PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Economic contribution and attitude towards alien freshwater ornamental fishes of pet store owners in Klang Valley, Malaysia
items: Modeling the bidirectional glutamine/ammonium conversion between cancer cells and cancer-associated fibroblasts
items: Ballroom dancers exhibit a dispositional need for arousal and elevated cerebral cortical activity during preferred melodic recall
items: Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics
items: The association between serum uric acid and diabetic complications in patients with type 2 diabetes mellitus by gender: a cross-sectional study
items: Improved salt tolerance of Chenopodium quinoa Willd. contributed by Pseudomonas sp. strain M30-35
items: Consistency of dark skeletal muscles in Thai native black-bone chickens (Gallus gallus domesticus)
items: Records of ctenophores from South Africa
items: Present practices and emerging opportunities in bioengineering for slope stabilization in Malaysia: An overview
items: Comment on Pescott & Jitlal 2020: Failure to account for measurement error undermines their conclusion of a weak impact of nitrogen deposition on plant species richness

Economic contribution and attitude towards alien freshwater ornamental fishes of pet store owners in Klang Valley, Malaysia
type: item
type: AcademicArticle
description: Malaysia is one of the top ten countries in the world that produce freshwater ornamental fishes. This industry can offer better livelihood opportunities to many poor households. However, most of the produced ornamental fishes are alien to Malaysia. In this study, we explore the contribution of alien freshwater fishes to the income of ornamental fish store owners and their attitude towards alien freshwater fishes within Klang Valley, Malaysia. Using a structured questionnaire, we surveyed 70 pet stores out of which 54 (81.42%) store owners responded. Most of the pet store owners were male (72%), Chinese (83%), and the highest educational level was at the secondary level (79%). Most of the pet store owners reported a monthly income of RM 2001–RM 5000 (78%) and were married (73%). Using Chi-square (χ2) test, significant relationships (p < 0.05) existed between the attitude of store owners towards alien ornamental fish species versus educational level (χ2 = 16.424, p = 0.007) and contribution of alien ornamental fishes to the pet store owners’ income (χ2 = 27.266, p = 0.003). Fish sales as the main income source also related significantly with the impact of fish selling business on income level (χ2 = 10.448, p = 0.007). This study showed that the ornamental fish sales contributed over half of the income (51–100%) from the businesses of store owners. Almost half of the respondents (42%) reported that alien ornamental fish was the highest contributor to their income from the ornamental fish sale. While the mismanagement of alien ornamental fishes could give various negative ecological impacts, the socio-economic benefits of these fishes cannot be denied.
format: application/pdf
format: text/html
creator: Abdulwakil Olawale Saba
creator: Ahmad Ismail
creator: Syaizwan Zahmir Zulkifli
creator: Shamarina Shohaimi
creator: Mohammad Noor Amal Azmai
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.10643
publisher: PeerJ Inc.
rights: © 2021 Saba et al.
abstract: Malaysia is one of the top ten countries in the world that produce freshwater ornamental fishes. This industry can offer better livelihood opportunities to many poor households. However, most of the produced ornamental fishes are alien to Malaysia. In this study, we explore the contribution of alien freshwater fishes to the income of ornamental fish store owners and their attitude towards alien freshwater fishes within Klang Valley, Malaysia. Using a structured questionnaire, we surveyed 70 pet stores out of which 54 (81.42%) store owners responded. Most of the pet store owners were male (72%), Chinese (83%), and the highest educational level was at the secondary level (79%). Most of the pet store owners reported a monthly income of RM 2001–RM 5000 (78%) and were married (73%). Using Chi-square (χ2) test, significant relationships (p < 0.05) existed between the attitude of store owners towards alien ornamental fish species versus educational level (χ2 = 16.424, p = 0.007) and contribution of alien ornamental fishes to the pet store owners’ income (χ2 = 27.266, p = 0.003). Fish sales as the main income source also related significantly with the impact of fish selling business on income level (χ2 = 10.448, p = 0.007). This study showed that the ornamental fish sales contributed over half of the income (51–100%) from the businesses of store owners. Almost half of the respondents (42%) reported that alien ornamental fish was the highest contributor to their income from the ornamental fish sale. While the mismanagement of alien ornamental fishes could give various negative ecological impacts, the socio-economic benefits of these fishes cannot be denied.
bibliographic citation: Saba et al. (2021) Economic contribution and attitude towards alien freshwater ornamental fishes of pet store owners in Klang Valley, Malaysia. PeerJ 9:e10643 https://doi.org/10.7717/peerj.10643
date submitted: 2020-09-18
date accepted: 2020-12-03
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saba
  given name: Abdulwakil Olawale
author list: Agent
  family name: Ismail
  given name: Ahmad
author list: Agent
  family name: Zulkifli
  given name: Syaizwan Zahmir
author list: Agent
  family name: Shohaimi
  given name: Shamarina
author list: Agent
  family name: Azmai
  given name: Mohammad Noor Amal
doi: 10.7717/peerj.10643
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Saba et al.
attribution name: Saba et al.

