zihan
author list: Agent
  family name: Fu
  given name: Zhiyuan
author list: Agent
  family name: Ren
  given name: Qiong
author list: Agent
  family name: Zhang
  given name: Jinchi
doi: 10.7717/peerj.9443
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-07
copyright: ©2020 Yue et al.
attribution name: Yue et al.

Silencing of the ARK5 gene reverses the drug resistance of multidrug-resistant SGC7901/DDP gastric cancer cells
type: item
type: AcademicArticle
description: For several years, the multidrug resistance (MDR) of gastric cancer cells has been a thorny issue worldwide regarding the chemotherapy process and needs to be solved. Here, we report that the ARK5 gene could promote the multidrug resistance of gastric cancer cells in vitro and in vivo. In this study, LV-ARK5-RNAi lentivirus was used to transfect the parental cell line SGC7901 and MDR cell line SGC7901/DDP to construct a stable model of ARK5 interference. Subsequently, the cells were treated with four chemotherapeutic drugs, cisplatin (DDP), adriamycin (ADR), 5-fluorouracil (5-FU) and docetaxel (DR) and were subjected to the CCK8, colony formation, adriamycin accumulation and retention, cell apoptosis and other assays. The study found that, in vitro, the expression of ARK5 in MDR gastric cancer cells was significantly higher than that in parental cells. Additionally, when treated with different chemotherapeutic drugs, compared with parental cells, MDR cells also had a higher cell survival rate, higher colony formation number, higher drug pump rate, and lower cell apoptosis rate. Additionally, in xenograft mouse models, MDR cells with high ARK5 expression showed higher resistance to chemotherapeutic drugs than parental cells. Overall, this study revealed that silencing the ARK5 gene can effectively reverse the drug resistance of MDR gastric cancer cells to chemotherapeutic drugs, providing insights into the mechanism of this process related to its inhibition of the active pump-out ability of MDR cells.
format: application/pdf
format: text/html
creator: Hongtao Wan
creator: Xiaowei Liu
creator: Yanglin Chen
creator: Ren Tang
creator: Bo Yi
creator: Dan Liu
subject: Biotechnology
subject: Cell Biology
subject: Genetics
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.9560
publisher: PeerJ Inc.
rights: © 2020 Wan et al.
abstract: For several years, the multidrug resistance (MDR) of gastric cancer cells has been a thorny issue worldwide regarding the chemotherapy process and needs to be solved. Here, we report that the ARK5 gene could promote the multidrug resistance of gastric cancer cells in vitro and in vivo. In this study, LV-ARK5-RNAi lentivirus was used to transfect the parental cell line SGC7901 and MDR cell line SGC7901/DDP to construct a stable model of ARK5 interference. Subsequently, the cells were treated with four chemotherapeutic drugs, cisplatin (DDP), adriamycin (ADR), 5-fluorouracil (5-FU) and docetaxel (DR) and were subjected to the CCK8, colony formation, adriamycin accumulation and retention, cell apoptosis and other assays. The study found that, in vitro, the expression of ARK5 in MDR gastric cancer cells was significantly higher than that in parental cells. Additionally, when treated with different chemotherapeutic drugs, compared with parental cells, MDR cells also had a higher cell survival rate, higher colony formation number, higher drug pump rate, and lower cell apoptosis rate. Additionally, in xenograft mouse models, MDR cells with high ARK5 expression showed higher resistance to chemotherapeutic drugs than parental cells. Overall, this study revealed that silencing the ARK5 gene can effectively reverse the drug resistance of MDR gastric cancer cells to chemotherapeutic drugs, providing insights into the mechanism of this process related to its inhibition of the active pump-out ability of MDR cells.
bibliographic citation: Wan et al. (2020) Silencing of the ARK5 gene reverses the drug resistance of multidrug-resistant SGC7901/DDP gastric cancer cells. PeerJ 8:e9560 https://doi.org/10.7717/peerj.9560
date submitted: 2020-03-03
date accepted: 2020-06-25
issued: 2020-08-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Hongtao
author list: Agent
  family name: Liu
  given name: Xiaowei
author list: Agent
  family name: Chen
  given name: Yanglin
author list: Agent
  family name: Tang
  given name: Ren
author list: Agent
  family name: Yi
  given name: Bo
author list: Agent
  family name: Liu
  given name: Dan
doi: 10.7717/peerj.9560
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-07
copyright: ©2020 Wan et al.
attribution name: Wan et al.

