PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: In silico identification and in vitro assessment of a potential anti-breast cancer activity of antimicrobial peptide retrieved from the ATMP1 Anabas testudineus fish peptide
items: Effects of salt stress on seed germination and respiratory metabolism in different Flueggea suffruticosa genotypes
items: Whistle characterization of long-beaked common dolphin (Delphinus delphis bairdii) in La Paz Bay, Gulf of California
items: Investigating the relationship between inbreeding and life expectancy in dogs: mongrels live longer than pure breeds
items: Difference in the recruitment of intrinsic foot muscles in the elderly under static and dynamic postural conditions
items: Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp
items: mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2
items: Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability
items: Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China
items: Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model

In silico identification and in vitro assessment of a potential anti-breast cancer activity of antimicrobial peptide retrieved from the ATMP1 Anabas testudineus fish peptide
type: item
type: AcademicArticle
description: A previous study has shown that synthetic antimicrobial peptides (AMPs) derived from Anabas testudineus (ATMP1) could in-vitro inhibit the progression of breast cancer cell lines. In this study, we are interested in studying altered versions of previous synthetic AMPs to gain some insight into the peptides functions. The AMPs were altered and subjected to bioinformatics prediction using four databases (ADP3, CAMP-R3, AMPfun, and ANTICP) to select the highest anticancer activity. The bioinformatics in silico analysis led to the selection of two AMPs, which are ATMP5 (THPPTTTTTTTTTTTYTAAPATTT) and ATMP6 (THPPTTTTTTTTTTTTTAAPARTT). The in silico analysis predicted that ATMP5 and ATMP6 have anticancer activity and lead to cell death. The ATMP5 and ATMP6 were submitted to deep learning databases (ToxIBTL and ToxinPred2) to predict the toxicity of the peptides and to (AllerTOP & AllergenFP) check the allergenicity. The results of databases indicated that AMPs are non-toxic to normal human cells and allergic to human immunoglobulin. The bioinformatics findings led to select the highest active peptide ATMP5, which was synthesised and applied for in-vitro experiments using cytotoxicity assay MTT Assay, apoptosis detection using the Annexin V FTIC-A assay, and gene expression using Apoptosis PCR Array to evaluate the AMP’s anticancer activity. The antimicrobial activity is approved by the disc diffusion method. The in-vitro experiments analysis showed that ATMP5 had the activity to inhibit the growth of the breast cancer cell line (MDA-MB-231) after 48 h and managed to arrest the cell cycle of the MDA-MB-231, apoptosis induction, and overexpression of the p53 by interaction with the related apoptotic genes. This research opened up new opportunities for developing potential and selective anticancer agents relying on antimicrobial peptide properties.
format: application/pdf
format: text/html
creator: Douglas Law
creator: Ahmed Abdulkareem Najm
creator: Jia Xuan Chong
creator: Joelene Zi Ying K’ng
creator: Mas Amran
creator: Huey Lih Ching
creator: Rui Rui Wong
creator: May Ho Leong
creator: Ibrahim Mahmood Mahdi
creator: Shazrul Fazry
subject: Cell Biology
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15651
publisher: PeerJ Inc.
rights: © 2023 Law et al.
abstract: A previous study has shown that synthetic antimicrobial peptides (AMPs) derived from Anabas testudineus (ATMP1) could in-vitro inhibit the progression of breast cancer cell lines. In this study, we are interested in studying altered versions of previous synthetic AMPs to gain some insight into the peptides functions. The AMPs were altered and subjected to bioinformatics prediction using four databases (ADP3, CAMP-R3, AMPfun, and ANTICP) to select the highest anticancer activity. The bioinformatics in silico analysis led to the selection of two AMPs, which are ATMP5 (THPPTTTTTTTTTTTYTAAPATTT) and ATMP6 (THPPTTTTTTTTTTTTTAAPARTT). The in silico analysis predicted that ATMP5 and ATMP6 have anticancer activity and lead to cell death. The ATMP5 and ATMP6 were submitted to deep learning databases (ToxIBTL and ToxinPred2) to predict the toxicity of the peptides and to (AllerTOP & AllergenFP) check the allergenicity. The results of databases indicated that AMPs are non-toxic to normal human cells and allergic to human immunoglobulin. The bioinformatics findings led to select the highest active peptide ATMP5, which was synthesised and applied for in-vitro experiments using cytotoxicity assay MTT Assay, apoptosis detection using the Annexin V FTIC-A assay, and gene expression using Apoptosis PCR Array to evaluate the AMP’s anticancer activity. The antimicrobial activity is approved by the disc diffusion method. The in-vitro experiments analysis showed that ATMP5 had the activity to inhibit the growth of the breast cancer cell line (MDA-MB-231) after 48 h and managed to arrest the cell cycle of the MDA-MB-231, apoptosis induction, and overexpression of the p53 by interaction with the related apoptotic genes. This research opened up new opportunities for developing potential and selective anticancer agents relying on antimicrobial peptide properties.
