PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: N-acetyl-L-tryptophan attenuates hepatic ischemia-reperfusion injury via regulating TLR4/NLRP3 signaling pathway in rats
items: Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition
items: The nutritional applications of garlic (Allium sativum) as natural feed additives in animals
items: The association of reactive balance control and spinal curvature under lumbar muscle fatigue
items: Icaritin protects SH-SY5Y cells transfected with TDP-43 by alleviating mitochondrial damage and oxidative stress
items: Disintegration half-life of biodegradable plastic films on different marine beach sediments
items: Cephalopod species identification using integrated analysis of machine learning and deep learning approaches
items: Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters
items: Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
items: Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress

N-acetyl-L-tryptophan attenuates hepatic ischemia-reperfusion injury via regulating TLR4/NLRP3 signaling pathway in rats
type: item
type: AcademicArticle
description: The aim of this study was to investigate the changes of TLR4/NLRP3 signal during hepatic ischemia-reperfusion injury (HIRI) and to verify whether N-acetyl-L-tryptophan (L-NAT) protected hepatocytes by regulating the activation of TLR4/NLRP3 signal. We have established the rat HIRI model and H2O2-induced cell damage model to simulate ischemia-reperfusion injury and detect the corresponding indicators. Compared with the sham group, Suzuki score and the level of serum ALT increased after HIRI, accompanied by an increased expression of NLRP3, ASC, Caspase-1, IL-1β, TLR4, and NF-κB. While L-NAT pretreatment reversed the above-mentioned changes. Compared with the control group, cells in the H2O2 treated group became smaller in cell volume and round in shape with unclear boundaries. Similar to the phenotypes in vivo, H2O2 treatment also induced significant increase in expression of pyroptosis-related proteins (NLRP3, ASC, Caspase-1 and IL-1β) and inflammatory factors (TLR4 and NF-κB). While L-NAT pretreatment attenuated injuries caused by H2O2. In conclusion, the present findings demonstrate that L-NAT alleviates HIRI by regulating activation of NLRP3 inflammasome, which may be related to the TLR4/NF-κB signaling pathway.
format: application/pdf
format: text/html
creator: Yitong Pan
creator: Shuna Yu
creator: Jianxin Wang
creator: Wanzhen Li
creator: Huiting Li
creator: Chen Bai
creator: Yaxin Sheng
creator: Ming Li
creator: Chenchen Wang
creator: Jiao Liu
creator: Peitong Xie
creator: Can Wang
creator: Jiying Jiang
creator: Jianguo Li
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.11909
publisher: PeerJ Inc.
rights: © 2021 Pan et al.
abstract: The aim of this study was to investigate the changes of TLR4/NLRP3 signal during hepatic ischemia-reperfusion injury (HIRI) and to verify whether N-acetyl-L-tryptophan (L-NAT) protected hepatocytes by regulating the activation of TLR4/NLRP3 signal. We have established the rat HIRI model and H2O2-induced cell damage model to simulate ischemia-reperfusion injury and detect the corresponding indicators. Compared with the sham group, Suzuki score and the level of serum ALT increased after HIRI, accompanied by an increased expression of NLRP3, ASC, Caspase-1, IL-1β, TLR4, and NF-κB. While L-NAT pretreatment reversed the above-mentioned changes. Compared with the control group, cells in the H2O2 treated group became smaller in cell volume and round in shape with unclear boundaries. Similar to the phenotypes in vivo, H2O2 treatment also induced significant increase in expression of pyroptosis-related proteins (NLRP3, ASC, Caspase-1 and IL-1β) and inflammatory factors (TLR4 and NF-κB). While L-NAT pretreatment attenuated injuries caused by H2O2. In conclusion, the present findings demonstrate that L-NAT alleviates HIRI by regulating activation of NLRP3 inflammasome, which may be related to the TLR4/NF-κB signaling pathway.