A note on the effects of epidemic forecasts on epidemic dynamics
type: item
type: AcademicArticle
description: The purpose of a forecast, in making an estimate about the future, is to give people information to act on. In the case of a coupled human system, a change in human behavior caused by the forecast can alter the course of events that were the subject of the forecast. In this context, the forecast is an integral part of the coupled human system, with two-way feedback between forecast output and human behavior. However, forecasting programs generally do not examine how the forecast might affect the system in question. This study examines how such a coupled system works using a model of viral infection—the susceptible-infected-removed (SIR) model—when the model is used in a forecasting context. Human behavior is modified by making the contact rate responsive to other dynamics, including forecasts, of the SIR system. This modification creates two-way feedback between the forecast and the infection dynamics. Results show that a faster rate of response by a population to system dynamics or forecasts leads to a significant decline in peak infections. Responding to a forecast leads to a lower infection peak than responding to current infection levels. Inaccurate forecasts can lead to either higher or lower peak infections depending on whether the forecast under-or over-estimates the peak. The direction of inaccuracy in a forecast determines whether the outcome is better or worse for the population. While work is still needed to constrain model functional forms, forecast feedback can be an important component of epidemic dynamics that should be considered in response planning.
format: application/pdf
format: text/html
creator: Nicholas R. Record
creator: Andrew Pershing
subject: Science Policy
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.9649
publisher: PeerJ Inc.
rights: © 2020 Record and Pershing
abstract: The purpose of a forecast, in making an estimate about the future, is to give people information to act on. In the case of a coupled human system, a change in human behavior caused by the forecast can alter the course of events that were the subject of the forecast. In this context, the forecast is an integral part of the coupled human system, with two-way feedback between forecast output and human behavior. However, forecasting programs generally do not examine how the forecast might affect the system in question. This study examines how such a coupled system works using a model of viral infection—the susceptible-infected-removed (SIR) model—when the model is used in a forecasting context. Human behavior is modified by making the contact rate responsive to other dynamics, including forecasts, of the SIR system. This modification creates two-way feedback between the forecast and the infection dynamics. Results show that a faster rate of response by a population to system dynamics or forecasts leads to a significant decline in peak infections. Responding to a forecast leads to a lower infection peak than responding to current infection levels. Inaccurate forecasts can lead to either higher or lower peak infections depending on whether the forecast under-or over-estimates the peak. The direction of inaccuracy in a forecast determines whether the outcome is better or worse for the population. While work is still needed to constrain model functional forms, forecast feedback can be an important component of epidemic dynamics that should be considered in response planning.
bibliographic citation: Record et al. (2020) A note on the effects of epidemic forecasts on epidemic dynamics. PeerJ 8:e9649 https://doi.org/10.7717/peerj.9649
date submitted: 2020-04-29
date accepted: 2020-07-13
issued: 2020-08-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Record
  given name: Nicholas R.
author list: Agent
  family name: Pershing
  given name: Andrew
doi: 10.7717/peerj.9649
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-07
copyright: © 2020 Record and Pershing
attribution name: Record and Pershing

High antibody titres induced by protein subunit vaccines using Mycobacterium ulcerans antigens Hsp18 and MUL_3720 with a TLR-2 agonist fail to protect against Buruli ulcer in mice
type: item
type: AcademicArticle
description: Background Mycobacterium ulcerans is the causative agent of a debilitating skin and soft tissue infection known as Buruli ulcer (BU). There is no vaccine against BU. The purpose of this study was to investigate the vaccine potential of two previously described immunogenic M. ulcerans proteins, MUL_3720 and Hsp18, using a mouse tail infection model of BU. Methods Recombinant versions of the two proteins were each electrostatically coupled with a previously described lipopeptide adjuvant. Seven C57BL/6 and seven BALB/c mice were vaccinated and boosted with each of the formulations. Vaccinated mice were then challenged with M. ulcerans via subcutaneous tail inoculation. Vaccine performance was assessed by time-to-ulceration compared to unvaccinated mice. Results The MUL_3720 and Hsp18 vaccines induced high titres of antigen-specific antibodies that were predominately subtype IgG1. However, all mice developed ulcers by day-40 post-M. ulcerans challenge. No significant difference was observed in the time-to-onset of ulceration between the experimental vaccine groups and unvaccinated animals. Conclusions These data align with previous vaccine experiments using Hsp18 and MUL_3720 that indicated these proteins may not be appropriate vaccine antigens. This work highlights the need to explore alternative vaccine targets and different approaches to understand the role antibodies might play in controlling BU.
format: application/pdf
format: text/html
creator: Kirstie M. Mangas
creator: Nicholas J. Tobias
creator: Estelle Marion
creator: Jérémie Babonneau
creator: Laurent Marsollier
creator: Jessica L. Porter
creator: Sacha J. Pidot
creator: Chinn Yi Wong
creator: David C. Jackson
creator: Brendon Y. Chua
creator: Timothy P. Stinear
subject: Microbiology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.9659
publisher: PeerJ Inc.
rights: © 2020 Mangas et al.
abstract: Background Mycobacterium ulcerans is the causative agent of a debilitating skin and soft tissue infection known as Buruli ulcer (BU). There is no vaccine against BU. The purpose of this study was to investigate the vaccine potential of two previously described immunogenic M. ulcerans proteins, MUL_3720 and Hsp18, using a mouse tail infection model of BU. Methods Recombinant versions of the two proteins were each electrostatically coupled with a previously described lipopeptide adjuvant. Seven C57BL/6 and seven BALB/c mice were vaccinated and boosted with each of the formulations. Vaccinated mice were then challenged with M. ulcerans via subcutaneous tail inoculation. Vaccine performance was assessed by time-to-ulceration compared to unvaccinated mice. Results The MUL_3720 and Hsp18 vaccines induced high titres of antigen-specific antibodies that were predominately subtype IgG1. However, all mice developed ulcers by day-40 post-M. ulcerans challenge. No significant difference was observed in the time-to-onset of ulceration between the experimental vaccine groups and unvaccinated animals. Conclusions These data align with previous vaccine experiments using Hsp18 and MUL_3720 that indicated these proteins may not be appropriate vaccine antigens. This work highlights the need to explore alternative vaccine targets and different approaches to understand the role antibodies might play in controlling BU.
bibliographic citation: Mangas et al. (2020) High antibody titres induced by protein subunit vaccines using Mycobacterium ulcerans antigens Hsp18 and MUL_3720 with a TLR-2 agonist fail to protect against Buruli ulcer in mice. PeerJ 8:e9659 https://doi.org/10.7717/peerj.9659
date submitted: 2020-02-19
date accepted: 2020-07-14
issued: 2020-08-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mangas
  given name: Kirstie M.
author list: Agent
  family name: Tobias
  given name: Nicholas J.
author list: Agent
  family name: Marion
  given name: Estelle
author list: Agent
  family name: Babonneau
  given name: Jérémie
author list: Agent
  family name: Marsollier
  given name: Laurent
author list: Agent
  family name: Porter
  given name: Jessica L.
author list: Agent
  family name: Pidot
  given name: Sacha J.
author list: Agent
  family name: Wong
  given name: Chinn Yi
author list: Agent
  family name: Jackson
  given name: David C.
author list: Agent
  family name: Chua
  given name: Brendon Y.
author list: Agent
  family name: Stinear
  given name: Timothy P.
doi: 10.7717/peerj.9659
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-07
copyright: ©2020 Mangas et al.
attribution name: Mangas et al.

