PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Foliar spraying of indoleacetic acid (IAA) enhances the phytostabilization of Pb in naturally tolerant ryegrass by limiting the root-to-shoot transfer of Pb and improving plant growth
items: Late Cretaceous coprolite from the Opole area (southern Poland) as evidence for a variable diet in shell-crushing shark Ptychodus (Elasmobranchii: Ptychodontidae)
items: Contributions of each of the four swimming strokes to elite 200-400 individual medley swimming performance in short and long course competitions
items: The relationship between leptin and periodontitis: a literature review
items: Effects of plyometric training on measures of physical fitness in racket sport athletes: a systematic review and meta-analysis
items: Validation of an algorithm to assess regular and irregular gait using inertial sensors in healthy and stroke individuals
items: Genome-wide identification and expression analysis of growth-regulating factors in Dendrobium officinale and Dendrobium chrysotoxum
items: Diagnostic value of albumin/fibrinogen ratio and C-reactive protein/albumin/globulin ratio for periprosthetic joint infection: a retrospective study
items: A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane
items: Analysis and pollution evaluation of heavy metal content in soil of the Yellow River Wetland Reserve in Henan

Foliar spraying of indoleacetic acid (IAA) enhances the phytostabilization of Pb in naturally tolerant ryegrass by limiting the root-to-shoot transfer of Pb and improving plant growth
type: item
type: AcademicArticle
description: Exogenous addition of IAA has the potential to improve the metal tolerance and phytostabilization of plants, but these effects have not been systematically investigated in naturally tolerant plants. Ryegrass (Lolium perenne L.) is a typical indigenous plant in the Lanping Pb/Zn mining area with high adaptability. This study investigated the phytostabilization ability and Pb tolerance mechanism of ryegrass in response to Pb, with or without foliar spraying of 0.1 mmol L−1 IAA. The results indicated that appropriate IAA treatment could be used to enhance the phytostabilization efficiency of naturally tolerant plants. Foliar spraying of IAA increased the aboveground and belowground biomass of ryegrass and improved root Pb phytostabilization. Compared to Pb-treated plants without exogenous IAA addition, Pb concentration in the shoots of ryegrass significantly decreased, then increased in the roots after the foliar spraying of IAA. In the 1,000 mg kg−1 Pb-treated plants, Pb concentration in the shoots decreased by 69.9% and increased by 79.1% in the roots after IAA treatment. IAA improved plant growth, especially in soils with higher Pb concentration. Foliar spraying of IAA increased shoot biomass by 35.9% and root biomass by 109.4% in 1,000 mg kg−1 Pb-treated plants, and increased shoot biomass by 196.5% and root biomass by 71.5% in 2,000 mg kg−1 Pb-treated plants. In addition, Pb stress significantly decreased the content of photosynthetic pigments and anti-oxidase activities in ryegrass, while foliar spraying of IAA remedied these negative impacts. In summary, foliar spraying of IAA could increase the biomass and improve the Pb tolerance of ryegrass.
format: application/pdf
format: text/html
creator: Chengqiang Zhu
creator: Runhai Jiang
creator: Shaofu Wen
creator: Tiyuan Xia
creator: Saiyong Zhu
creator: Xiuli Hou
subject: Plant Science
subject: Soil Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.16560
publisher: PeerJ Inc.
rights: © 2023 Zhu et al.
abstract: Exogenous addition of IAA has the potential to improve the metal tolerance and phytostabilization of plants, but these effects have not been systematically investigated in naturally tolerant plants. Ryegrass (Lolium perenne L.) is a typical indigenous plant in the Lanping Pb/Zn mining area with high adaptability. This study investigated the phytostabilization ability and Pb tolerance mechanism of ryegrass in response to Pb, with or without foliar spraying of 0.1 mmol L−1 IAA. The results indicated that appropriate IAA treatment could be used to enhance the phytostabilization efficiency of naturally tolerant plants. Foliar spraying of IAA increased the aboveground and belowground biomass of ryegrass and improved root Pb phytostabilization. Compared to Pb-treated plants without exogenous IAA addition, Pb concentration in the shoots of ryegrass significantly decreased, then increased in the roots after the foliar spraying of IAA. In the 1,000 mg kg−1 Pb-treated plants, Pb concentration in the shoots decreased by 69.9% and increased by 79.1% in the roots after IAA treatment. IAA improved plant growth, especially in soils with higher Pb concentration. Foliar spraying of IAA increased shoot biomass by 35.9% and root biomass by 109.4% in 1,000 mg kg−1 Pb-treated plants, and increased shoot biomass by 196.5% and root biomass by 71.5% in 2,000 mg kg−1 Pb-treated plants. In addition, Pb stress significantly decreased the content of photosynthetic pigments and anti-oxidase activities in ryegrass, while foliar spraying of IAA remedied these negative impacts. In summary, foliar spraying of IAA could increase the biomass and improve the Pb tolerance of ryegrass.