bibliographic citation: Pan et al. (2021) N-acetyl-L-tryptophan attenuates hepatic ischemia-reperfusion injury via regulating TLR4/NLRP3 signaling pathway in rats. PeerJ 9:e11909 https://doi.org/10.7717/peerj.11909
date submitted: 2021-01-05
date accepted: 2021-07-14
issued: 2021-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Yitong
author list: Agent
  family name: Yu
  given name: Shuna
author list: Agent
  family name: Wang
  given name: Jianxin
author list: Agent
  family name: Li
  given name: Wanzhen
author list: Agent
  family name: Li
  given name: Huiting
author list: Agent
  family name: Bai
  given name: Chen
author list: Agent
  family name: Sheng
  given name: Yaxin
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Wang
  given name: Chenchen
author list: Agent
  family name: Liu
  given name: Jiao
author list: Agent
  family name: Xie
  given name: Peitong
author list: Agent
  family name: Wang
  given name: Can
author list: Agent
  family name: Jiang
  given name: Jiying
author list: Agent
  family name: Li
  given name: Jianguo
doi: 10.7717/peerj.11909
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-10
copyright: ©2021 Pan et al.
attribution name: Pan et al.

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition
type: item
type: AcademicArticle
description: Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial eco…
format: application/pdf
format: text/html
creator: Laura T. Leonard
creator: Eoin L. Brodie
creator: Kenneth H. Williams
creator: Jonathan O. Sharp
subject: Soil Science
subject: Climate Change Biology
subject: Biogeochemistry
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.11926
publisher: PeerJ Inc.
rights: © 2021 Leonard et al.
abstract: Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial eco…
bibliographic citation: Leonard et al. (2021) Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition. PeerJ 9:e11926 https://doi.org/10.7717/peerj.11926
date submitted: 2021-04-13
date accepted: 2021-07-17
issued: 2021-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leonard
  given name: Laura T.
author list: Agent
  family name: Brodie
  given name: Eoin L.
author list: Agent
  family name: Williams
  given name: Kenneth H.
author list: Agent
  family name: Sharp
  given name: Jonathan O.
doi: 10.7717/peerj.11926
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-10
copyright: © 2021 Leonard et al.
attribution name: Leonard et al.

The nutritional applications of garlic (Allium sativum) as natural feed additives in animals
type: item
type: AcademicArticle
description: Garlic (Allium sativum) is an essential vegetable that has been widely utilized as seasoning, flavoring, culinary and in herbal remedies. Garlic contains several characteristic organosulfur compounds, such as diallyl sulfide, allicin (diallyl thiosulphate), γ-glutamylcysteine, and S-allyl cysteine (alliin) and ajoene, which garlic has beneficial effects on inflammation, oxidative stress markers, hypertension, hyperlipidaemia and endothelial function in vitro or in animal model. These bioactive molecules are also playing pivotal role in livestock and fisheries production apart from its application in humans. Supplementation of animal feed with garlic and its related products is consistent with the modern agricultural concept of organic animal husbandry. This review compiles the information describing the effects of feeding garlic and its extracts on selected performance parameters in animals (chicken, rabbits, ruminants, pigs and fish). This review may provide reference for scientists and entrepreneurs to investigate the applications of feeds added with garlic and allicin by-products for the improvement of animal husbandry and aquatic production.
format: application/pdf
format: text/html
creator: Jiashun Chen
creator: Fang Wang
creator: Yexin Yin
creator: Xiaokang Ma
subject: Agricultural Science
subject: Plant Science
subject: Veterinary Medicine
description: doi:10.7717/peerj.11934
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Garlic (Allium sativum) is an essential vegetable that has been widely utilized as seasoning, flavoring, culinary and in herbal remedies. Garlic contains several characteristic organosulfur compounds, such as diallyl sulfide, allicin (diallyl thiosulphate), γ-glutamylcysteine, and S-allyl cysteine (alliin) and ajoene, which garlic has beneficial effects on inflammation, oxidative stress markers, hypertension, hyperlipidaemia and endothelial function in vitro or in animal model. These bioactive molecules are also playing pivotal role in livestock and fisheries production apart from its application in humans. Supplementation of animal feed with garlic and its related products is consistent with the modern agricultural concept of organic animal husbandry. This review compiles the information describing the effects of feeding garlic and its extracts on selected performance parameters in animals (chicken, rabbits, ruminants, pigs and fish). This review may provide reference for scientists and entrepreneurs to investigate the applications of feeds added with garlic and allicin by-products for the improvement of animal husbandry and aquatic production.
