PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A plant-derived biostimulant Aminolom Enzimatico® application stimulates chlorophyll content, electrolyte leakage, stomata density and root yield of radishes under salinity stress
items: Chitosan-DNA nanoparticles: synthesis and optimization for long-term storage and effective delivery
items: Geochemical signatures and nanomechanical properties of echinoid tests from nearshore habitats of Florida: environmental and physiological controls on echinoid biomineralization
items: Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community—Leishan County, Guizhou Province, Southwest China
items: The influence of physical activity levels on lactate production during squat training using a functional electromechanical dynamometer
items: Analysing head and trunk motion in the judo osoto-gari technique: relationship to sweeping-leg velocity
items: The bacterial composition signatures of perianal abscess and origin of infecting microbes
items: Evolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus Euplotes (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits
items: Re-evaluation of mastodon material from Oregon and Washington, USA, Alberta, Canada, and Hidalgo and Jalisco, Mexico
items: Deep water vetulicolians from the lower Cambrian of China

A plant-derived biostimulant Aminolom Enzimatico® application stimulates chlorophyll content, electrolyte leakage, stomata density and root yield of radishes under salinity stress
type: item
type: AcademicArticle
description: Biostimulants stimulate plant growth and tolerance to salinity stress, which creates unfavorable conditions for plant growth from emergence to harvest; however, little is known about their roles in triggering salt tolerance. Therefore, the study aimed to determine how applying a foliar plant-derived biostimulant (Aminolom Enzimatico® 24%) affects the growth (leaf area, biomass weight, root diameter, root fresh weight, and water-soluble dry matter), physiology (chlorophyll content, electrolyte leakage, cell membrane stability, and relative water content), and stomata of the lower and upper parts of leaves in radish plants (Raphanus sativus L.) under salinity stress. Radish plantlets at 7 d old were irrigated with saline water (i.e., 50, 100, 150, and 200 mM NaCl), and the biostimulant was sprayed twice at 7 d intervals. Under salinity stress, increased water-soluble dry matter content was detected, along with reduced plant biomass weight, root fresh weight, and root diameter. Meanwhile, the foliar biostimulant increased the mean root fresh weight, biomass fresh weight, and leaf area by 12%, 13.6%, and 24% compared to the control, respectively. Increasing NaCl dramatically reduced leaf area and relative water content, whereas chlorophyll content and stomata densities on both sides of the leaves improved. By regulating physiological parameters and thereby promoting root and leaf growth, the biostimulant application improved the radish plants’ tolerance to salinity stress up to 100 mM NaCl. Spraying the biostimulant can also boost plant growth, root yield, and radish quality under moderate salinity stress.
format: application/pdf
format: text/html
creator: Gamze Kaya
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.18804
publisher: PeerJ Inc.
rights: © 2025 Kaya
abstract: Biostimulants stimulate plant growth and tolerance to salinity stress, which creates unfavorable conditions for plant growth from emergence to harvest; however, little is known about their roles in triggering salt tolerance. Therefore, the study aimed to determine how applying a foliar plant-derived biostimulant (Aminolom Enzimatico® 24%) affects the growth (leaf area, biomass weight, root diameter, root fresh weight, and water-soluble dry matter), physiology (chlorophyll content, electrolyte leakage, cell membrane stability, and relative water content), and stomata of the lower and upper parts of leaves in radish plants (Raphanus sativus L.) under salinity stress. Radish plantlets at 7 d old were irrigated with saline water (i.e., 50, 100, 150, and 200 mM NaCl), and the biostimulant was sprayed twice at 7 d intervals. Under salinity stress, increased water-soluble dry matter content was detected, along with reduced plant biomass weight, root fresh weight, and root diameter. Meanwhile, the foliar biostimulant increased the mean root fresh weight, biomass fresh weight, and leaf area by 12%, 13.6%, and 24% compared to the control, respectively. Increasing NaCl dramatically reduced leaf area and relative water content, whereas chlorophyll content and stomata densities on both sides of the leaves improved. By regulating physiological parameters and thereby promoting root and leaf growth, the biostimulant application improved the radish plants’ tolerance to salinity stress up to 100 mM NaCl. Spraying the biostimulant can also boost plant growth, root yield, and radish quality under moderate salinity stress.