bibliographic citation: Zhu et al. (2023) Foliar spraying of indoleacetic acid (IAA) enhances the phytostabilization of Pb in naturally tolerant ryegrass by limiting the root-to-shoot transfer of Pb and improving plant growth. PeerJ 11:e16560 https://doi.org/10.7717/peerj.16560
date submitted: 2023-05-24
date accepted: 2023-11-10
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Chengqiang
author list: Agent
  family name: Jiang
  given name: Runhai
author list: Agent
  family name: Wen
  given name: Shaofu
author list: Agent
  family name: Xia
  given name: Tiyuan
author list: Agent
  family name: Zhu
  given name: Saiyong
author list: Agent
  family name: Hou
  given name: Xiuli
doi: 10.7717/peerj.16560
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: ©2023 Zhu et al.
attribution name: Zhu et al.

Late Cretaceous coprolite from the Opole area (southern Poland) as evidence for a variable diet in shell-crushing shark Ptychodus (Elasmobranchii: Ptychodontidae)
type: item
type: AcademicArticle
description: Background Coprolites, i.e., fossilized faeces, are an important source of knowledge on the diet and food processing mechanisms in the fossil record. Direct and indirect evidences for the dietary preferences of extinct sharks are rare in the fossil record. The first coprolite attributable to Ptychodus containing prey remains from the European Cretaceous is documented here. Methods A coprolite from the Late Cretaceous of Opole (southern Poland) was scanned using micro-computed tomography to show the arrangement of the inclusions. In addition, the cross-section was examined under the SEM/EDS to analyse the microstructure and chemical composition of the inclusions. Results Brachiopod shell fragments and foraminiferan shells are recognized and identified among the variously shaped inclusions detected through the performed analysis. Conclusions The extinct shell-crushing shark Ptychodus has been identified as the likely producer of the examined coprolite. The presence of brachiopod shell fragments indicates that at least some species of this durophagous predatory shark may have preyed on small benthic elements on the sea bottom.
format: application/pdf
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creator: Dawid Mazurek
creator: Mateusz Antczak
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.16598
publisher: PeerJ Inc.
rights: © 2023 Mazurek and Antczak
abstract: Background Coprolites, i.e., fossilized faeces, are an important source of knowledge on the diet and food processing mechanisms in the fossil record. Direct and indirect evidences for the dietary preferences of extinct sharks are rare in the fossil record. The first coprolite attributable to Ptychodus containing prey remains from the European Cretaceous is documented here. Methods A coprolite from the Late Cretaceous of Opole (southern Poland) was scanned using micro-computed tomography to show the arrangement of the inclusions. In addition, the cross-section was examined under the SEM/EDS to analyse the microstructure and chemical composition of the inclusions. Results Brachiopod shell fragments and foraminiferan shells are recognized and identified among the variously shaped inclusions detected through the performed analysis. Conclusions The extinct shell-crushing shark Ptychodus has been identified as the likely producer of the examined coprolite. The presence of brachiopod shell fragments indicates that at least some species of this durophagous predatory shark may have preyed on small benthic elements on the sea bottom.
bibliographic citation: Mazurek et al. (2023) Late Cretaceous coprolite from the Opole area (southern Poland) as evidence for a variable diet in shell-crushing shark Ptychodus (Elasmobranchii: Ptychodontidae). PeerJ 11:e16598 https://doi.org/10.7717/peerj.16598
date submitted: 2023-04-13
date accepted: 2023-11-15
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mazurek
  given name: Dawid
author list: Agent
  family name: Antczak
  given name: Mateusz
doi: 10.7717/peerj.16598
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: © 2023 Mazurek and Antczak
attribution name: Mazurek and Antczak

Contributions of each of the four swimming strokes to elite 200-400 individual medley swimming performance in short and long course competitions
type: item
type: AcademicArticle
description: Objectives The relative contribution of each of the four strokes to performance, and whether these contributions differ substantially between short course and long course competitions is unclear. To clarify these issues the aim of this study was to assess the strokes that have more influence on the performance in the 200 and 400 m IM swimming performances of elite male and female swimmers, participating in major events: Olympic Games (OG) and World Championship (WC) in short-course and long-course from 2012 to 2021. Methods Data from 1,095 swimmers (501 women and 594 men) who competed in 200 and 400-m IM were obtained with a minimum level of 800 FINA points. Linear regression modelling and classification trees were employed to quantify differences between strokes and short/long course swimming. Results Regression analysis indicated that breaststroke (β = − 0.191; p < 0.000) and backstroke (β = − 0.185; p < 0.000) had a bigger effect on IM performance, with butterfly (β = − 0.101; p < 0.000) having a lesser impact. The classification trees showed threshold performance standards in terms of 50-m times in form-stroke events must be fulfilled to attain medal-winning performances. Conclusions These form-stroke standards represent important milestones for designing medal-oriented training strategies for both 200 IM and 400 m IM. Achieving a medallist position in 200 and 400 m IM requires obtaining specified lap times in butterfly, breaststroke and backstroke for males and females in long-course competitions, and breaststroke and backstroke for short-course competitions. The OG presents more exigent demands of lap times in butterfly, crawl and backstroke for IM swimmers.