bibliographic citation: Law et al. (2023) In silico identification and in vitro assessment of a potential anti-breast cancer activity of antimicrobial peptide retrieved from the ATMP1 Anabas testudineus fish peptide. PeerJ 11:e15651 https://doi.org/10.7717/peerj.15651
date submitted: 2023-01-19
date accepted: 2023-06-06
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Law
  given name: Douglas
author list: Agent
  family name: Abdulkareem Najm
  given name: Ahmed
author list: Agent
  family name: Chong
  given name: Jia Xuan
author list: Agent
  family name: K’ng
  given name: Joelene Zi Ying
author list: Agent
  family name: Amran
  given name: Mas
author list: Agent
  family name: Ching
  given name: Huey Lih
author list: Agent
  family name: Wong
  given name: Rui Rui
author list: Agent
  family name: Leong
  given name: May Ho
author list: Agent
  family name: Mahdi
  given name: Ibrahim Mahmood
author list: Agent
  family name: Fazry
  given name: Shazrul
doi: 10.7717/peerj.15651
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Law et al.
attribution name: Law et al.

Effects of salt stress on seed germination and respiratory metabolism in different Flueggea suffruticosa genotypes
type: item
type: AcademicArticle
description: The selection and utilization of ornamental plants that are highly tolerant to salt are helpful for landscape construction and the ecological protection of coastal and arid areas. To evaluate salt tolerance, one of the most used methods is the observation of seed germination under salt stress. Therefore, this work aimed to evaluate the influence of different concentrations of NaCl in water absorption, germination, and respiratory metabolism in seeds of different Flueggea suffruticosa genotypes. P2 and P27, salt-sensitive and salt-tolerant line s of F. suffruticosa, were chosen for treatment with 0, 40, 80, 120, 160, 200, and 240 mM NaCl. F. suffruticosa under salt stress exhibited inhibition of seed germination. The seeds of F. suffruticosa have different times for the physiological phases of water absorption with different NaCl concentrations. Salt stress retarded the seed water absorption process, and it depended on seed genotypes for F. suffruticosa. Soluble sugars accumulated in both P2 and P27 under salt stress. Meanwhile, the activities of hexokinase, 6-phosphofructokinase, pyruvate kinase, pyruvate dehydrogenase, citrate synthase, and glucose-6-phosphate dehydrogenase were overall increased in P27 after salt treatment, which caused increases in pyruvic acid and citric acid. The citrate synthase and glucose-6-phosphate dehydrogenase activities decreased in P2. These results suggest that the respiratory metabolism of salt-tolerant F. suffruticosa was enhanced, compared with the salt-sensitive line, to ameliorate the repression of seed germination under salt stress. The different changes in respiratory metabolism could influence the degree of salt tolerance.
format: application/pdf
format: text/html
creator: Ningwei Xu
creator: Bin Lu
creator: Yang Wang
creator: Xiaoyue Yu
creator: Nan Yao
creator: Qijuan Lin
creator: Xingyou Xu
creator: Bingshe Lu
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.15668
publisher: PeerJ Inc.
rights: © 2023 Xu et al.
abstract: The selection and utilization of ornamental plants that are highly tolerant to salt are helpful for landscape construction and the ecological protection of coastal and arid areas. To evaluate salt tolerance, one of the most used methods is the observation of seed germination under salt stress. Therefore, this work aimed to evaluate the influence of different concentrations of NaCl in water absorption, germination, and respiratory metabolism in seeds of different Flueggea suffruticosa genotypes. P2 and P27, salt-sensitive and salt-tolerant line s of F. suffruticosa, were chosen for treatment with 0, 40, 80, 120, 160, 200, and 240 mM NaCl. F. suffruticosa under salt stress exhibited inhibition of seed germination. The seeds of F. suffruticosa have different times for the physiological phases of water absorption with different NaCl concentrations. Salt stress retarded the seed water absorption process, and it depended on seed genotypes for F. suffruticosa. Soluble sugars accumulated in both P2 and P27 under salt stress. Meanwhile, the activities of hexokinase, 6-phosphofructokinase, pyruvate kinase, pyruvate dehydrogenase, citrate synthase, and glucose-6-phosphate dehydrogenase were overall increased in P27 after salt treatment, which caused increases in pyruvic acid and citric acid. The citrate synthase and glucose-6-phosphate dehydrogenase activities decreased in P2. These results suggest that the respiratory metabolism of salt-tolerant F. suffruticosa was enhanced, compared with the salt-sensitive line, to ameliorate the repression of seed germination under salt stress. The different changes in respiratory metabolism could influence the degree of salt tolerance.
bibliographic citation: Xu et al. (2023) Effects of salt stress on seed germination and respiratory metabolism in different Flueggea suffruticosa genotypes. PeerJ 11:e15668 https://doi.org/10.7717/peerj.15668
date submitted: 2023-02-15
date accepted: 2023-06-09
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Xu
  given name: Ningwei
author list: Agent
  family name: Lu
  given name: Bin
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Yu
  given name: Xiaoyue
author list: Agent
  family name: Yao
  given name: Nan
author list: Agent
  family name: Lin
  given name: Qijuan
author list: Agent
  family name: Xu
  given name: Xingyou
author list: Agent
  family name: Lu
  given name: Bingshe
doi: 10.7717/peerj.15668
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Xu et al.
attribution name: Xu et al.