bibliographic citation: Chen et al. (2021) The nutritional applications of garlic (Allium sativum) as natural feed additives in animals. PeerJ 9:e11934 https://doi.org/10.7717/peerj.11934
date submitted: 2020-12-30
date accepted: 2021-07-19
issued: 2021-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jiashun
author list: Agent
  family name: Wang
  given name: Fang
author list: Agent
  family name: Yin
  given name: Yexin
author list: Agent
  family name: Ma
  given name: Xiaokang
doi: 10.7717/peerj.11934
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-10
copyright: © 2021 Chen et al.
attribution name: Chen et al.

The association of reactive balance control and spinal curvature under lumbar muscle fatigue
type: item
type: AcademicArticle
description: Background Although low back fatigue is an important intervening factor for physical functioning among sedentary people, little is known about its possible significance in relation to the spinal posture and compensatory postural responses to unpredictable stimuli. This study investigates the effect of lumbar muscle fatigue on spinal curvature and reactive balance control in response to externally induced perturbations. Methods A group of 38 young sedentary individuals underwent a perturbation-based balance test by applying a 2 kg load release. Sagittal spinal curvature and pelvic tilt was measured in both a normal and Matthiass standing posture both with and without a hand-held 2 kg load, and before and after the Sørensen fatigue test. Results Both the peak anterior and peak posterior center of pressure (CoP) displacements and the corresponding time to peak anterior and peak posterior CoP displacements significantly increased after the Sørensen fatigue test (all at p < 0.001). A lumbar muscle fatigue led to a decrease of the lumbar lordosis in the Matthiass posture while holding a 2 kg load in front of the body when compared to pre-fatigue conditions both without a load (p = 0.011, d = 0.35) and with a 2 kg load (p = 0.000, d = 0.51). Also the sacral inclination in the Matthiass posture with a 2 kg additional load significantly decreased under fatigue when compared to all postures in pre-fatigue conditions (p = 0.01, d = 0.48). Contrary to pre-fatigue conditions, variables of the perturbation-based balance test were closely associated with those of lumbar curvature while standing in the Matthiass posture with a 2 kg additional load after the Sørensen fatigue test (r values in range from −0.520 to −0.631, all at p < 0.05). Conclusion These findings indicate that lumbar muscle fatigue causes changes in the lumbar spinal curvature and this is functionally relevant in explaining the impaired ability to maintain balance after externally induced perturbations. This emphas…
format: application/pdf
format: text/html
creator: Erika Zemková
creator: Alena Cepková
creator: José M. Muyor
subject: Kinesiology
description: doi:10.7717/peerj.11969
publisher: PeerJ Inc.
rights: © 2021 Zemková et al.
abstract: Background Although low back fatigue is an important intervening factor for physical functioning among sedentary people, little is known about its possible significance in relation to the spinal posture and compensatory postural responses to unpredictable stimuli. This study investigates the effect of lumbar muscle fatigue on spinal curvature and reactive balance control in response to externally induced perturbations. Methods A group of 38 young sedentary individuals underwent a perturbation-based balance test by applying a 2 kg load release. Sagittal spinal curvature and pelvic tilt was measured in both a normal and Matthiass standing posture both with and without a hand-held 2 kg load, and before and after the Sørensen fatigue test. Results Both the peak anterior and peak posterior center of pressure (CoP) displacements and the corresponding time to peak anterior and peak posterior CoP displacements significantly increased after the Sørensen fatigue test (all at p < 0.001). A lumbar muscle fatigue led to a decrease of the lumbar lordosis in the Matthiass posture while holding a 2 kg load in front of the body when compared to pre-fatigue conditions both without a load (p = 0.011, d = 0.35) and with a 2 kg load (p = 0.000, d = 0.51). Also the sacral inclination in the Matthiass posture with a 2 kg additional load significantly decreased under fatigue when compared to all postures in pre-fatigue conditions (p = 0.01, d = 0.48). Contrary to pre-fatigue conditions, variables of the perturbation-based balance test were closely associated with those of lumbar curvature while standing in the Matthiass posture with a 2 kg additional load after the Sørensen fatigue test (r values in range from −0.520 to −0.631, all at p < 0.05). Conclusion These findings indicate that lumbar muscle fatigue causes changes in the lumbar spinal curvature and this is functionally relevant in explaining the impaired ability to maintain balance after externally induced perturbations. This emphas…
bibliographic citation: Zemková et al. (2021) The association of reactive balance control and spinal curvature under lumbar muscle fatigue. PeerJ 9:e11969 https://doi.org/10.7717/peerj.11969
date submitted: 2020-12-23
date accepted: 2021-07-23
issued: 2021-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zemková
  given name: Erika
author list: Agent
  family name: Cepková
  given name: Alena
author list: Agent
  family name: Muyor
  given name: José M.