Modeling the bidirectional glutamine/ammonium conversion between cancer cells and cancer-associated fibroblasts
type: item
type: AcademicArticle
description: Like in an ecosystem, cancer and other cells residing in the tumor microenvironment engage in various modes of interactions to buffer the negative effects of environmental changes. One such change is the consumption of common nutrients (such as glutamine/Gln) and the consequent accumulation of toxic metabolic byproducts (such as ammonium/NH4). Ammonium is a waste product of cellular metabolism whose accumulation causes cell stress. In tumors, it is known that it can be recycled into nutrients by cancer associated fibroblasts (CAFs). Here we present monoculture and coculture growth of cancer cells and CAFs on different substrates: glutamine and ammonium. We propose a mathematical model to aid our understanding. We find that cancer cells are able to survive on ammonium and recycle it to glutamine for limited periods of time. CAFs are able to even grow on ammonium. In coculture, the presence of CAFs results in an improved survival of cancer cells compared to their monoculture when exposed to ammonium. Interestingly, the ratio between the two cell populations is maintained under various concentrations of NH4, suggesting the ability of the mixed cell system to survive temporary metabolic stress and sustain the size and cell composition as a stable entity.
format: application/pdf
format: text/html
creator: Peter Hinow
creator: Gabriella Pinter
creator: Wei Yan
creator: Shizhen Emily Wang
subject: Biochemistry
subject: Cell Biology
subject: Mathematical Biology
subject: Oncology
description: doi:10.7717/peerj.10648
publisher: PeerJ Inc.
rights: © 2021 Hinow et al.
abstract: Like in an ecosystem, cancer and other cells residing in the tumor microenvironment engage in various modes of interactions to buffer the negative effects of environmental changes. One such change is the consumption of common nutrients (such as glutamine/Gln) and the consequent accumulation of toxic metabolic byproducts (such as ammonium/NH4). Ammonium is a waste product of cellular metabolism whose accumulation causes cell stress. In tumors, it is known that it can be recycled into nutrients by cancer associated fibroblasts (CAFs). Here we present monoculture and coculture growth of cancer cells and CAFs on different substrates: glutamine and ammonium. We propose a mathematical model to aid our understanding. We find that cancer cells are able to survive on ammonium and recycle it to glutamine for limited periods of time. CAFs are able to even grow on ammonium. In coculture, the presence of CAFs results in an improved survival of cancer cells compared to their monoculture when exposed to ammonium. Interestingly, the ratio between the two cell populations is maintained under various concentrations of NH4, suggesting the ability of the mixed cell system to survive temporary metabolic stress and sustain the size and cell composition as a stable entity.
bibliographic citation: Hinow et al. (2021) Modeling the bidirectional glutamine/ammonium conversion between cancer cells and cancer-associated fibroblasts. PeerJ 9:e10648 https://doi.org/10.7717/peerj.10648
date submitted: 2020-09-10
date accepted: 2020-12-04
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hinow
  given name: Peter
author list: Agent
  family name: Pinter
  given name: Gabriella
author list: Agent
  family name: Yan
  given name: Wei
author list: Agent
  family name: Wang
  given name: Shizhen Emily
doi: 10.7717/peerj.10648
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Hinow et al.
attribution name: Hinow et al.

Ballroom dancers exhibit a dispositional need for arousal and elevated cerebral cortical activity during preferred melodic recall
type: item
type: AcademicArticle
description: Background Although the association of human temperament and preference has been studied previously, few investigations have examined cerebral cortical activation to assess brain dynamics associated with the motivation to engage in performance. The present study adopted a personality and cognitive neuroscience approach to investigate if participation in ballroom dancing is associated with sensation-seeking temperament and elevated cerebral cortical arousal during freely chosen musical recall. Methods Preferred tempo, indicated by tapping speed during melodic recall, and a measure of fundamental disposition or temperament were assessed in 70 ballroom dancers and 71 nondancers. All participants completed a trait personality inventory (i.e., the Chen Huichang 60 Temperaments Inventory) to determine four primary types: choleric, sanguine, phlegmatic and melancholic. Participants separately recalled their favorite musical piece and tapped to it with their index finger for 40 beats using a computer keyboard. A subset of 59 participants (29 ballroom dancers and 30 nondancers) also repeated the same tapping task while electroencephalographic (EEG) activity was recorded. Results The results revealed that the dancers were more extraverted, indicative of a heightened need for arousal, exhibited a preference for faster musical tempo, and exhibited elevated EEG beta power during the musical recall task relative to nondancers. Paradoxically, dancers also showed elevated introversion (i.e., melancholic score) relative to nondancers, which can be resolved by consideration of interactional personality theory if one assumes reasonably that dance performance environment is perceived in a stimulating manner. Conclusion The results are generally consistent with arousal theory, and suggest that ballroom dancers seek elevated stimulation and, thereby, choose to engage with active and energetic rhythmic auditory stimulation, thus providing the nervous system with the requisite stimulation …
format: application/pdf
format: text/html
creator: Xinhong Jin
creator: Yingzhi Lu
creator: Bradley D. Hatfield
creator: Xiaoyu Wang
creator: Biye Wang
creator: Chenglin Zhou
subject: Neuroscience
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10658
publisher: PeerJ Inc.