format: application/pdf
format: text/html
creator: José María González-Ravé
creator: Jesus Santos-Cerro
creator: Patricia González-Megía
creator: David Pyne
subject: Kinesiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.16612
publisher: PeerJ Inc.
rights: © 2023 González-Ravé et al.
abstract: Objectives The relative contribution of each of the four strokes to performance, and whether these contributions differ substantially between short course and long course competitions is unclear. To clarify these issues the aim of this study was to assess the strokes that have more influence on the performance in the 200 and 400 m IM swimming performances of elite male and female swimmers, participating in major events: Olympic Games (OG) and World Championship (WC) in short-course and long-course from 2012 to 2021. Methods Data from 1,095 swimmers (501 women and 594 men) who competed in 200 and 400-m IM were obtained with a minimum level of 800 FINA points. Linear regression modelling and classification trees were employed to quantify differences between strokes and short/long course swimming. Results Regression analysis indicated that breaststroke (β = − 0.191; p < 0.000) and backstroke (β = − 0.185; p < 0.000) had a bigger effect on IM performance, with butterfly (β = − 0.101; p < 0.000) having a lesser impact. The classification trees showed threshold performance standards in terms of 50-m times in form-stroke events must be fulfilled to attain medal-winning performances. Conclusions These form-stroke standards represent important milestones for designing medal-oriented training strategies for both 200 IM and 400 m IM. Achieving a medallist position in 200 and 400 m IM requires obtaining specified lap times in butterfly, breaststroke and backstroke for males and females in long-course competitions, and breaststroke and backstroke for short-course competitions. The OG presents more exigent demands of lap times in butterfly, crawl and backstroke for IM swimmers.
bibliographic citation: González-Ravé et al. (2023) Contributions of each of the four swimming strokes to elite 200-400 individual medley swimming performance in short and long course competitions. PeerJ 11:e16612 https://doi.org/10.7717/peerj.16612
date submitted: 2023-06-13
date accepted: 2023-11-15
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: González-Ravé
  given name: José María
author list: Agent
  family name: Santos-Cerro
  given name: Jesus
author list: Agent
  family name: González-Megía
  given name: Patricia
author list: Agent
  family name: Pyne
  given name: David
doi: 10.7717/peerj.16612
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: ©2023 González-Ravé et al.
attribution name: González-Ravé et al.

The relationship between leptin and periodontitis: a literature review
type: item
type: AcademicArticle
description: Leptin is a peptide hormone that regulates energy balance, immune inflammatory response, and bone metabolism. Several studies have demonstrated a relationship between leptin and periodontitis, a local inflammatory disease that progressively weakens the supporting structures of the teeth, eventually leading to tooth loss. This article reviews the existing literature and discusses leptin’s basic characteristics, its relationship with periodontitis, and its effects on periodontal tissue metabolism.
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creator: Zhijiao Guo
creator: Yanhui Peng
creator: Qiaoyu Hu
creator: Na Liu
creator: Qing Liu
subject: Allergy and Clinical Immunology
subject: Dentistry
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.16633
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: Leptin is a peptide hormone that regulates energy balance, immune inflammatory response, and bone metabolism. Several studies have demonstrated a relationship between leptin and periodontitis, a local inflammatory disease that progressively weakens the supporting structures of the teeth, eventually leading to tooth loss. This article reviews the existing literature and discusses leptin’s basic characteristics, its relationship with periodontitis, and its effects on periodontal tissue metabolism.
bibliographic citation: Guo et al. (2023) The relationship between leptin and periodontitis: a literature review. PeerJ 11:e16633 https://doi.org/10.7717/peerj.16633
date submitted: 2023-08-17
date accepted: 2023-11-17
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Zhijiao
author list: Agent
  family name: Peng
  given name: Yanhui
author list: Agent
  family name: Hu
  given name: Qiaoyu
author list: Agent
  family name: Liu
  given name: Na
author list: Agent
  family name: Liu
  given name: Qing
doi: 10.7717/peerj.16633
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: © 2023 Guo et al.
attribution name: Guo et al.