bibliographic citation: Kaya (2025) A plant-derived biostimulant Aminolom Enzimatico® application stimulates chlorophyll content, electrolyte leakage, stomata density and root yield of radishes under salinity stress. PeerJ 13:e18804 https://doi.org/10.7717/peerj.18804
date submitted: 2024-09-23
date accepted: 2024-12-11
issued: 2025-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaya
  given name: Gamze
doi: 10.7717/peerj.18804
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-24
copyright: © 2025 Kaya
attribution name: Kaya

Chitosan-DNA nanoparticles: synthesis and optimization for long-term storage and effective delivery
type: item
type: AcademicArticle
description: Background Chitosan nanoparticles (CsNPs) are an effective and inexpensive approach for DNA delivery into live cells. However, most CsNP synthesis protocols are not optimized to allow long-term storage of CsNPs without loss of function. Here, we describe a protocol for CsNP synthesis, lyophilization, and sonication, to store CsNPs and maintain transfection efficiency. Methods The size and zeta potential of CsNPs were analyzed by dynamic light scattering (DLS) and the morphology of CsNPs was assessed by transmission electron microscopy (TEM). HEK293 cells were transfected with CsNPs, and expression of H2B-CMV-mScarlet plasmid was assessed by flow cytometry. Confocal microscopy was used to visualize post-transfection gene expression. Time, volume, and effect of sonication were tested to optimize the lyophilization process. Results DLS and TEM analysis indicated amine groups on chitosan to phosphate groups on DNA (N:P) ratios yielded smaller CsNPs sizes. Transfection efficiency, measured by FACS and confocal microscopy, peaked at N:P ratios of 2:1 and 3:1 for both fresh and lyophilized CsNPs. Chitosan/DNA complexes remained stable in solution for at least 72 h at a ratio ≥2:1 as assessed by agarose gel electrophoresis. A lower surface charge with lower N:P ratios was indicated by zeta potential measurements. Lyophilized CsNPs lost 50% transfection efficiency compared to those freshly made. In contrast, sonication of lyophilized CsNPs restored their transfection efficiency to the level of fresh CsNPs. Sonicated CsNPs maintained spherical morphology, while unsonicated CsNPs showed aggregates. Cytotoxicity assays revealed high cell viability (>90%) after CsNPs transfection for a ratio of 2:1 or 3:1. Conclusion This optimized CsNPs synthesis protocol opens the possibility of long-term storage for CsNPs, which would provide broader applications of this technology.
format: application/pdf
format: text/html
creator: Aigul Raimbekova
creator: Ulpan Kart
creator: Akbayan Yerishova
creator: Timur Elebessov
creator: Sergey Yegorov
creator: Tri Thanh Pham
creator: Gonzalo Hortelano
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.18750
publisher: PeerJ Inc.
rights: © 2025 Raimbekova et al.
abstract: Background Chitosan nanoparticles (CsNPs) are an effective and inexpensive approach for DNA delivery into live cells. However, most CsNP synthesis protocols are not optimized to allow long-term storage of CsNPs without loss of function. Here, we describe a protocol for CsNP synthesis, lyophilization, and sonication, to store CsNPs and maintain transfection efficiency. Methods The size and zeta potential of CsNPs were analyzed by dynamic light scattering (DLS) and the morphology of CsNPs was assessed by transmission electron microscopy (TEM). HEK293 cells were transfected with CsNPs, and expression of H2B-CMV-mScarlet plasmid was assessed by flow cytometry. Confocal microscopy was used to visualize post-transfection gene expression. Time, volume, and effect of sonication were tested to optimize the lyophilization process. Results DLS and TEM analysis indicated amine groups on chitosan to phosphate groups on DNA (N:P) ratios yielded smaller CsNPs sizes. Transfection efficiency, measured by FACS and confocal microscopy, peaked at N:P ratios of 2:1 and 3:1 for both fresh and lyophilized CsNPs. Chitosan/DNA complexes remained stable in solution for at least 72 h at a ratio ≥2:1 as assessed by agarose gel electrophoresis. A lower surface charge with lower N:P ratios was indicated by zeta potential measurements. Lyophilized CsNPs lost 50% transfection efficiency compared to those freshly made. In contrast, sonication of lyophilized CsNPs restored their transfection efficiency to the level of fresh CsNPs. Sonicated CsNPs maintained spherical morphology, while unsonicated CsNPs showed aggregates. Cytotoxicity assays revealed high cell viability (>90%) after CsNPs transfection for a ratio of 2:1 or 3:1. Conclusion This optimized CsNPs synthesis protocol opens the possibility of long-term storage for CsNPs, which would provide broader applications of this technology.
bibliographic citation: Raimbekova et al. (2025) Chitosan-DNA nanoparticles: synthesis and optimization for long-term storage and effective delivery. PeerJ 13:e18750 https://doi.org/10.7717/peerj.18750
date submitted: 2024-09-06
date accepted: 2024-12-02
issued: 2025-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raimbekova
  given name: Aigul
author list: Agent
  family name: Kart
  given name: Ulpan
author list: Agent
  family name: Yerishova
  given name: Akbayan
author list: Agent
  family name: Elebessov
  given name: Timur
author list: Agent
  family name: Yegorov
  given name: Sergey
author list: Agent
  family name: Pham
  given name: Tri Thanh
author list: Agent
  family name: Hortelano
  given name: Gonzalo
doi: 10.7717/peerj.18750
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-24
copyright: © 2025 Raimbekova et al.
attribution name: Raimbekova et al.