rights: © 2021 Jin et al.
abstract: Background Although the association of human temperament and preference has been studied previously, few investigations have examined cerebral cortical activation to assess brain dynamics associated with the motivation to engage in performance. The present study adopted a personality and cognitive neuroscience approach to investigate if participation in ballroom dancing is associated with sensation-seeking temperament and elevated cerebral cortical arousal during freely chosen musical recall. Methods Preferred tempo, indicated by tapping speed during melodic recall, and a measure of fundamental disposition or temperament were assessed in 70 ballroom dancers and 71 nondancers. All participants completed a trait personality inventory (i.e., the Chen Huichang 60 Temperaments Inventory) to determine four primary types: choleric, sanguine, phlegmatic and melancholic. Participants separately recalled their favorite musical piece and tapped to it with their index finger for 40 beats using a computer keyboard. A subset of 59 participants (29 ballroom dancers and 30 nondancers) also repeated the same tapping task while electroencephalographic (EEG) activity was recorded. Results The results revealed that the dancers were more extraverted, indicative of a heightened need for arousal, exhibited a preference for faster musical tempo, and exhibited elevated EEG beta power during the musical recall task relative to nondancers. Paradoxically, dancers also showed elevated introversion (i.e., melancholic score) relative to nondancers, which can be resolved by consideration of interactional personality theory if one assumes reasonably that dance performance environment is perceived in a stimulating manner. Conclusion The results are generally consistent with arousal theory, and suggest that ballroom dancers seek elevated stimulation and, thereby, choose to engage with active and energetic rhythmic auditory stimulation, thus providing the nervous system with the requisite stimulation …
bibliographic citation: Jin et al. (2021) Ballroom dancers exhibit a dispositional need for arousal and elevated cerebral cortical activity during preferred melodic recall. PeerJ 9:e10658 https://doi.org/10.7717/peerj.10658
date submitted: 2020-07-31
date accepted: 2020-12-07
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Xinhong
author list: Agent
  family name: Lu
  given name: Yingzhi
author list: Agent
  family name: Hatfield
  given name: Bradley D.
author list: Agent
  family name: Wang
  given name: Xiaoyu
author list: Agent
  family name: Wang
  given name: Biye
author list: Agent
  family name: Zhou
  given name: Chenglin
doi: 10.7717/peerj.10658
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Jin et al.
attribution name: Jin et al.

Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics
type: item
type: AcademicArticle
description: Motivation Analysis of singe cell RNA sequencing (scRNA-seq) typically consists of different steps including quality control, batch correction, clustering, cell identification and characterization, and visualization. The amount of scRNA-seq data is growing extremely fast, and novel algorithmic approaches improving these steps are key to extract more biological information. Here, we introduce: (i) two methods for automatic cell type identification (i.e., without expert curator) based on a voting algorithm and a Hopfield classifier, (ii) a method for cell anomaly quantification based on isolation forest, and (iii) a tool for the visualization of cell phenotypic landscapes based on Hopfield energy-like functions. These new approaches are integrated in a software platform that includes many other state-of-the-art methodologies and provides a self-contained toolkit for scRNA-seq analysis. Results We present a suite of software elements for the analysis of scRNA-seq data. This Python-based open source software, Digital Cell Sorter (DCS), consists in an extensive toolkit of methods for scRNA-seq analysis. We illustrate the capability of the software using data from large datasets of peripheral blood mononuclear cells (PBMC), as well as plasma cells of bone marrow samples from healthy donors and multiple myeloma patients. We test the novel algorithms by evaluating their ability to deconvolve cell mixtures and detect small numbers of anomalous cells in PBMC data. Availability The DCS toolkit is available for download and installation through the Python Package Index (PyPI). The software can be deployed using the Python import function following installation. Source code is also available for download on Zenodo: DOI 10.5281/zenodo.2533377. Supplementary information Supplemental Materials are available at PeerJ online.
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creator: Sergii Domanskyi
creator: Alex Hakansson
creator: Thomas J. Bertus
creator: Giovanni Paternostro
creator: Carlo Piermarocchi
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Computational Science
description: doi:10.7717/peerj.10670
publisher: PeerJ Inc.
rights: © 2021 Domanskyi et al.