Effects of plyometric training on measures of physical fitness in racket sport athletes: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Over the past decade, the popularity of racket sports has surged. Plyometric training (PT) has been the focus of extensive research because of the proven benefits it provides to athletes. However, there is a lack of systematic reviews and meta-analyses specifically evaluating the impact of PT on physical fitness metrics in racket sport athletes. This study aimed to conduct a comprehensive review and analysis of evidence derived from randomized controlled trials (RCTs) to evaluate the effects of PT on measures of physical fitness among racket sports athletes. Methods The electronic databases PubMed, Web of Science, SCOPUS, and SPORTDiscus were systematically searched up to June 2023 without placing any restrictions on the publication dates. The PICOS method was adopted to establish the inclusion criteria: (a) healthy athletes who participate in racket sports; (b) a PT program; (c) a control group; (d) assessment of physical fitness components pre- and post-PT; and (e) RCTs. The records’ methodological quality was assessed utilizing the Physiotherapy Evidence Database (PEDro) scale. The certainty in the evidence related to each outcome was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) assessment. A random-effects model was used to calculate effect sizes (ES; Hedges’ g) between experimental and control groups. Results There were 14 eligible studies of moderate-to-high-quality, involving 746 athletes in total. The results revealed small-to-moderate effects (p < 0.05) of PT on muscle power (ES = 0.46), muscle strength (ES = 0.50), sprint speed (ES = 0.45), change of direction ability (ES = 0.76), and reaction time (ES = 0.67), while no clear evidence was found on balance and flexibility. The training-induced changes in muscle power showed no significant difference (p > 0.05) between youth (ES = 0.72) and adults (ES = 0.40). There were also similar muscle power improvements (ES = 0.36–0.54 vs 0.38–0.56, all p > 0…
format: application/pdf
format: text/html
creator: Nuannuan Deng
creator: Kim Geok Soh
creator: Borhannudin Abdullah
creator: Dandan Huang
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.16638
publisher: PeerJ Inc.
rights: © 2023 Deng et al.
abstract: Background Over the past decade, the popularity of racket sports has surged. Plyometric training (PT) has been the focus of extensive research because of the proven benefits it provides to athletes. However, there is a lack of systematic reviews and meta-analyses specifically evaluating the impact of PT on physical fitness metrics in racket sport athletes. This study aimed to conduct a comprehensive review and analysis of evidence derived from randomized controlled trials (RCTs) to evaluate the effects of PT on measures of physical fitness among racket sports athletes. Methods The electronic databases PubMed, Web of Science, SCOPUS, and SPORTDiscus were systematically searched up to June 2023 without placing any restrictions on the publication dates. The PICOS method was adopted to establish the inclusion criteria: (a) healthy athletes who participate in racket sports; (b) a PT program; (c) a control group; (d) assessment of physical fitness components pre- and post-PT; and (e) RCTs. The records’ methodological quality was assessed utilizing the Physiotherapy Evidence Database (PEDro) scale. The certainty in the evidence related to each outcome was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) assessment. A random-effects model was used to calculate effect sizes (ES; Hedges’ g) between experimental and control groups. Results There were 14 eligible studies of moderate-to-high-quality, involving 746 athletes in total. The results revealed small-to-moderate effects (p < 0.05) of PT on muscle power (ES = 0.46), muscle strength (ES = 0.50), sprint speed (ES = 0.45), change of direction ability (ES = 0.76), and reaction time (ES = 0.67), while no clear evidence was found on balance and flexibility. The training-induced changes in muscle power showed no significant difference (p > 0.05) between youth (ES = 0.72) and adults (ES = 0.40). There were also similar muscle power improvements (ES = 0.36–0.54 vs 0.38–0.56, all p > 0…
bibliographic citation: Deng et al. (2023) Effects of plyometric training on measures of physical fitness in racket sport athletes: a systematic review and meta-analysis. PeerJ 11:e16638 https://doi.org/10.7717/peerj.16638
date submitted: 2023-07-28
date accepted: 2023-11-19
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Nuannuan
author list: Agent
  family name: Soh
  given name: Kim Geok
author list: Agent
  family name: Abdullah
  given name: Borhannudin
author list: Agent
  family name: Huang
  given name: Dandan
doi: 10.7717/peerj.16638
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: © 2023 Deng et al.
attribution name: Deng et al.