doi: 10.7717/peerj.11969
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-10
copyright: ©2021 Zemková et al.
attribution name: Zemková et al.

Icaritin protects SH-SY5Y cells transfected with TDP-43 by alleviating mitochondrial damage and oxidative stress
type: item
type: AcademicArticle
description: Background The aim of this study was to investigate the effect of icaritin (ICT) on TAR DNA-binding protein 43 (TDP-43)-induced neuroblastoma (SH-SY5Y) cell damage and to further explore its underlying mechanisms. Methods To investigate the possible mechanism, TDP-43 was used to induce SH-SY5Y cell injury. Cell viability was evaluated by the CCK-8 assay. The mitochondrial membrane potential (MMP) was determined with JC-1. The expression levels of TDP-43 and cytochrome C (CytC) were measuring by Western blotting. Changes in adenosine 5′-triphosphate (ATP) content, total antioxidative capacity (T-AOC), glutathione peroxidase (GSH-Px) activity, superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were detected with specific kits. Results The results showed that ICT reduced the cell damage induced by TDP-43. ICT reduced the expression level of TDP-43; increased ATP content and the MMP; decreased CytC expression; increased T-AOC and GSH-Px, total SOD (T-SOD), copper/zinc SOD (CuZn-SOD), and manganese SOD (Mn-SOD) activity; and decreased MDA content. Conclusions The results suggest that ICT has a protective effect on TDP-43-transfected SH-SY5Y cells that is related to reductions in TDP-43 expression and mitochondrial damage and alleviation of oxidative stress.
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creator: Yongjian Zhou
creator: Nanqu Huang
creator: Yuanyuan Li
creator: Zhisheng Ba
creator: Yanjun Zhou
creator: Yong Luo
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11978
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Background The aim of this study was to investigate the effect of icaritin (ICT) on TAR DNA-binding protein 43 (TDP-43)-induced neuroblastoma (SH-SY5Y) cell damage and to further explore its underlying mechanisms. Methods To investigate the possible mechanism, TDP-43 was used to induce SH-SY5Y cell injury. Cell viability was evaluated by the CCK-8 assay. The mitochondrial membrane potential (MMP) was determined with JC-1. The expression levels of TDP-43 and cytochrome C (CytC) were measuring by Western blotting. Changes in adenosine 5′-triphosphate (ATP) content, total antioxidative capacity (T-AOC), glutathione peroxidase (GSH-Px) activity, superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were detected with specific kits. Results The results showed that ICT reduced the cell damage induced by TDP-43. ICT reduced the expression level of TDP-43; increased ATP content and the MMP; decreased CytC expression; increased T-AOC and GSH-Px, total SOD (T-SOD), copper/zinc SOD (CuZn-SOD), and manganese SOD (Mn-SOD) activity; and decreased MDA content. Conclusions The results suggest that ICT has a protective effect on TDP-43-transfected SH-SY5Y cells that is related to reductions in TDP-43 expression and mitochondrial damage and alleviation of oxidative stress.
bibliographic citation: Zhou et al. (2021) Icaritin protects SH-SY5Y cells transfected with TDP-43 by alleviating mitochondrial damage and oxidative stress. PeerJ 9:e11978 https://doi.org/10.7717/peerj.11978
date submitted: 2021-04-02
date accepted: 2021-07-24
issued: 2021-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yongjian
author list: Agent
  family name: Huang
  given name: Nanqu
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Ba
  given name: Zhisheng
author list: Agent
  family name: Zhou
  given name: Yanjun
author list: Agent
  family name: Luo
  given name: Yong
doi: 10.7717/peerj.11978
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-10
copyright: ©2021 Zhou et al.
attribution name: Zhou et al.