abstract: Motivation Analysis of singe cell RNA sequencing (scRNA-seq) typically consists of different steps including quality control, batch correction, clustering, cell identification and characterization, and visualization. The amount of scRNA-seq data is growing extremely fast, and novel algorithmic approaches improving these steps are key to extract more biological information. Here, we introduce: (i) two methods for automatic cell type identification (i.e., without expert curator) based on a voting algorithm and a Hopfield classifier, (ii) a method for cell anomaly quantification based on isolation forest, and (iii) a tool for the visualization of cell phenotypic landscapes based on Hopfield energy-like functions. These new approaches are integrated in a software platform that includes many other state-of-the-art methodologies and provides a self-contained toolkit for scRNA-seq analysis. Results We present a suite of software elements for the analysis of scRNA-seq data. This Python-based open source software, Digital Cell Sorter (DCS), consists in an extensive toolkit of methods for scRNA-seq analysis. We illustrate the capability of the software using data from large datasets of peripheral blood mononuclear cells (PBMC), as well as plasma cells of bone marrow samples from healthy donors and multiple myeloma patients. We test the novel algorithms by evaluating their ability to deconvolve cell mixtures and detect small numbers of anomalous cells in PBMC data. Availability The DCS toolkit is available for download and installation through the Python Package Index (PyPI). The software can be deployed using the Python import function following installation. Source code is also available for download on Zenodo: DOI 10.5281/zenodo.2533377. Supplementary information Supplemental Materials are available at PeerJ online.
bibliographic citation: Domanskyi et al. (2021) Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics. PeerJ 9:e10670 https://doi.org/10.7717/peerj.10670
date submitted: 2020-10-09
date accepted: 2020-12-08
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Domanskyi
  given name: Sergii
author list: Agent
  family name: Hakansson
  given name: Alex
author list: Agent
  family name: Bertus
  given name: Thomas J.
author list: Agent
  family name: Paternostro
  given name: Giovanni
author list: Agent
  family name: Piermarocchi
  given name: Carlo
doi: 10.7717/peerj.10670
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Domanskyi et al.
attribution name: Domanskyi et al.

The association between serum uric acid and diabetic complications in patients with type 2 diabetes mellitus by gender: a cross-sectional study
type: item
type: AcademicArticle
description: Background The relationship between serum uric acid (SUA) and several diabetic complications or co-morbidities remains a matter of debate. The study aims to explore the association between SUA levels and the prevalence of non-alcoholic fatty liver disease (NAFLD), diabetic retinopathy (DR), diabetic nephropathy (DN) and diabetic peripheral neuropathy (DPN) in patients with type 2 diabetes mellitus (T2DM). Methods A total of 2,809 participants (1,784 males and 1,025 females) were included in this cross-sectional study. Clinical characteristics and the prevalence of each of the four diseases were analyzed based on gender-specific quartiles of SUA levels. The Pearson correlation analysis and linear-regression analysis were used to access the correlation between SUA levels and clinical characteristics. Furthermore, a binary logistic regression analysis was carried out to determine whether SUA was an independent risk factor for each of the four complications. Results SUA levels were positively correlated to BMI, BUN, Scr and TG, but negatively associated with eGFR, HDL, FBG, 2h-PG and HbA1c% for the patients with T2DM. The prevalence of NAFLD and DN, but not DR or DPN, were increased with SUA levels from the first to the fourth quartile. Binary logistic regression further disclosed that SUA was an independent risk factor for NAFLD (ORs Male = 1.002, ∗P = 0.0013; ORs Female = 1.002, ∗P = 0.015) and DN (ORs Male = 1.006, ∗P < 0.001; ORs Female = 1.005, ∗P < 0.001), but not for DR and DPN. After adjustment for the confounders, SUA levels were significantly associated with NAFLD within the 3rd (ORs = 1.829, P = 0.004) and 4th quartile (ORs = 2.064, P = 0.001) for women, but not independently associated with SUA for man. On the other hand, our results revealed increased prevalence of DN for SUA quartile 2 (ORs = 3.643, P = 0.039), quartile 3 (ORs = 3.967, P = 0.024) and quartile 4 (ORs = 9.133, P < 0.001) in men; however, SUA quartiles were significantly associated with DN on…
format: application/pdf
format: text/html
creator: Yimeng Hu
creator: Qinge Li
creator: Rui Min
creator: Yingfeng Deng
creator: Yancheng Xu
creator: Ling Gao
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Hematology
description: doi:10.7717/peerj.10691
publisher: PeerJ Inc.
rights: © 2021 Hu et al.