Validation of an algorithm to assess regular and irregular gait using inertial sensors in healthy and stroke individuals
type: item
type: AcademicArticle
description: Background Studies using inertial measurement units (IMUs) for gait assessment have shown promising results regarding accuracy of gait event detection and spatiotemporal parameters. However, performance of such algorithms is challenged in irregular walking patterns, such as in individuals with gait deficits. Based on the literature, we developed an algorithm to detect initial contact (IC) and terminal contact (TC) and calculate spatiotemporal gait parameters. We evaluated the validity of this algorithm for regular and irregular gait patterns against a 3D optical motion capture system (OMCS). Methods Twenty healthy participants (aged 59 ± 12 years) and 10 people in the chronic phase after stroke (aged 61 ± 11 years) were equipped with 4 IMUs: on both feet, sternum and lower back (MTw Awinda, Xsens) and 26 reflective makers. Participants walked on an instrumented treadmill for 2 minutes (i) with their preferred stride lengths and (ii) once with irregular stride lengths (±20% deviation) induced by light projected stepping stones. Accuracy of the algorithm was evaluated on stride-by-stride agreement of IC, TC, stride time, length and velocity with OMCS. Bland-Altman-like plots were made for the spatiotemporal parameters, while differences in detection of IC and TC time instances were shown in histogram plots. Performance of the algorithm was compared between regular and irregular gait with a linear mixed model. This was done by comparing the performance in healthy participants in the regular vs irregular walking condition, and by comparing the agreement in healthy participants with stroke participants in the regular walking condition. Results For each condition at least 1,500 strides were included for analysis. Compared to OMCS, IMU-based IC detection in both groups and condition was on average 9–17 (SD ranging from 7 to 35) ms, while IMU-based TC was on average 15–24 (SD ranging from 12 to 35) ms earlier. When comparing regular and irregular gait in healthy participant…
format: application/pdf
format: text/html
creator: Carmen Ensink
creator: Katrijn Smulders
creator: Jolien Warnar
creator: Noel Keijsers
subject: Kinesiology
subject: Biomechanics
subject: Sports Injury
subject: Rehabilitation
description: doi:10.7717/peerj.16641
publisher: PeerJ Inc.
rights: © 2023 Ensink et al.
abstract: Background Studies using inertial measurement units (IMUs) for gait assessment have shown promising results regarding accuracy of gait event detection and spatiotemporal parameters. However, performance of such algorithms is challenged in irregular walking patterns, such as in individuals with gait deficits. Based on the literature, we developed an algorithm to detect initial contact (IC) and terminal contact (TC) and calculate spatiotemporal gait parameters. We evaluated the validity of this algorithm for regular and irregular gait patterns against a 3D optical motion capture system (OMCS). Methods Twenty healthy participants (aged 59 ± 12 years) and 10 people in the chronic phase after stroke (aged 61 ± 11 years) were equipped with 4 IMUs: on both feet, sternum and lower back (MTw Awinda, Xsens) and 26 reflective makers. Participants walked on an instrumented treadmill for 2 minutes (i) with their preferred stride lengths and (ii) once with irregular stride lengths (±20% deviation) induced by light projected stepping stones. Accuracy of the algorithm was evaluated on stride-by-stride agreement of IC, TC, stride time, length and velocity with OMCS. Bland-Altman-like plots were made for the spatiotemporal parameters, while differences in detection of IC and TC time instances were shown in histogram plots. Performance of the algorithm was compared between regular and irregular gait with a linear mixed model. This was done by comparing the performance in healthy participants in the regular vs irregular walking condition, and by comparing the agreement in healthy participants with stroke participants in the regular walking condition. Results For each condition at least 1,500 strides were included for analysis. Compared to OMCS, IMU-based IC detection in both groups and condition was on average 9–17 (SD ranging from 7 to 35) ms, while IMU-based TC was on average 15–24 (SD ranging from 12 to 35) ms earlier. When comparing regular and irregular gait in healthy participant…
bibliographic citation: Ensink et al. (2023) Validation of an algorithm to assess regular and irregular gait using inertial sensors in healthy and stroke individuals. PeerJ 11:e16641 https://doi.org/10.7717/peerj.16641
date submitted: 2023-05-22
date accepted: 2023-11-19
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ensink
  given name: Carmen
author list: Agent
  family name: Smulders
  given name: Katrijn
author list: Agent
  family name: Warnar
  given name: Jolien
author list: Agent
  family name: Keijsers
  given name: Noel
doi: 10.7717/peerj.16641
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: ©2023 Ensink et al.
attribution name: Ensink et al.