Disintegration half-life of biodegradable plastic films on different marine beach sediments
type: item
type: AcademicArticle
description: The seafloor is considered the major sink for plastic debris in the world’s oceans. Biodegradable polymers are available on the market as a substitute for conventional plastic and could potentially end up in the same environment. To gain more insight into the effects of different sediments on the degradation rate of biodegradable plastic we performed two iterative seawater tank experiments. First, to test the effect of sediment grain size, film of Mater-Bi HF03V, a blend of thermoplastic starch and biodegradable polyesters, was placed on the surface of mud as well as on four different grain size fractions of beach sand. Disintegration half-life was shortest on mud (139 days) and increased with the grain size of the beach sediment fractions (63–250 µm: 296 days; 250–500 µm: 310 days; 500–1,000 µm: 438 days; >1,000 µm: 428 days). We assume that the higher surface-to-volume ratio in fine sediment compared to coarse sediment led to a higher bacterial abundance and thus to faster disintegration rates. In a follow-up experiment, the <500 µm fraction of sediment from four different beaches around Isola d’Elba, Italy, was used to test plastic disintegration as above. Additionally, polyhydroxybutyrate (PHB, MIREL P5001) was used as a positive control and high-density polyethylene (HD-PE) as a negative control. No disintegration was observed for HD-PE. Mater-Bi HF03V and PHB disintegrated significantly differently on sediment from different sites, with half-lives of Mater-Bi HF03V ranging from 72 to 368 days and of PHB from 112 to 215 days. Here, the half-life was shortest on slightly coarser sediment and at potentially anthropogenically impacted sites. We assume that the effect of the grain size on the disintegration rate was masked by other parameters influencing the microbial community and activity. Understanding the parameters driving biodegradation is key to reliably report the range of disintegration rates occurring under the various conditions in different ecosystems.
format: application/pdf
format: text/html
creator: Andreas Eich
creator: Miriam Weber
creator: Christian Lott
subject: Marine Biology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11981
publisher: PeerJ Inc.
rights: © 2021 Eich et al.
abstract: The seafloor is considered the major sink for plastic debris in the world’s oceans. Biodegradable polymers are available on the market as a substitute for conventional plastic and could potentially end up in the same environment. To gain more insight into the effects of different sediments on the degradation rate of biodegradable plastic we performed two iterative seawater tank experiments. First, to test the effect of sediment grain size, film of Mater-Bi HF03V, a blend of thermoplastic starch and biodegradable polyesters, was placed on the surface of mud as well as on four different grain size fractions of beach sand. Disintegration half-life was shortest on mud (139 days) and increased with the grain size of the beach sediment fractions (63–250 µm: 296 days; 250–500 µm: 310 days; 500–1,000 µm: 438 days; >1,000 µm: 428 days). We assume that the higher surface-to-volume ratio in fine sediment compared to coarse sediment led to a higher bacterial abundance and thus to faster disintegration rates. In a follow-up experiment, the <500 µm fraction of sediment from four different beaches around Isola d’Elba, Italy, was used to test plastic disintegration as above. Additionally, polyhydroxybutyrate (PHB, MIREL P5001) was used as a positive control and high-density polyethylene (HD-PE) as a negative control. No disintegration was observed for HD-PE. Mater-Bi HF03V and PHB disintegrated significantly differently on sediment from different sites, with half-lives of Mater-Bi HF03V ranging from 72 to 368 days and of PHB from 112 to 215 days. Here, the half-life was shortest on slightly coarser sediment and at potentially anthropogenically impacted sites. We assume that the effect of the grain size on the disintegration rate was masked by other parameters influencing the microbial community and activity. Understanding the parameters driving biodegradation is key to reliably report the range of disintegration rates occurring under the various conditions in different ecosystems.