abstract: Background The relationship between serum uric acid (SUA) and several diabetic complications or co-morbidities remains a matter of debate. The study aims to explore the association between SUA levels and the prevalence of non-alcoholic fatty liver disease (NAFLD), diabetic retinopathy (DR), diabetic nephropathy (DN) and diabetic peripheral neuropathy (DPN) in patients with type 2 diabetes mellitus (T2DM). Methods A total of 2,809 participants (1,784 males and 1,025 females) were included in this cross-sectional study. Clinical characteristics and the prevalence of each of the four diseases were analyzed based on gender-specific quartiles of SUA levels. The Pearson correlation analysis and linear-regression analysis were used to access the correlation between SUA levels and clinical characteristics. Furthermore, a binary logistic regression analysis was carried out to determine whether SUA was an independent risk factor for each of the four complications. Results SUA levels were positively correlated to BMI, BUN, Scr and TG, but negatively associated with eGFR, HDL, FBG, 2h-PG and HbA1c% for the patients with T2DM. The prevalence of NAFLD and DN, but not DR or DPN, were increased with SUA levels from the first to the fourth quartile. Binary logistic regression further disclosed that SUA was an independent risk factor for NAFLD (ORs Male = 1.002, ∗P = 0.0013; ORs Female = 1.002, ∗P = 0.015) and DN (ORs Male = 1.006, ∗P < 0.001; ORs Female = 1.005, ∗P < 0.001), but not for DR and DPN. After adjustment for the confounders, SUA levels were significantly associated with NAFLD within the 3rd (ORs = 1.829, P = 0.004) and 4th quartile (ORs = 2.064, P = 0.001) for women, but not independently associated with SUA for man. On the other hand, our results revealed increased prevalence of DN for SUA quartile 2 (ORs = 3.643, P = 0.039), quartile 3 (ORs = 3.967, P = 0.024) and quartile 4 (ORs = 9.133, P < 0.001) in men; however, SUA quartiles were significantly associated with DN on…
bibliographic citation: Hu et al. (2021) The association between serum uric acid and diabetic complications in patients with type 2 diabetes mellitus by gender: a cross-sectional study. PeerJ 9:e10691 https://doi.org/10.7717/peerj.10691
date submitted: 2020-08-24
date accepted: 2020-12-11
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Yimeng
author list: Agent
  family name: Li
  given name: Qinge
author list: Agent
  family name: Min
  given name: Rui
author list: Agent
  family name: Deng
  given name: Yingfeng
author list: Agent
  family name: Xu
  given name: Yancheng
author list: Agent
  family name: Gao
  given name: Ling
doi: 10.7717/peerj.10691
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Hu et al.
attribution name: Hu et al.

Improved salt tolerance of Chenopodium quinoa Willd. contributed by Pseudomonas sp. strain M30-35
type: item
type: AcademicArticle
description: Background Plant-growth-promoting rhizobacteria (PGPR) can promote plant growth and enhance plant tolerance to salt stress. Pseudomonas sp. strain M30-35 might confer abiotic stress tolerance to its host plants. We evaluated the effects of M30-35 inoculation on the growth and metabolite accumulation of Chenopodium quinoa Willd. during salt stress growth conditions. Methods The effects of M30-35 on the growth of C. quinoa seedlings were tested under salt stress. Seedling growth parameters measured included chlorophyll content, root activity, levels of plant- phosphorus (P), and saponin content. Results M30-35 increased biomass production and root activity compared to non-inoculated plants fertilized with rhizobia and plants grown under severe salt stress conditions. The photosynthetic pigment content of chlorophyll a and b were higher in M30-35-inoculated C. quinoa seedlings under high salt stress conditions compared to non-inoculated seedlings. The stability of P content was also maintained. The content of saponin, an important secondary metabolite in C. quinoa, was increased by the inoculation of M30-35 under 300 mM NaCl conditions. Conclusion Inoculation of M30-35 rescues the growth diminution of C. quinoa seedlings under salt stress.
format: application/pdf
format: text/html
creator: Deyu Cai
creator: Ying Xu
creator: Fei Zhao
creator: Yan Zhang
creator: Huirong Duan
creator: Xiaonong Guo
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.10702
publisher: PeerJ Inc.
rights: © 2021 Cai et al.
abstract: Background Plant-growth-promoting rhizobacteria (PGPR) can promote plant growth and enhance plant tolerance to salt stress. Pseudomonas sp. strain M30-35 might confer abiotic stress tolerance to its host plants. We evaluated the effects of M30-35 inoculation on the growth and metabolite accumulation of Chenopodium quinoa Willd. during salt stress growth conditions. Methods The effects of M30-35 on the growth of C. quinoa seedlings were tested under salt stress. Seedling growth parameters measured included chlorophyll content, root activity, levels of plant- phosphorus (P), and saponin content. Results M30-35 increased biomass production and root activity compared to non-inoculated plants fertilized with rhizobia and plants grown under severe salt stress conditions. The photosynthetic pigment content of chlorophyll a and b were higher in M30-35-inoculated C. quinoa seedlings under high salt stress conditions compared to non-inoculated seedlings. The stability of P content was also maintained. The content of saponin, an important secondary metabolite in C. quinoa, was increased by the inoculation of M30-35 under 300 mM NaCl conditions. Conclusion Inoculation of M30-35 rescues the growth diminution of C. quinoa seedlings under salt stress.
bibliographic citation: Cai et al. (2021) Improved salt tolerance of Chenopodium quinoa Willd. contributed by Pseudomonas sp. strain M30-35. PeerJ 9:e10702 https://doi.org/10.7717/peerj.10702
date submitted: 2020-09-08
date accepted: 2020-12-14
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Deyu
author list: Agent
  family name: Xu
  given name: Ying
author list: Agent
  family name: Zhao
  given name: Fei
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Duan
  given name: Huirong
author list: Agent
  family name: Guo
  given name: Xiaonong
doi: 10.7717/peerj.10702
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Cai et al.
attribution name: Cai et al.