Genome-wide identification and expression analysis of growth-regulating factors in Dendrobium officinale and Dendrobium chrysotoxum
type: item
type: AcademicArticle
description: Background Dendrobium, one of the largest genera in Orchidaceae, is popular not only for its aesthetic appeal but for its significant medicinal value. Growth-regulating factors (GRFs) play an essential role in plant growth and development. However, there is still a lack of information about the evolution and biological function analysis of the GRF gene family among Dendrobiumspecies. Methods Growth-regulating factors from Dendrobium officinale Kimura et Migo and Dendrobium chrysotoxum Lindl. were identified by HMMER and BLAST. Detailed bioinformatics analysis was conducted to explore the evolution and function of GRF gene family in D. officinale and D. chrysotoxum using genomic data, transcriptome data and qRT-PCR technology. Results Here, we evaluated the evolution of the GRF gene family based on the genome sequences of D. officinale and D. chrysotoxum. Inferred from phylogenetic trees, the GRF genes were classified into two clades, and each clade contains three subclades. Sequence comparison analysis revealed relatively conserved gene structures and motifs among members of the same subfamily, indicating a conserved evolution of GRF genes within Dendrobiumspecies. However, considering the distribution of orthologous DoGRFs and DcGRFs, and the differences in the number of GRFs among species, we suggest that the GRF gene family has undergone different evolutionary processes. A total of 361 cis-elements were detected, with 33, 141, and 187 related to plant growth and development, stress, and hormones, respectively. The tissue-specific expression of GRFs showed that DoGRF8 may have a significant function in the stem elongation of D. officinale. Moreover, four genes were up-regulated under Methyl-jasmonic acid/methyl jasmonate (MeJA) treatment, showing that DoGRFs and DcGRFs play a crucial role in stress response. These findings provide valuable information for further investigations into the evolution and function of GRF genes in D. officinale and D. chrysotoxum.
format: application/pdf
format: text/html
creator: Shuying Zhu
creator: Hongman Wang
creator: Qiqian Xue
creator: Huasong Zou
creator: Wei Liu
creator: Qingyun Xue
creator: Xiao-Yu Ding
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16644
publisher: PeerJ Inc.
rights: © 2023 Zhu et al.
abstract: Background Dendrobium, one of the largest genera in Orchidaceae, is popular not only for its aesthetic appeal but for its significant medicinal value. Growth-regulating factors (GRFs) play an essential role in plant growth and development. However, there is still a lack of information about the evolution and biological function analysis of the GRF gene family among Dendrobiumspecies. Methods Growth-regulating factors from Dendrobium officinale Kimura et Migo and Dendrobium chrysotoxum Lindl. were identified by HMMER and BLAST. Detailed bioinformatics analysis was conducted to explore the evolution and function of GRF gene family in D. officinale and D. chrysotoxum using genomic data, transcriptome data and qRT-PCR technology. Results Here, we evaluated the evolution of the GRF gene family based on the genome sequences of D. officinale and D. chrysotoxum. Inferred from phylogenetic trees, the GRF genes were classified into two clades, and each clade contains three subclades. Sequence comparison analysis revealed relatively conserved gene structures and motifs among members of the same subfamily, indicating a conserved evolution of GRF genes within Dendrobiumspecies. However, considering the distribution of orthologous DoGRFs and DcGRFs, and the differences in the number of GRFs among species, we suggest that the GRF gene family has undergone different evolutionary processes. A total of 361 cis-elements were detected, with 33, 141, and 187 related to plant growth and development, stress, and hormones, respectively. The tissue-specific expression of GRFs showed that DoGRF8 may have a significant function in the stem elongation of D. officinale. Moreover, four genes were up-regulated under Methyl-jasmonic acid/methyl jasmonate (MeJA) treatment, showing that DoGRFs and DcGRFs play a crucial role in stress response. These findings provide valuable information for further investigations into the evolution and function of GRF genes in D. officinale and D. chrysotoxum.
bibliographic citation: Zhu et al. (2023) Genome-wide identification and expression analysis of growth-regulating factors in Dendrobium officinale and Dendrobium chrysotoxum. PeerJ 11:e16644 https://doi.org/10.7717/peerj.16644
date submitted: 2023-08-16
date accepted: 2023-11-20
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Shuying
author list: Agent
  family name: Wang
  given name: Hongman
author list: Agent
  family name: Xue
  given name: Qiqian
author list: Agent
  family name: Zou
  given name: Huasong
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Xue
  given name: Qingyun
author list: Agent
  family name: Ding
  given name: Xiao-Yu
doi: 10.7717/peerj.16644
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: ©2023 Zhu et al.
attribution name: Zhu et al.