Geochemical signatures and nanomechanical properties of echinoid tests from nearshore habitats of Florida: environmental and physiological controls on echinoid biomineralization
type: item
type: AcademicArticle
description: The mechanisms that regulate minor and trace element biomineralization in the echinoid skeleton can be primarily controlled biologically (i.e., by the organism and its vital effects) or by extrinsic environmental factors. Assessing the relative role of those controls is essential for understanding echinoid biomineralization, taphonomy, diagenesis, and their potential as geochemical archives. In this study, we (1) contrast geochemical signatures of specimens collected across multiple taxa and environmental settings to assess in situ the effects of environmental and physiological factors on skeletal biomineralogy; and (2) analyze the nanomechanical properties of the echinoid skeleton to assess potential linkages between magnesium/calcium (Mg/Ca) ratios and skeletal nanohardness. Live specimens of sand dollars and sea biscuits (Mellita tenuis, Encope spp., Leodia sexiesperforata, and Clypeaster subdepressus) were collected from three different salinity regimes: (1) a coastal region of Cedar Key influenced by freshwater input from Suwannee River, with low and fluctuating salinity; (2) St. James Bay with less fluctuating, higher salinity; and (3) Florida Keys with stable, fully marine salinity conditions. No clear relationship was found between the bulk skeletal barium/calcium (Ba/Ca), zinc/calcium (Zn/Ca), sodium/calcium (Na/Ca), cadmium/calcium (Cd/Ca), copper/calcium (Cu/Ca), phosphorous/calcium (P/Ca), lead/calcium (Pb/Ca), boron/calcium (B/Ca), manganese/calcium (Mn/Ca) ratios pooled across all taxa. In contrast, bulk Mg/Ca, strontium/calcium (Sr/Ca), sulfur/calcium (S/Ca) and lithium/calcium (Li/Ca) ratios exhibited notable differences between the three regions, indicating that distribution of these elements can be at least partly influenced by environmental factors such as salinity. However, such patterns were highly variable across taxa and regions, indicating that both environmental and physiological factors influenced geochemical signatures to varying degrees, …
format: application/pdf
format: text/html
creator: Przemysław Gorzelak
creator: Luis Torres Jr.
creator: Dorota Kołbuk
creator: Tobias B. Grun
creator: Michał Kowalewski
subject: Biochemistry
subject: Bioengineering
subject: Marine Biology
subject: Paleontology
subject: Ecotoxicology
description: doi:10.7717/peerj.18688
publisher: PeerJ Inc.
rights: © 2025 Gorzelak et al.
abstract: The mechanisms that regulate minor and trace element biomineralization in the echinoid skeleton can be primarily controlled biologically (i.e., by the organism and its vital effects) or by extrinsic environmental factors. Assessing the relative role of those controls is essential for understanding echinoid biomineralization, taphonomy, diagenesis, and their potential as geochemical archives. In this study, we (1) contrast geochemical signatures of specimens collected across multiple taxa and environmental settings to assess in situ the effects of environmental and physiological factors on skeletal biomineralogy; and (2) analyze the nanomechanical properties of the echinoid skeleton to assess potential linkages between magnesium/calcium (Mg/Ca) ratios and skeletal nanohardness. Live specimens of sand dollars and sea biscuits (Mellita tenuis, Encope spp., Leodia sexiesperforata, and Clypeaster subdepressus) were collected from three different salinity regimes: (1) a coastal region of Cedar Key influenced by freshwater input from Suwannee River, with low and fluctuating salinity; (2) St. James Bay with less fluctuating, higher salinity; and (3) Florida Keys with stable, fully marine salinity conditions. No clear relationship was found between the bulk skeletal barium/calcium (Ba/Ca), zinc/calcium (Zn/Ca), sodium/calcium (Na/Ca), cadmium/calcium (Cd/Ca), copper/calcium (Cu/Ca), phosphorous/calcium (P/Ca), lead/calcium (Pb/Ca), boron/calcium (B/Ca), manganese/calcium (Mn/Ca) ratios pooled across all taxa. In contrast, bulk Mg/Ca, strontium/calcium (Sr/Ca), sulfur/calcium (S/Ca) and lithium/calcium (Li/Ca) ratios exhibited notable differences between the three regions, indicating that distribution of these elements can be at least partly influenced by environmental factors such as salinity. However, such patterns were highly variable across taxa and regions, indicating that both environmental and physiological factors influenced geochemical signatures to varying degrees, …
bibliographic citation: Gorzelak et al. (2025) Geochemical signatures and nanomechanical properties of echinoid tests from nearshore habitats of Florida: environmental and physiological controls on echinoid biomineralization. PeerJ 13:e18688 https://doi.org/10.7717/peerj.18688
date submitted: 2024-09-11
date accepted: 2024-11-20
issued: 2025-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gorzelak
  given name: Przemysław
author list: Agent
  family name: Torres Jr.