Whistle characterization of long-beaked common dolphin (Delphinus delphis bairdii) in La Paz Bay, Gulf of California
type: item
type: AcademicArticle
description: Long-beaked common dolphin (Delphinus delphis bairdii) distribution is limited to the Eastern North Pacific Ocean. Its whistle repertoire is poorly investigated, with no studies in the Gulf of California. The aim of the present study is to characterize the whistles of this species and compare their parameters with different populations. Acoustic monitoring was conducted in La Paz Bay, Gulf of California. Recordings were inspected in spectrogram view in Raven Pro, selecting good quality whistles (n = 270). In the software Luscinia, contours were manually traced to obtain whistle frequencies and duration. Number of steps, inflection points and contour type were visually determined. We calculated the descriptive statistics of the selected whistle parameters and we compared the results with a dolphins population from the Eastern Pacific Ocean. Permutational multivariate analysis of variance (PERMANOVA) was performed to test the intraspecific variation of the whistle parameters among groups. In the present study the mean values (±SD) of the whistle parameters were: maximum frequency = 14.13 ± 3.71 kHz, minimum frequency = 8.44 ± 2.58 kHz and duration = 0.44 ± 0.31 s. Whistles with the upsweep contour were the most common ones (34.44%). The coefficient of variation (CV) values for modulation parameters were high (>100%), in accordance with other studies on dolphins. Whistle parameters showed significant differences among groups. Finally, ending and maximum frequencies, duration and inflection points of the whistles recorded in the present study were lower compared with the parameters of the long-beaked common dolphins from the Eastern Pacific Ocean. This study provides the first whistle characterization of long-beaked common dolphin from the Gulf of California and it will help future passive acoustic monitoring applications in the study area.
format: application/pdf
format: text/html
creator: Óscar Carlón-Beltrán
creator: Lorena Viloria-Gómora
creator: Jorge Urbán R.
creator: Sergio Martínez-Aguilar
creator: Simone Antichi
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.15687
publisher: PeerJ Inc.
rights: © 2023 Carlón-Beltrán et al.
abstract: Long-beaked common dolphin (Delphinus delphis bairdii) distribution is limited to the Eastern North Pacific Ocean. Its whistle repertoire is poorly investigated, with no studies in the Gulf of California. The aim of the present study is to characterize the whistles of this species and compare their parameters with different populations. Acoustic monitoring was conducted in La Paz Bay, Gulf of California. Recordings were inspected in spectrogram view in Raven Pro, selecting good quality whistles (n = 270). In the software Luscinia, contours were manually traced to obtain whistle frequencies and duration. Number of steps, inflection points and contour type were visually determined. We calculated the descriptive statistics of the selected whistle parameters and we compared the results with a dolphins population from the Eastern Pacific Ocean. Permutational multivariate analysis of variance (PERMANOVA) was performed to test the intraspecific variation of the whistle parameters among groups. In the present study the mean values (±SD) of the whistle parameters were: maximum frequency = 14.13 ± 3.71 kHz, minimum frequency = 8.44 ± 2.58 kHz and duration = 0.44 ± 0.31 s. Whistles with the upsweep contour were the most common ones (34.44%). The coefficient of variation (CV) values for modulation parameters were high (>100%), in accordance with other studies on dolphins. Whistle parameters showed significant differences among groups. Finally, ending and maximum frequencies, duration and inflection points of the whistles recorded in the present study were lower compared with the parameters of the long-beaked common dolphins from the Eastern Pacific Ocean. This study provides the first whistle characterization of long-beaked common dolphin from the Gulf of California and it will help future passive acoustic monitoring applications in the study area.
bibliographic citation: Carlón-Beltrán et al. (2023) Whistle characterization of long-beaked common dolphin (Delphinus delphis bairdii) in La Paz Bay, Gulf of California. PeerJ 11:e15687 https://doi.org/10.7717/peerj.15687
date submitted: 2023-01-09
date accepted: 2023-06-14
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carlón-Beltrán
  given name: Óscar
author list: Agent
  family name: Viloria-Gómora
  given name: Lorena
author list: Agent
  family name: Urbán R.
  given name: Jorge
author list: Agent
  family name: Martínez-Aguilar
  given name: Sergio
author list: Agent
  family name: Antichi
  given name: Simone
doi: 10.7717/peerj.15687
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Carlón-Beltrán et al.
attribution name: Carlón-Beltrán et al.