Consistency of dark skeletal muscles in Thai native black-bone chickens (Gallus gallus domesticus)
type: item
type: AcademicArticle
description: Black-bone chickens (Gallus gallus domesticus) have become economically valuable, particularly in Southeast Asia as a consequence of popular traditional Chinese medical practices. Chickens with whole body organ darkness are considered to have higher value and are, therefore, more often requested. This research study aimed to investigate the darkness in 34 skeletal muscles of 10 Thai black-bone chickens (five males and five females). The evaluation of muscle darkness was done on two levels: (i) a color chart was employed at the macroanatomical level and (ii) by using melanin pigment to evaluate the structure at the microanatomy level. The results revealed that the accumulation of melanin pigment in the muscle tissue was observed in the endomysium, perimysium and epimysium. With respect to the results of the color chart test, iliotibialis lateralis pars preacetabularis, gastrocnemius, fibularis longus and puboischiofemoralis pars medialis showed the highest degree of darkness, while serratus profundus, pectoralis, iliotibialis cranialis, flexor cruris lateralis, and flexor cruris medialis appeared to be the least dark. In addition, we found that the highest and lowest amounts of melanin pigment was noted in the flexor carpi ulnaris and pectoralis (p < 0.05), respectively; however, there was no significant difference (p > 0.05) observed between the sexes. These results reveal that the 34 specified muscles of black-bone chickens showed uneven distribution of darkness due to the differing accumulations of melanin pigments of each muscle.This information may provide background knowledge for a better understanding of melanin accumulation and lead to breeding improvements in Thai black-bone chickens.
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creator: Wannapimol Kriangwanich
creator: Promporn Piboon
creator: Wirakorn Sakorn
creator: Kittisak Buddhachat
creator: Varankpicha Kochagul
creator: Kidsadagon Pringproa
creator: Supamit Mekchay
creator: Korakot Nganvongpanit
subject: Agricultural Science
subject: Food Science and Technology
subject: Veterinary Medicine
subject: Nutrition
subject: Histology
description: doi:10.7717/peerj.10728
publisher: PeerJ Inc.
rights: © 2021 Kriangwanich et al.
abstract: Black-bone chickens (Gallus gallus domesticus) have become economically valuable, particularly in Southeast Asia as a consequence of popular traditional Chinese medical practices. Chickens with whole body organ darkness are considered to have higher value and are, therefore, more often requested. This research study aimed to investigate the darkness in 34 skeletal muscles of 10 Thai black-bone chickens (five males and five females). The evaluation of muscle darkness was done on two levels: (i) a color chart was employed at the macroanatomical level and (ii) by using melanin pigment to evaluate the structure at the microanatomy level. The results revealed that the accumulation of melanin pigment in the muscle tissue was observed in the endomysium, perimysium and epimysium. With respect to the results of the color chart test, iliotibialis lateralis pars preacetabularis, gastrocnemius, fibularis longus and puboischiofemoralis pars medialis showed the highest degree of darkness, while serratus profundus, pectoralis, iliotibialis cranialis, flexor cruris lateralis, and flexor cruris medialis appeared to be the least dark. In addition, we found that the highest and lowest amounts of melanin pigment was noted in the flexor carpi ulnaris and pectoralis (p < 0.05), respectively; however, there was no significant difference (p > 0.05) observed between the sexes. These results reveal that the 34 specified muscles of black-bone chickens showed uneven distribution of darkness due to the differing accumulations of melanin pigments of each muscle.This information may provide background knowledge for a better understanding of melanin accumulation and lead to breeding improvements in Thai black-bone chickens.
bibliographic citation: Kriangwanich et al. (2021) Consistency of dark skeletal muscles in Thai native black-bone chickens (Gallus gallus domesticus). PeerJ 9:e10728 https://doi.org/10.7717/peerj.10728
date submitted: 2020-08-17
date accepted: 2020-12-17
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kriangwanich
  given name: Wannapimol
author list: Agent
  family name: Piboon
  given name: Promporn
author list: Agent
  family name: Sakorn
  given name: Wirakorn
author list: Agent
  family name: Buddhachat
  given name: Kittisak
author list: Agent
  family name: Kochagul
  given name: Varankpicha
author list: Agent
  family name: Pringproa
  given name: Kidsadagon
author list: Agent
  family name: Mekchay
  given name: Supamit
author list: Agent
  family name: Nganvongpanit
  given name: Korakot
doi: 10.7717/peerj.10728
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Kriangwanich et al.
attribution name: Kriangwanich et al.