Diagnostic value of albumin/fibrinogen ratio and C-reactive protein/albumin/globulin ratio for periprosthetic joint infection: a retrospective study
type: item
type: AcademicArticle
description: Background The study aims to explore diagnostic value of albumin/fibrinogen ratio (AFR) and C-reactive protein (CRP)/albumin (ALB)/globulin (GLO) ratio (CAGR) for periprosthetic joint infection (PJI). Methods A retrospective analysis was conducted on clinical data collected from 190 patients who had joint replacement surgery in Qilu Hospital of Shandong University (Qingdao), from January 2017 to December 2022. Based on the occurrence of PJI after surgery, patients were divided as an infection group (10 cases) and non-infection group (180 cases). Diagnostic indicators were analyzed, univariate and multivariate logistic regression analyses were further performed to identify factors related to PJI. Sensitivity and specificity of AFR and CAGR, both individually and in combination, were calculated using ROC curves, and their diagnostic performance was compared based on the area under the curve (AUC). Results Levels of CRP, ESR, FIB, GLO, and CAGR were significantly higher in the infection group than in non-infection group (P < 0.05). Levels of ALB and AFR were significantly lower in infection group (P < 0.05). Multivariate logistic regression analysis reviewed that CRP (OR = 3.324), ESR (OR = 2.118), FIB (OR = 3.142), ALB (OR = 0.449), GLO (OR = 1.985), AFR (OR = 0.587), and CAGR (OR = 2.469) were factors influencing PJI (P < 0.05). The AUC for AFR and CAGR in diagnosing PJI were 0.739 and 0.780, while AUC for their combined detection was 0.858. Conclusion Abnormal levels of AFR and CAGR are associated with PJI, and their combined use has certain diagnostic value for PJI.
format: application/pdf
format: text/html
creator: Wei Ji
creator: Zemiao Liu
creator: Tao Lin
subject: Hematology
subject: Orthopedics
description: doi:10.7717/peerj.16662
publisher: PeerJ Inc.
rights: © 2023 Ji et al.
abstract: Background The study aims to explore diagnostic value of albumin/fibrinogen ratio (AFR) and C-reactive protein (CRP)/albumin (ALB)/globulin (GLO) ratio (CAGR) for periprosthetic joint infection (PJI). Methods A retrospective analysis was conducted on clinical data collected from 190 patients who had joint replacement surgery in Qilu Hospital of Shandong University (Qingdao), from January 2017 to December 2022. Based on the occurrence of PJI after surgery, patients were divided as an infection group (10 cases) and non-infection group (180 cases). Diagnostic indicators were analyzed, univariate and multivariate logistic regression analyses were further performed to identify factors related to PJI. Sensitivity and specificity of AFR and CAGR, both individually and in combination, were calculated using ROC curves, and their diagnostic performance was compared based on the area under the curve (AUC). Results Levels of CRP, ESR, FIB, GLO, and CAGR were significantly higher in the infection group than in non-infection group (P < 0.05). Levels of ALB and AFR were significantly lower in infection group (P < 0.05). Multivariate logistic regression analysis reviewed that CRP (OR = 3.324), ESR (OR = 2.118), FIB (OR = 3.142), ALB (OR = 0.449), GLO (OR = 1.985), AFR (OR = 0.587), and CAGR (OR = 2.469) were factors influencing PJI (P < 0.05). The AUC for AFR and CAGR in diagnosing PJI were 0.739 and 0.780, while AUC for their combined detection was 0.858. Conclusion Abnormal levels of AFR and CAGR are associated with PJI, and their combined use has certain diagnostic value for PJI.
bibliographic citation: Ji et al. (2023) Diagnostic value of albumin/fibrinogen ratio and C-reactive protein/albumin/globulin ratio for periprosthetic joint infection: a retrospective study. PeerJ 11:e16662 https://doi.org/10.7717/peerj.16662
date submitted: 2023-09-26
date accepted: 2023-11-21
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Wei
author list: Agent
  family name: Liu
  given name: Zemiao
author list: Agent
  family name: Lin
  given name: Tao
doi: 10.7717/peerj.16662
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: © 2023 Ji et al.
attribution name: Ji et al.

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane
type: item
type: AcademicArticle
description: Background Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations. Methods After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model. Results The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10−6 to 4.35 × 10−2, as well as some cane yield component traits with p values of 1.61 × 10−4 to 3.35 × 10−2. The significant association is consistent across four environments. Conclusion Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This mark…
format: application/pdf
format: text/html
creator: Supaporn Khanbo
creator: Suthasinee Somyong
creator: Phakamas Phetchawang
creator: Warodom Wirojsirasak
creator: Kittipat Ukoskit
creator: Peeraya Klomsa-ard
creator: Wirulda Pootakham
creator: Sithichoke Tangphatsornruang
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16667
publisher: PeerJ Inc.
rights: © 2023 Khanbo et al.
abstract: Background Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations. Methods After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model. Results The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10−6 to 4.35 × 10−2, as well as some cane yield component traits with p values of 1.61 × 10−4 to 3.35 × 10−2. The significant association is consistent across four environments. Conclusion Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This mark…
bibliographic citation: Khanbo et al. (2023) A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane. PeerJ 11:e16667 https://doi.org/10.7717/peerj.16667
date submitted: 2023-08-21
date accepted: 2023-11-21
issued: 2023-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khanbo
  given name: Supaporn
author list: Agent
  family name: Somyong
  given name: Suthasinee
author list: Agent
  family name: Phetchawang
  given name: Phakamas
author list: Agent
  family name: Wirojsirasak
  given name: Warodom
author list: Agent
  family name: Ukoskit
  given name: Kittipat
author list: Agent
  family name: Klomsa-ard
  given name: Peeraya
author list: Agent
  family name: Pootakham
  given name: Wirulda
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
doi: 10.7717/peerj.16667
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-15
copyright: © 2023 Khanbo et al.
attribution name: Khanbo et al.