Investigating the relationship between inbreeding and life expectancy in dogs: mongrels live longer than pure breeds
type: item
type: AcademicArticle
description: This study aimed to investigate the establishment of relationship between inbreeding and life expectancy in dogs. A dataset of N = 30,563 dogs sourced from the VetCompass™ Program, UK was made available by the Royal Veterinary College, University of London, containing information about breed and longevity and was subject to survival analysis. A Cox regression proportional hazards model was used to differentiate survivability in three groups of dogs (mongrel, cross-bred and pure breed). The model was found highly significant (p < 0.001) and we found that mongrel dog had the highest life expectancy, followed by cross-bred dogs with only one purebred ancestor and purebred dogs had the lowest life expectancy. A second Cox regression was also found highly significant (p < 0.001) differentiating the lifespan of different dog breed and correlating positively the hazard ratio and the Genetic Illness Severity Index for Dogs (GISID). The results show that survivability is higher in mongrel dogs followed by cross-bred with one of the ancestor only as a pure breed, and pure breed dog have the highest morbidity level. Higher morbidity is associated with higher GISID scores, and therefore, higher inbreeding coefficients. These findings have important implications for dog breeders, owners, and animal welfare organizations seeking to promote healthier, longer-lived dogs.
format: application/pdf
format: text/html
creator: Fernando Mata
creator: Andreia Mata
subject: Veterinary Medicine
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.15718
publisher: PeerJ Inc.
rights: © 2023 Mata et al.
abstract: This study aimed to investigate the establishment of relationship between inbreeding and life expectancy in dogs. A dataset of N = 30,563 dogs sourced from the VetCompass™ Program, UK was made available by the Royal Veterinary College, University of London, containing information about breed and longevity and was subject to survival analysis. A Cox regression proportional hazards model was used to differentiate survivability in three groups of dogs (mongrel, cross-bred and pure breed). The model was found highly significant (p < 0.001) and we found that mongrel dog had the highest life expectancy, followed by cross-bred dogs with only one purebred ancestor and purebred dogs had the lowest life expectancy. A second Cox regression was also found highly significant (p < 0.001) differentiating the lifespan of different dog breed and correlating positively the hazard ratio and the Genetic Illness Severity Index for Dogs (GISID). The results show that survivability is higher in mongrel dogs followed by cross-bred with one of the ancestor only as a pure breed, and pure breed dog have the highest morbidity level. Higher morbidity is associated with higher GISID scores, and therefore, higher inbreeding coefficients. These findings have important implications for dog breeders, owners, and animal welfare organizations seeking to promote healthier, longer-lived dogs.
bibliographic citation: Mata et al. (2023) Investigating the relationship between inbreeding and life expectancy in dogs: mongrels live longer than pure breeds. PeerJ 11:e15718 https://doi.org/10.7717/peerj.15718
date submitted: 2023-02-28
date accepted: 2023-06-16
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mata
  given name: Fernando
author list: Agent
  family name: Mata
  given name: Andreia
doi: 10.7717/peerj.15718
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Mata et al.
attribution name: Mata et al.

Difference in the recruitment of intrinsic foot muscles in the elderly under static and dynamic postural conditions
type: item
type: AcademicArticle
description: Background The effect of foot, especially intrinsic muscles, on postural control and its related mechanisms remain unclear due to the complex structure. Therefore, this study aims to investigate the activation of intrinsic foot muscles in the elderly under static and dynamic postural tasks. Methods Twenty-one elderly participants were included to perform different postural tests (sensory organization test (SOT), motor control test (MCT), limit of stability test (LOS), and unilateral stance test) by a NeuroCom Balance Manager System. The participants were instructed to maintain postural stability under conditions with combined different sensory inputs (vision, vestibular, and proprioception) in SOT as well as conditions with translation disturbance in MCT, and to perform an active weight-shifting tasks in LOS. During these tasks, muscle activation were simultaneously acquired from intrinsic foot muscles (abductor halluces (AbH) and flexor digitorum brevis (FDB)) and ankle muscles (anterior tibialis, medial head of gastrocnemius, lateral head of gastrocnemius, and peroneus longus). The root-mean-square amplitude of these muscles in postural tasks was calculated and normalized with the EMG activity in unilateral stance task. Results The activation of intrinsic foot muscles significantly differed among different SOT tasks (p < 0.001). Post-hoc tests showed that compared with that under normal condition 1 without sensory interference, EMGs increased significantly under sensory disturbance (conditions 2–6). By contrast, compared with that under the single-sensory disturbed conditions (conditions 2–4; 2 for disturbed vision, 3 for disturbed vestibular sensation, 4 for disturbed proprioception), activation was significantly greater under the dual-sensory disturbed postural tasks (conditions 5 and 6; 5 for disturbed vision and proprioception, 6 for disturbed vestibular sensation and proprioception). In MCT, EMGs of foot muscles increased significantly under different transla…
format: application/pdf
format: text/html
creator: Zhangqi Lai
creator: Ruiyan Wang
creator: Bangguo Zhou
creator: Jing Chen
creator: Lin Wang
subject: Geriatrics
subject: Kinesiology
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.15719
publisher: PeerJ Inc.