bibliographic citation: Eich et al. (2021) Disintegration half-life of biodegradable plastic films on different marine beach sediments. PeerJ 9:e11981 https://doi.org/10.7717/peerj.11981
date submitted: 2021-03-29
date accepted: 2021-07-25
issued: 2021-08-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eich
  given name: Andreas
author list: Agent
  family name: Weber
  given name: Miriam
author list: Agent
  family name: Lott
  given name: Christian
doi: 10.7717/peerj.11981
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-10
copyright: © 2021 Eich et al.
attribution name: Eich et al.

Cephalopod species identification using integrated analysis of machine learning and deep learning approaches
type: item
type: AcademicArticle
description: Background Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images. Methods A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance. Results The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of th…
format: application/pdf
format: text/html
creator: Hui Yuan Tan
creator: Zhi Yun Goh
creator: Kar-Hoe Loh
creator: Amy Yee-Hui Then
creator: Hasmahzaiti Omar
creator: Siow-Wee Chang
subject: Computational Biology
subject: Marine Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.11825
publisher: PeerJ Inc.
rights: © 2021 Tan et al.
abstract: Background Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images. Methods A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance. Results The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of th…
bibliographic citation: Tan et al. (2021) Cephalopod species identification using integrated analysis of machine learning and deep learning approaches. PeerJ 9:e11825 https://doi.org/10.7717/peerj.11825
date submitted: 2020-11-13
date accepted: 2021-06-30
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Hui Yuan
author list: Agent
  family name: Goh
  given name: Zhi Yun
author list: Agent
  family name: Loh
  given name: Kar-Hoe
author list: Agent
  family name: Then
  given name: Amy Yee-Hui
author list: Agent
  family name: Omar
  given name: Hasmahzaiti
author list: Agent
  family name: Chang
  given name: Siow-Wee
doi: 10.7717/peerj.11825
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Tan et al.
attribution name: Tan et al.

Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters
type: item
type: AcademicArticle
description: Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
format: application/pdf
format: text/html
creator: Jake J. Ponce
creator: Ivan Arismendi
creator: Austen Thomas
subject: Ecology
subject: Molecular Biology
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.11835
publisher: PeerJ Inc.
rights: © 2021 Ponce et al.
abstract: Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
bibliographic citation: Ponce et al. (2021) Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters. PeerJ 9:e11835 https://doi.org/10.7717/peerj.11835
date submitted: 2021-01-11
date accepted: 2021-07-01
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponce
  given name: Jake J.
author list: Agent
  family name: Arismendi
  given name: Ivan
author list: Agent
  family name: Thomas
  given name: Austen
doi: 10.7717/peerj.11835
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Ponce et al.
attribution name: Ponce et al.

Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
type: item
type: AcademicArticle
description: Background Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomass. Interestingly, engineering of a single gene from such photorespiratory bypasses has also improved photosynthesis and plant productivity. Although single gene transformations may not completely reduce photorespiration, increases in plant biomass accumulation have still been observed indicating an alternative role in regulating different metabolic processes. Therefore, the current study was aimed at evaluating the underlying mechanism (s) associated with the effects of introducing a single cyanobacterial glycolate decarboxylation pathway gene on photosynthesis and plant performance. Methods Transgenic Arabidopsis thaliana plants (GD, HD, OX) expressing independently cyanobacterial decarboxylation pathway genes i.e., glycolate dehydrogenase, hydroxyacid dehydrogenase, and oxalate decarboxylase, respectively, were utilized. Photosynthetic, fluorescence related, and growth parameters were analyzed. Additionally, transcriptomic analysis of GD transgenic plants was also performed. Results The GD plants exhibited a significant increase (16%) in net photosynthesis rate while both HD and OX plants showed a non-significant (11%) increase as compared to wild type plants (WT). The stomatal conductance was significantly higher (24%) in GD and HD plants than the WT plants. The quantum efficiencies of photosystem II, carbon dioxide assimilation and the chlorophyll fluorescence-based photosynthetic electron transport rate were also higher than WT plants. The OX plants displayed significant reductions in the rate of photorespiration relative to gross photosynthesis and increase in the ratio of the photosynthetic electron flow attributable …
format: application/pdf
format: text/html
creator: Anum Zeb Abbasi
creator: Misbah Bilal
creator: Ghazal Khurshid
creator: Charilaos Yiotis
creator: Iftikhar Zeb
creator: Jamshaid Hussain
creator: Ayesha Baig
creator: Mohammad Maroof Shah
creator: Safee Ullah Chaudhary
creator: Bruce Osborne
creator: Raza Ahmad
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.11860
publisher: PeerJ Inc.