Dissecting molecular network structures using a network subgraph approach
type: item
type: AcademicArticle
description: Biological processes are based on molecular networks, which exhibit biological functions through interactions of genetic elements or proteins. This study presents a graph-based method to characterize molecular networks by decomposing the networks into directed multigraphs: network subgraphs. Spectral graph theory, reciprocity and complexity measures were used to quantify the network subgraphs. Graph energy, reciprocity and cyclomatic complexity can optimally specify network subgraphs with some degree of degeneracy. Seventy-one molecular networks were analyzed from three network types: cancer networks, signal transduction networks, and cellular processes. Molecular networks are built from a finite number of subgraph patterns and subgraphs with large graph energies are not present, which implies a graph energy cutoff. In addition, certain subgraph patterns are absent from the three network types. Thus, the Shannon entropy of the subgraph frequency distribution is not maximal. Furthermore, frequently-observed subgraphs are irreducible graphs. These novel findings warrant further investigation and may lead to important applications. Finally, we observed that cancer-related cellular processes are enriched with subgraph-associated driver genes. Our study provides a systematic approach for dissecting biological networks and supports the conclusion that there are organizational principles underlying molecular networks.
format: application/pdf
format: text/html
creator: Chien-Hung Huang
creator: Efendi Zaenudin
creator: Jeffrey J.P. Tsai
creator: Nilubon Kurubanjerdjit
creator: Eskezeia Y. Dessie
creator: Ka-Lok Ng
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.9556
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Biological processes are based on molecular networks, which exhibit biological functions through interactions of genetic elements or proteins. This study presents a graph-based method to characterize molecular networks by decomposing the networks into directed multigraphs: network subgraphs. Spectral graph theory, reciprocity and complexity measures were used to quantify the network subgraphs. Graph energy, reciprocity and cyclomatic complexity can optimally specify network subgraphs with some degree of degeneracy. Seventy-one molecular networks were analyzed from three network types: cancer networks, signal transduction networks, and cellular processes. Molecular networks are built from a finite number of subgraph patterns and subgraphs with large graph energies are not present, which implies a graph energy cutoff. In addition, certain subgraph patterns are absent from the three network types. Thus, the Shannon entropy of the subgraph frequency distribution is not maximal. Furthermore, frequently-observed subgraphs are irreducible graphs. These novel findings warrant further investigation and may lead to important applications. Finally, we observed that cancer-related cellular processes are enriched with subgraph-associated driver genes. Our study provides a systematic approach for dissecting biological networks and supports the conclusion that there are organizational principles underlying molecular networks.
bibliographic citation: Huang et al. (2020) Dissecting molecular network structures using a network subgraph approach. PeerJ 8:e9556 https://doi.org/10.7717/peerj.9556
date submitted: 2020-01-08
date accepted: 2020-06-25
issued: 2020-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Chien-Hung
author list: Agent
  family name: Zaenudin
  given name: Efendi
author list: Agent
  family name: Tsai
  given name: Jeffrey J.P.
author list: Agent
  family name: Kurubanjerdjit
  given name: Nilubon
author list: Agent
  family name: Dessie
  given name: Eskezeia Y.
author list: Agent
  family name: Ng
  given name: Ka-Lok
doi: 10.7717/peerj.9556
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-06
copyright: © 2020 Huang et al.
attribution name: Huang et al.

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