rights: © 2023 Lai et al.
abstract: Background The effect of foot, especially intrinsic muscles, on postural control and its related mechanisms remain unclear due to the complex structure. Therefore, this study aims to investigate the activation of intrinsic foot muscles in the elderly under static and dynamic postural tasks. Methods Twenty-one elderly participants were included to perform different postural tests (sensory organization test (SOT), motor control test (MCT), limit of stability test (LOS), and unilateral stance test) by a NeuroCom Balance Manager System. The participants were instructed to maintain postural stability under conditions with combined different sensory inputs (vision, vestibular, and proprioception) in SOT as well as conditions with translation disturbance in MCT, and to perform an active weight-shifting tasks in LOS. During these tasks, muscle activation were simultaneously acquired from intrinsic foot muscles (abductor halluces (AbH) and flexor digitorum brevis (FDB)) and ankle muscles (anterior tibialis, medial head of gastrocnemius, lateral head of gastrocnemius, and peroneus longus). The root-mean-square amplitude of these muscles in postural tasks was calculated and normalized with the EMG activity in unilateral stance task. Results The activation of intrinsic foot muscles significantly differed among different SOT tasks (p < 0.001). Post-hoc tests showed that compared with that under normal condition 1 without sensory interference, EMGs increased significantly under sensory disturbance (conditions 2–6). By contrast, compared with that under the single-sensory disturbed conditions (conditions 2–4; 2 for disturbed vision, 3 for disturbed vestibular sensation, 4 for disturbed proprioception), activation was significantly greater under the dual-sensory disturbed postural tasks (conditions 5 and 6; 5 for disturbed vision and proprioception, 6 for disturbed vestibular sensation and proprioception). In MCT, EMGs of foot muscles increased significantly under different transla…
bibliographic citation: Lai et al. (2023) Difference in the recruitment of intrinsic foot muscles in the elderly under static and dynamic postural conditions. PeerJ 11:e15719 https://doi.org/10.7717/peerj.15719
date submitted: 2023-03-14
date accepted: 2023-06-16
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Zhangqi
author list: Agent
  family name: Wang
  given name: Ruiyan
author list: Agent
  family name: Zhou
  given name: Bangguo
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Wang
  given name: Lin
doi: 10.7717/peerj.15719
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Lai et al.
attribution name: Lai et al.

Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp
type: item
type: AcademicArticle
description: Faba bean water extract (FBW) and vitamin K3 (VK3) have been demonstrated to improve the muscle textural quality of fish. To better apply these two feed additives in commercial aquaculture setting, four experimental diets (control, commercial feed group; 15% FBW, 15% faba bean water extract group; 2.5% VK3, 2.5% vitamin K3 group; combined group, 15% faba bean water extract + 2.5% vitamin K3 group) were formulated to explore their combined effects of FBW and VK3 on the growth, health status, and muscle textural quality of grass carp. The growth performance, textural quality, intestinal characteristics, and oxidative and immune responses were analyzed on days 40, 80 and 120. The results showed that supplementation with higher doses of FBW and VK3 have no influence on growth-related parameters and immune parameters of grass carp. Notably, compared with the control, fish in the combined group had the highest textural qualities (hardness, chewiness and adhesiveness), followed by those in 15% FBW and 2.5% VK3 groups (P < 0.05). Also, FBW and VK3, to some extent, may lower antioxidative ability of grass carp, as illustrated by lower levels of GSH and CAT in 15% FBW, 2.5% VK3, and combined groups on day 120 (P < 0.05). In addition, enhanced lipase activity was observed in the 15% FBW group. Taken together, the combined supplementation of FBW and VK3 was demonstrated to be a more advanced option than their individual supplementation in a commercial setting owing to the resulting combined effects on both the textural quality and health status of grass carp.