Analysis and pollution evaluation of heavy metal content in soil of the Yellow River Wetland Reserve in Henan
type: item
type: AcademicArticle
description: Objective This study aims to assess the contamination levels of six heavy metals, namely arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), and lead (Pb), in the soil of the Henan Yellow River Wetland Reserve. It seeks to reveal the spatial distribution and trends of heavy metal pollution, providing a scientific basis for the rational utilization and effective protection of soil. Additionally, it aims to propose targeted management and remediation recommendations to mitigate or prevent soil pollution. Method A total of 706 soil samples were collected in this area in combination with the land use type map. As and Hg were determined by atomic fluorescence spectrometry, and Cr, Cu, Pb and Cd were determined by inductively coupled plasma mass spectrometry. Taking the soil pollution risk screening value of agricultural land (GB15618-2018) as a reference value, the sample data were statistically analyzed, and the Nemerow comprehensive pollution index method combined with ArcGIS technology was used to evaluate the soil environmental quality. Result The comprehensive pollution index of the soil in the Yellow River Wetland Reserve was 0.42, ranging from 0.17 to 2.38, which was safe and not polluted (I grade). Out of 706 sampling locations, 674 remained uncontaminated, while 26 exhibited cleanliness. Although they were in the warning line, they did not exceed the standard, accounting for 3.68% of the total number of sampling points. Five sample points were slightly polluted, accounting for 0.71% of the total sample points, and one sample point was moderately polluted, accounting for 0.14% of the total sample points. It can be seen that there are few agricultural land pollution points in the Yellow River Wetland Reserve, and the soil environment quality is generally good. Conclusion The soil in the Yellow River Wetland Reserve in Henan has a very small amount of mild and moderate pollution, and there is no severe pollution. The cleanliness is currently high.
format: application/pdf
format: text/html
creator: Xiaolong Chen
creator: Cora Un In Wong
creator: Hongfeng Zhang
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.16454
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Objective This study aims to assess the contamination levels of six heavy metals, namely arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), and lead (Pb), in the soil of the Henan Yellow River Wetland Reserve. It seeks to reveal the spatial distribution and trends of heavy metal pollution, providing a scientific basis for the rational utilization and effective protection of soil. Additionally, it aims to propose targeted management and remediation recommendations to mitigate or prevent soil pollution. Method A total of 706 soil samples were collected in this area in combination with the land use type map. As and Hg were determined by atomic fluorescence spectrometry, and Cr, Cu, Pb and Cd were determined by inductively coupled plasma mass spectrometry. Taking the soil pollution risk screening value of agricultural land (GB15618-2018) as a reference value, the sample data were statistically analyzed, and the Nemerow comprehensive pollution index method combined with ArcGIS technology was used to evaluate the soil environmental quality. Result The comprehensive pollution index of the soil in the Yellow River Wetland Reserve was 0.42, ranging from 0.17 to 2.38, which was safe and not polluted (I grade). Out of 706 sampling locations, 674 remained uncontaminated, while 26 exhibited cleanliness. Although they were in the warning line, they did not exceed the standard, accounting for 3.68% of the total number of sampling points. Five sample points were slightly polluted, accounting for 0.71% of the total sample points, and one sample point was moderately polluted, accounting for 0.14% of the total sample points. It can be seen that there are few agricultural land pollution points in the Yellow River Wetland Reserve, and the soil environment quality is generally good. Conclusion The soil in the Yellow River Wetland Reserve in Henan has a very small amount of mild and moderate pollution, and there is no severe pollution. The cleanliness is currently high.
bibliographic citation: Chen et al. (2023) Analysis and pollution evaluation of heavy metal content in soil of the Yellow River Wetland Reserve in Henan. PeerJ 11:e16454 https://doi.org/10.7717/peerj.16454
date submitted: 2023-08-25
date accepted: 2023-10-23
issued: 2023-12-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaolong
author list: Agent
  family name: Wong
  given name: Cora Un In
author list: Agent
  family name: Zhang
  given name: Hongfeng
doi: 10.7717/peerj.16454
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-12-14
copyright: © 2023 Chen et al.
attribution name: Chen et al.

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