rights: © 2021 Abbasi et al.
abstract: Background Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomass. Interestingly, engineering of a single gene from such photorespiratory bypasses has also improved photosynthesis and plant productivity. Although single gene transformations may not completely reduce photorespiration, increases in plant biomass accumulation have still been observed indicating an alternative role in regulating different metabolic processes. Therefore, the current study was aimed at evaluating the underlying mechanism (s) associated with the effects of introducing a single cyanobacterial glycolate decarboxylation pathway gene on photosynthesis and plant performance. Methods Transgenic Arabidopsis thaliana plants (GD, HD, OX) expressing independently cyanobacterial decarboxylation pathway genes i.e., glycolate dehydrogenase, hydroxyacid dehydrogenase, and oxalate decarboxylase, respectively, were utilized. Photosynthetic, fluorescence related, and growth parameters were analyzed. Additionally, transcriptomic analysis of GD transgenic plants was also performed. Results The GD plants exhibited a significant increase (16%) in net photosynthesis rate while both HD and OX plants showed a non-significant (11%) increase as compared to wild type plants (WT). The stomatal conductance was significantly higher (24%) in GD and HD plants than the WT plants. The quantum efficiencies of photosystem II, carbon dioxide assimilation and the chlorophyll fluorescence-based photosynthetic electron transport rate were also higher than WT plants. The OX plants displayed significant reductions in the rate of photorespiration relative to gross photosynthesis and increase in the ratio of the photosynthetic electron flow attributable …
bibliographic citation: Abbasi et al. (2021) Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana. PeerJ 9:e11860 https://doi.org/10.7717/peerj.11860
date submitted: 2021-02-28
date accepted: 2021-07-05
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abbasi
  given name: Anum Zeb
author list: Agent
  family name: Bilal
  given name: Misbah
author list: Agent
  family name: Khurshid
  given name: Ghazal
author list: Agent
  family name: Yiotis
  given name: Charilaos
author list: Agent
  family name: Zeb
  given name: Iftikhar
author list: Agent
  family name: Hussain
  given name: Jamshaid
author list: Agent
  family name: Baig
  given name: Ayesha
author list: Agent
  family name: Shah
  given name: Mohammad Maroof
author list: Agent
  family name: Chaudhary
  given name: Safee Ullah
author list: Agent
  family name: Osborne
  given name: Bruce
author list: Agent
  family name: Ahmad
  given name: Raza
doi: 10.7717/peerj.11860
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: © 2021 Abbasi et al.
attribution name: Abbasi et al.

Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress
type: item
type: AcademicArticle
description: Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.
format: application/pdf
format: text/html
creator: Hong Jiang
creator: Zhiyuan Li
creator: Xiumei Jiang
creator: Yong Qin
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11888
publisher: PeerJ Inc.
rights: © 2021 Jiang et al.
abstract: Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.
bibliographic citation: Jiang et al. (2021) Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress. PeerJ 9:e11888 https://doi.org/10.7717/peerj.11888
date submitted: 2020-10-26
date accepted: 2021-07-09
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Hong
author list: Agent
  family name: Li
  given name: Zhiyuan
author list: Agent
  family name: Jiang
  given name: Xiumei
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.11888
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Jiang et al.
attribution name: Jiang et al.

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