Records of ctenophores from South Africa
type: item
type: AcademicArticle
description: Although ctenophores can be conspicuous components of the plankton in coastal marine ecosystems, only six species have been formally described from around South Africa. Using photographs from local community scientists, we add a further three species (Cestum veneris, Beroe forskalii?, Ocyropsis maculata?) and six morphospecies to the regional fauna. These additions suggest that South Africa has a ctenophore fauna that is amongst the most diverse, globally; an observation in agreement with information from other taxa. Tips on how community scientists can improve their photographic contributions to understanding ctenophore diversity are provided.
format: application/pdf
format: text/html
creator: Mark J. Gibbons
creator: Steve H.D. Haddock
creator: George I. Matsumoto
creator: Craig Foster
subject: Biodiversity
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.10697
publisher: PeerJ Inc.
rights: © 2021 Gibbons et al.
abstract: Although ctenophores can be conspicuous components of the plankton in coastal marine ecosystems, only six species have been formally described from around South Africa. Using photographs from local community scientists, we add a further three species (Cestum veneris, Beroe forskalii?, Ocyropsis maculata?) and six morphospecies to the regional fauna. These additions suggest that South Africa has a ctenophore fauna that is amongst the most diverse, globally; an observation in agreement with information from other taxa. Tips on how community scientists can improve their photographic contributions to understanding ctenophore diversity are provided.
bibliographic citation: Gibbons et al. (2021) Records of ctenophores from South Africa. PeerJ 9:e10697 https://doi.org/10.7717/peerj.10697
date submitted: 2020-09-08
date accepted: 2020-12-12
issued: 2021-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gibbons
  given name: Mark J.
author list: Agent
  family name: Haddock
  given name: Steve H.D.
author list: Agent
  family name: Matsumoto
  given name: George I.
author list: Agent
  family name: Foster
  given name: Craig
doi: 10.7717/peerj.10697
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-12
copyright: ©2021 Gibbons et al.
attribution name: Gibbons et al.

Present practices and emerging opportunities in bioengineering for slope stabilization in Malaysia: An overview
type: item
type: AcademicArticle
description: Population increase and the demand for infrastructure development such as construction of highways and road widening are intangible, leading up to mass land clearing. As flat terrains become scarce, infrastructure expansions have moved on to hilly terrains, cutting through slopes and forests. Unvegetated or bare slopes are prone to erosion due to the lack of or insufficient surface cover. The combination of exposed slope, uncontrolled slope management practices, poor slope planning and high rainfall as in Malaysia could steer towards slope failures which then results in landslides under acute situation. Moreover, due to the tropical weather, the soils undergo intense chemical weathering and leaching that elevates soil erosion and surface runoff. Mitigation measures are vital to address slope failures as they lead to economic loss and loss of lives. Since there is minimal or limited information and investigations on slope stabilization methods in Malaysia, this review deciphers into the current slope management practices such as geotextiles, brush layering, live poles, rock buttress and concrete structures. However, these methods have their drawbacks. Thus, as a way forward, we highlight the potential application of soil bioengineering methods especially on the use of whole plants. Here, we discuss the general attributions of a plant in slope stabilization including its mechanical, hydrological and hydraulic effects. Subsequently, we focus on species selection, and engineering properties of vegetation especially rooting structures and architecture. Finally, the review will dissect and assess the ecological principles for vegetation establishment with an emphasis on adopting the mix-culture approach as a slope failure mitigation measure. Nevertheless, the use of soil bioengineering is limited to low to moderate risk slopes only, while in high-risk slopes, the use of traditional engineering measure is deemed more appropriate and remain to be the solution for slope stab…
format: application/pdf
format: text/html
creator: Deivaseeno Dorairaj
creator: Normaniza Osman
subject: Bioengineering
subject: Ecology
subject: Soil Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.10477
publisher: PeerJ Inc.