format: application/pdf
format: text/html
creator: Yichao Li
creator: Bin Chen
creator: Junming Zhang
creator: Guangjun Wang
creator: Wangbao Gong
creator: Jingjing Tian
creator: Hongyan Li
creator: Kai Zhang
creator: Yun Xia
creator: Zhifei Li
creator: Jun Xie
creator: Ermeng Yu
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Zoology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.15733
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Faba bean water extract (FBW) and vitamin K3 (VK3) have been demonstrated to improve the muscle textural quality of fish. To better apply these two feed additives in commercial aquaculture setting, four experimental diets (control, commercial feed group; 15% FBW, 15% faba bean water extract group; 2.5% VK3, 2.5% vitamin K3 group; combined group, 15% faba bean water extract + 2.5% vitamin K3 group) were formulated to explore their combined effects of FBW and VK3 on the growth, health status, and muscle textural quality of grass carp. The growth performance, textural quality, intestinal characteristics, and oxidative and immune responses were analyzed on days 40, 80 and 120. The results showed that supplementation with higher doses of FBW and VK3 have no influence on growth-related parameters and immune parameters of grass carp. Notably, compared with the control, fish in the combined group had the highest textural qualities (hardness, chewiness and adhesiveness), followed by those in 15% FBW and 2.5% VK3 groups (P < 0.05). Also, FBW and VK3, to some extent, may lower antioxidative ability of grass carp, as illustrated by lower levels of GSH and CAT in 15% FBW, 2.5% VK3, and combined groups on day 120 (P < 0.05). In addition, enhanced lipase activity was observed in the 15% FBW group. Taken together, the combined supplementation of FBW and VK3 was demonstrated to be a more advanced option than their individual supplementation in a commercial setting owing to the resulting combined effects on both the textural quality and health status of grass carp.
bibliographic citation: Li et al. (2023) Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp. PeerJ 11:e15733 https://doi.org/10.7717/peerj.15733
date submitted: 2023-03-20
date accepted: 2023-06-19
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yichao
author list: Agent
  family name: Chen
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Junming
author list: Agent
  family name: Wang
  given name: Guangjun
author list: Agent
  family name: Gong
  given name: Wangbao
author list: Agent
  family name: Tian
  given name: Jingjing
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Xia
  given name: Yun
author list: Agent
  family name: Li
  given name: Zhifei
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Yu
  given name: Ermeng
doi: 10.7717/peerj.15733
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Li et al.
attribution name: Li et al.

mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2
type: item
type: AcademicArticle
description: After myocardial injury, cardiac fibroblasts (CFs) differentiate into myofibroblasts, which express and secrete extracellular matrix (ECM) components for myocardial repair, but also promote myocardial fibrosis. Recombinant fibroblast growth factor 2 (FGF2) protein drug with low molecular weight can promote cell survival and angiogenesis, and it was found that FGF2 could inhibit the activation of CFs, suggesting FGF2 has great potential in myocardial repair. However, the regulatory role of FGF2 on CFs has not been fully elucidated. Here, we found that recombinant FGF2 significantly suppressed the expression of alpha smooth muscle actin (α-SMA) in CFs. Through RNA sequencing, we analyzed mRNA expression in CFs and the differently expressed genes regulated by FGF2, including 430 up-regulated genes and 391 down-regulated genes. Gene ontology analysis revealed that the differentially expressed genes were strongly enriched in multiple biological functions, including ECM organization, cell adhesion, actin filament organization and axon guidance. The results of gene set enrichment analysis (GSEA) show that ECM organization and actin filament organization are down-regulated, while axon guidance is up-regulated. Further cellular experiments indicate that the regulatory functions of FGF2 are consistent with the findings of the gene enrichment analysis. This study provides valuable insights into the potential therapeutic role of FGF2 in treating cardiac fibrosis and establishes a foundation for further research to uncover the underlying mechanisms of CFs gene expression regulated by FGF2.
format: application/pdf
format: text/html
creator: Changye Sun
creator: Mengru Bai
creator: Yangyang Jia
creator: Xiangqin Tian
creator: Yonglong Guo
creator: Xinhui Xu
creator: Zhikun Guo
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Cardiology
description: doi:10.7717/peerj.15736
publisher: PeerJ Inc.
rights: © 2023 Sun et al.
abstract: After myocardial injury, cardiac fibroblasts (CFs) differentiate into myofibroblasts, which express and secrete extracellular matrix (ECM) components for myocardial repair, but also promote myocardial fibrosis. Recombinant fibroblast growth factor 2 (FGF2) protein drug with low molecular weight can promote cell survival and angiogenesis, and it was found that FGF2 could inhibit the activation of CFs, suggesting FGF2 has great potential in myocardial repair. However, the regulatory role of FGF2 on CFs has not been fully elucidated. Here, we found that recombinant FGF2 significantly suppressed the expression of alpha smooth muscle actin (α-SMA) in CFs. Through RNA sequencing, we analyzed mRNA expression in CFs and the differently expressed genes regulated by FGF2, including 430 up-regulated genes and 391 down-regulated genes. Gene ontology analysis revealed that the differentially expressed genes were strongly enriched in multiple biological functions, including ECM organization, cell adhesion, actin filament organization and axon guidance. The results of gene set enrichment analysis (GSEA) show that ECM organization and actin filament organization are down-regulated, while axon guidance is up-regulated. Further cellular experiments indicate that the regulatory functions of FGF2 are consistent with the findings of the gene enrichment analysis. This study provides valuable insights into the potential therapeutic role of FGF2 in treating cardiac fibrosis and establishes a foundation for further research to uncover the underlying mechanisms of CFs gene expression regulated by FGF2.
bibliographic citation: Sun et al. (2023) mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2. PeerJ 11:e15736 https://doi.org/10.7717/peerj.15736
date submitted: 2023-02-09
date accepted: 2023-06-20
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Changye
author list: Agent
  family name: Bai
  given name: Mengru
author list: Agent
  family name: Jia
  given name: Yangyang
author list: Agent
  family name: Tian
  given name: Xiangqin
author list: Agent
  family name: Guo
  given name: Yonglong
author list: Agent
  family name: Xu
  given name: Xinhui
author list: Agent
  family name: Guo
  given name: Zhikun
doi: 10.7717/peerj.15736
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Sun et al.
attribution name: Sun et al.

Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability
type: item
type: AcademicArticle
description: Background Leaf nutrient resorption is a key strategy in plant conservation that minimizes nutrient loss and enhances productivity. However, the differences of the nutrient resorption among garden tree species in urban ecosystems were not clearly understood, especially the differences of nitrogen resorption efficiency (NRE) and phosphorous resorption efficiency (PRE) between evergreen and deciduous trees. Methods We selected 40 most generally used garden tree specie belonged two life forms (evergreen and deciduous) and investigated the nitrogen (N) and phosphorus (P) concentrations in green and senesced leaves and soil nutrient concentrations of nine samples trees for each species. Then, the nutrient concentrations and resorption efficiency were compared, and the soil nutrients utilization strategies were further analyzed. Results The results showed that the N concentration was significantly higher in the green and senesced leaves of deciduous trees than in the leaves of evergreen trees. The two life-form trees were both N limited and evergreen trees were more sensitive to N limitation. The NRE and PRE in the deciduous trees were significantly higher than those in the evergreen trees. The NRE was significantly positively correlated with the PRE in the deciduous trees. As the soil N and P concentrations increased, the nutrient resorption efficiency (NuRE) of the evergreen trees increased, but that of the deciduous trees decreased. Compared with the deciduous trees, the evergreen trees were more sensitive to the feedback of soil N and P concentrations. These findings reveal the N and P nutrient resorption mechanism of evergreen and deciduous trees and fill a gap in the understanding of nutrient resorption in urban ecosystems.
format: application/pdf
format: text/html
creator: Ruyuan Hu
creator: Tairui Liu
creator: Yunxiang Zhang
creator: Rongrong Zheng
creator: Jinping Guo
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15738
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Leaf nutrient resorption is a key strategy in plant conservation that minimizes nutrient loss and enhances productivity. However, the differences of the nutrient resorption among garden tree species in urban ecosystems were not clearly understood, especially the differences of nitrogen resorption efficiency (NRE) and phosphorous resorption efficiency (PRE) between evergreen and deciduous trees. Methods We selected 40 most generally used garden tree specie belonged two life forms (evergreen and deciduous) and investigated the nitrogen (N) and phosphorus (P) concentrations in green and senesced leaves and soil nutrient concentrations of nine samples trees for each species. Then, the nutrient concentrations and resorption efficiency were compared, and the soil nutrients utilization strategies were further analyzed. Results The results showed that the N concentration was significantly higher in the green and senesced leaves of deciduous trees than in the leaves of evergreen trees. The two life-form trees were both N limited and evergreen trees were more sensitive to N limitation. The NRE and PRE in the deciduous trees were significantly higher than those in the evergreen trees. The NRE was significantly positively correlated with the PRE in the deciduous trees. As the soil N and P concentrations increased, the nutrient resorption efficiency (NuRE) of the evergreen trees increased, but that of the deciduous trees decreased. Compared with the deciduous trees, the evergreen trees were more sensitive to the feedback of soil N and P concentrations. These findings reveal the N and P nutrient resorption mechanism of evergreen and deciduous trees and fill a gap in the understanding of nutrient resorption in urban ecosystems.
bibliographic citation: Hu et al. (2023) Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability. PeerJ 11:e15738 https://doi.org/10.7717/peerj.15738
date submitted: 2023-02-01
date accepted: 2023-06-20
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Ruyuan
author list: Agent
  family name: Liu
  given name: Tairui
author list: Agent
  family name: Zhang
  given name: Yunxiang
author list: Agent
  family name: Zheng
  given name: Rongrong
author list: Agent
  family name: Guo
  given name: Jinping
doi: 10.7717/peerj.15738
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Hu et al.
attribution name: Hu et al.

Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China
type: item
type: AcademicArticle
description: Long-term shallow tillage leads to poor development of root system and deterioration of soil quality. Field experiments were conducted during 2019–2021 to explore the effects of different tillage depths on rice root system, stem lodging resistance, rice yield and quality. The experimental treatments were comprised of four tillage depths i.e., 14 cm (TD 14) as the control, 17 cm (TD17), 20 cm (TD20), and 23 cm (TD23) by using a tractor- mounted hydraulic-adjustable. Results indicated that the TD17 treatment substantially improved the breaking resistance by 39.45–72.37% and decreased the lodging index by 11.73–29.94% of first to third node attribute, increased the stem diameter and unit length dry weight and decreased the internode length, compared with control. The TD17 treatment also reduced the chalkiness, chalkiness rate by 26.23% and 32.30%, respectively. Moreover, the viscosity value and cooking and eating quality of rice in TD17 treatment were improved 27.30% and 12.33%, respectively, compared to control. Moreover, the TD20 treatment enhanced the grain yield by 9.18% owing to the higher panicle number and grain number per panicle. The highest photosynthetic rate was also found in the TD20 treatment, which was significant higher 15.57% than TD14 treatment. Overall, the 17–20 cm was found the optimum tillage depth and therefore recommended to the farmers to get improved rice yield with minimum lodging in the rice production systems of the Northeast China.
format: application/pdf
format: text/html
creator: Diankai Gong
creator: Guijin Dai
creator: Ying Chen
creator: Guangxing Yu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15739
publisher: PeerJ Inc.
rights: © 2023 Gong et al.
abstract: Long-term shallow tillage leads to poor development of root system and deterioration of soil quality. Field experiments were conducted during 2019–2021 to explore the effects of different tillage depths on rice root system, stem lodging resistance, rice yield and quality. The experimental treatments were comprised of four tillage depths i.e., 14 cm (TD 14) as the control, 17 cm (TD17), 20 cm (TD20), and 23 cm (TD23) by using a tractor- mounted hydraulic-adjustable. Results indicated that the TD17 treatment substantially improved the breaking resistance by 39.45–72.37% and decreased the lodging index by 11.73–29.94% of first to third node attribute, increased the stem diameter and unit length dry weight and decreased the internode length, compared with control. The TD17 treatment also reduced the chalkiness, chalkiness rate by 26.23% and 32.30%, respectively. Moreover, the viscosity value and cooking and eating quality of rice in TD17 treatment were improved 27.30% and 12.33%, respectively, compared to control. Moreover, the TD20 treatment enhanced the grain yield by 9.18% owing to the higher panicle number and grain number per panicle. The highest photosynthetic rate was also found in the TD20 treatment, which was significant higher 15.57% than TD14 treatment. Overall, the 17–20 cm was found the optimum tillage depth and therefore recommended to the farmers to get improved rice yield with minimum lodging in the rice production systems of the Northeast China.
bibliographic citation: Gong et al. (2023) Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China. PeerJ 11:e15739 https://doi.org/10.7717/peerj.15739
date submitted: 2023-02-20
date accepted: 2023-06-20
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gong
  given name: Diankai
author list: Agent
  family name: Dai
  given name: Guijin
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Yu
  given name: Guangxing
doi: 10.7717/peerj.15739
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Gong et al.
attribution name: Gong et al.

Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model
type: item
type: AcademicArticle
description: This article proposes a combined prediction model based on a bidirectional long short-term memory (BiLSTM) neural network optimized by the snake optimizer (SO) under complete ensemble empirical mode decomposition with adaptive noise. First, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) was used to decompose the sea ice area time series data into a series of eigenmodes and perform noise reduction to enhance the stationarity and smoothness of the time series. Second, this article used a bidirectional long short-term memory neural network optimized by the snake optimizer to fully exploit the characteristics of each eigenmode of the time series to achieve the prediction of each. Finally, the predicted values of each mode are superimposed and reconstructed as the final prediction values. Our model achieves a good score of RMSE: 1.047, MAE: 0.815, and SMAPE: 3.938 on the test set.
format: application/pdf
format: text/html
creator: Qiao Guo
creator: Haoyu Zhang
creator: Yuhao Zhang
creator: Xuchu Jiang
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Aquatic and Marine Chemistry
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.15748
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: This article proposes a combined prediction model based on a bidirectional long short-term memory (BiLSTM) neural network optimized by the snake optimizer (SO) under complete ensemble empirical mode decomposition with adaptive noise. First, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) was used to decompose the sea ice area time series data into a series of eigenmodes and perform noise reduction to enhance the stationarity and smoothness of the time series. Second, this article used a bidirectional long short-term memory neural network optimized by the snake optimizer to fully exploit the characteristics of each eigenmode of the time series to achieve the prediction of each. Finally, the predicted values of each mode are superimposed and reconstructed as the final prediction values. Our model achieves a good score of RMSE: 1.047, MAE: 0.815, and SMAPE: 3.938 on the test set.
bibliographic citation: Guo et al. (2023) Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model. PeerJ 11:e15748 https://doi.org/10.7717/peerj.15748
date submitted: 2023-03-10
date accepted: 2023-06-22
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Qiao
author list: Agent
  family name: Zhang
  given name: Haoyu
author list: Agent
  family name: Zhang
  given name: Yuhao
author list: Agent
  family name: Jiang
  given name: Xuchu
doi: 10.7717/peerj.15748
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Guo et al.
attribution name: Guo et al.

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