rights: © 2021 Dorairaj and Osman
abstract: Population increase and the demand for infrastructure development such as construction of highways and road widening are intangible, leading up to mass land clearing. As flat terrains become scarce, infrastructure expansions have moved on to hilly terrains, cutting through slopes and forests. Unvegetated or bare slopes are prone to erosion due to the lack of or insufficient surface cover. The combination of exposed slope, uncontrolled slope management practices, poor slope planning and high rainfall as in Malaysia could steer towards slope failures which then results in landslides under acute situation. Moreover, due to the tropical weather, the soils undergo intense chemical weathering and leaching that elevates soil erosion and surface runoff. Mitigation measures are vital to address slope failures as they lead to economic loss and loss of lives. Since there is minimal or limited information and investigations on slope stabilization methods in Malaysia, this review deciphers into the current slope management practices such as geotextiles, brush layering, live poles, rock buttress and concrete structures. However, these methods have their drawbacks. Thus, as a way forward, we highlight the potential application of soil bioengineering methods especially on the use of whole plants. Here, we discuss the general attributions of a plant in slope stabilization including its mechanical, hydrological and hydraulic effects. Subsequently, we focus on species selection, and engineering properties of vegetation especially rooting structures and architecture. Finally, the review will dissect and assess the ecological principles for vegetation establishment with an emphasis on adopting the mix-culture approach as a slope failure mitigation measure. Nevertheless, the use of soil bioengineering is limited to low to moderate risk slopes only, while in high-risk slopes, the use of traditional engineering measure is deemed more appropriate and remain to be the solution for slope stab…
bibliographic citation: Dorairaj et al. (2021) Present practices and emerging opportunities in bioengineering for slope stabilization in Malaysia: An overview. PeerJ 9:e10477 https://doi.org/10.7717/peerj.10477
date submitted: 2020-05-11
date accepted: 2020-11-11
issued: 2021-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dorairaj
  given name: Deivaseeno
author list: Agent
  family name: Osman
  given name: Normaniza
doi: 10.7717/peerj.10477
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-12
copyright: © 2021 Dorairaj and Osman
attribution name: Dorairaj and Osman

Comment on Pescott & Jitlal 2020: Failure to account for measurement error undermines their conclusion of a weak impact of nitrogen deposition on plant species richness
type: item
type: AcademicArticle
description: Estimation of the impacts of atmospheric nitrogen (N) deposition on ecosystems and biodiversity is a research imperative. Analyses of large-scale spatial gradients, where an observed response is correlated with measured or modelled deposition, have been an important source of evidence. A number of problems beset this approach. For example, if responses are spatially aggregated then treating each location as statistically independent can lead to biased confidence intervals and a greater probably of false positive results. Using methods that account for residual spatial autocorrelation, Pescott & Jitlal (2020) re-analysed two large-scale spatial gradient datasets from Britain where modelled N deposition at 5 × 5 km resolution had been previously correlated with species richness in small quadrats. They found that N deposition effects were weaker than previously demonstrated leading them to conclude that “previous estimates of Ndep impacts on richness from space-for-time substitution studies are likely to have been over-estimated”. We use a simulation study to show that their conclusion is unreliable despite them recognising that an influential fraction of the residual spatially structured variation could itself be attributable to N deposition. This arises because the covariate used was modelled N deposition at 5 × 5 km resolution leaving open the possibility that measured or modelled N deposition at finer resolutions could explain more variance in the response. Explicitly treating this as spatially auto-correlated error ignores this possibility and leads directly to their unreliable conclusion. We further demonstrate the plausibility of this scenario by showing that significant variation in N deposition at the 1 km square resolution is indeed averaged at 5 × 5 km resolution. Further analyses are required to explore whether estimation of the size of the N deposition effect on plant species richness and other measures of biodiversity is indeed dependent on the accuracy a…
format: application/pdf
format: text/html
creator: Simon M. Smart
creator: Carly J. Stevens
creator: Sam J. Tomlinson
creator: Lindsay C. Maskell
creator: Peter A. Henrys
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.10632
publisher: PeerJ Inc.
rights: © 2021 Smart et al.
abstract: Estimation of the impacts of atmospheric nitrogen (N) deposition on ecosystems and biodiversity is a research imperative. Analyses of large-scale spatial gradients, where an observed response is correlated with measured or modelled deposition, have been an important source of evidence. A number of problems beset this approach. For example, if responses are spatially aggregated then treating each location as statistically independent can lead to biased confidence intervals and a greater probably of false positive results. Using methods that account for residual spatial autocorrelation, Pescott & Jitlal (2020) re-analysed two large-scale spatial gradient datasets from Britain where modelled N deposition at 5 × 5 km resolution had been previously correlated with species richness in small quadrats. They found that N deposition effects were weaker than previously demonstrated leading them to conclude that “previous estimates of Ndep impacts on richness from space-for-time substitution studies are likely to have been over-estimated”. We use a simulation study to show that their conclusion is unreliable despite them recognising that an influential fraction of the residual spatially structured variation could itself be attributable to N deposition. This arises because the covariate used was modelled N deposition at 5 × 5 km resolution leaving open the possibility that measured or modelled N deposition at finer resolutions could explain more variance in the response. Explicitly treating this as spatially auto-correlated error ignores this possibility and leads directly to their unreliable conclusion. We further demonstrate the plausibility of this scenario by showing that significant variation in N deposition at the 1 km square resolution is indeed averaged at 5 × 5 km resolution. Further analyses are required to explore whether estimation of the size of the N deposition effect on plant species richness and other measures of biodiversity is indeed dependent on the accuracy a…
bibliographic citation: Smart et al. (2021) Comment on Pescott & Jitlal 2020: Failure to account for measurement error undermines their conclusion of a weak impact of nitrogen deposition on plant species richness. PeerJ 9:e10632 https://doi.org/10.7717/peerj.10632
date submitted: 2020-06-12
date accepted: 2020-12-01
issued: 2021-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smart
  given name: Simon M.
author list: Agent
  family name: Stevens
  given name: Carly J.
author list: Agent
  family name: Tomlinson
  given name: Sam J.
author list: Agent
  family name: Maskell
  given name: Lindsay C.
author list: Agent
  family name: Henrys
  given name: Peter A.
doi: 10.7717/peerj.10632
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-12
copyright: ©2021 Smart et al.
attribution name: Smart et al.

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