  given name: Luis
author list: Agent
  family name: Kołbuk
  given name: Dorota
author list: Agent
  family name: Grun
  given name: Tobias B.
author list: Agent
  family name: Kowalewski
  given name: Michał
doi: 10.7717/peerj.18688
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-24
copyright: ©2025 Gorzelak et al.
attribution name: Gorzelak et al.

Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community—Leishan County, Guizhou Province, Southwest China
type: item
type: AcademicArticle
description: Background Camellia sinensis is an important cash crop in southwestern China, with soil organic carbon playing a vital role in soil fertility, and microorganisms contributing significantly to nutrient cycling, thus both of them influencing tea tree growth and development. However, existing studies primarily focus on soil organic carbon, neglecting carbon fractions, and the relationship between soil organic carbon fractions and microbial communities is unclear. Consequently, this study aims to clarify the impact of different tea planting durations on soil organic carbon fractions and microbial communities and identify the main factors influencing microbial communities. It provides a theoretical basis for soil quality evaluation in the study area and scientific guidance for tea plantation management, thus fostering the region’s economic sustainability. Methods This study selected tea plantations with different tea planting durations of 3–5 years (Y5), 12–16 years (Y15), 18–22 years (Y20), 40–42 years (Y40), and 48–50 years (Y50), as research subjects and adjacent uncultivated forest without a history of tea planting (CK) served as controls. Soil organic carbon (SOC), particulate organic carbon (POC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacterial diversity were measured in the 0–20 cm and 20–40 cm soil layers, respectively. Results Compared to the adjacent uncultivated forest (CK), the soil organic carbon (SOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) contents in a 40-year tea plantation significantly increased. Nonetheless, the microbial biomass carbon (MBC) content notably decreased. POC/SOC ratios rose with prolonged planting, signifying enhanced conversion of organic carbon into particulate forms. Bacterial community diversity peaked at 15 years and declined by 40 years post-planting and after tea planting dominated by Acidobacteriota…
format: application/pdf
format: text/html
creator: Yingge Shu
creator: Shan Xie
creator: Hong Fan
creator: Chun Duan
creator: Yuansheng Liu
creator: Zuyong Chen
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.18683
publisher: PeerJ Inc.
rights: © 2025 Shu et al.
abstract: Background Camellia sinensis is an important cash crop in southwestern China, with soil organic carbon playing a vital role in soil fertility, and microorganisms contributing significantly to nutrient cycling, thus both of them influencing tea tree growth and development. However, existing studies primarily focus on soil organic carbon, neglecting carbon fractions, and the relationship between soil organic carbon fractions and microbial communities is unclear. Consequently, this study aims to clarify the impact of different tea planting durations on soil organic carbon fractions and microbial communities and identify the main factors influencing microbial communities. It provides a theoretical basis for soil quality evaluation in the study area and scientific guidance for tea plantation management, thus fostering the region’s economic sustainability. Methods This study selected tea plantations with different tea planting durations of 3–5 years (Y5), 12–16 years (Y15), 18–22 years (Y20), 40–42 years (Y40), and 48–50 years (Y50), as research subjects and adjacent uncultivated forest without a history of tea planting (CK) served as controls. Soil organic carbon (SOC), particulate organic carbon (POC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacterial diversity were measured in the 0–20 cm and 20–40 cm soil layers, respectively. Results Compared to the adjacent uncultivated forest (CK), the soil organic carbon (SOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) contents in a 40-year tea plantation significantly increased. Nonetheless, the microbial biomass carbon (MBC) content notably decreased. POC/SOC ratios rose with prolonged planting, signifying enhanced conversion of organic carbon into particulate forms. Bacterial community diversity peaked at 15 years and declined by 40 years post-planting and after tea planting dominated by Acidobacteriota…
bibliographic citation: Shu et al. (2025) Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community—Leishan County, Guizhou Province, Southwest China. PeerJ 13:e18683 https://doi.org/10.7717/peerj.18683
date submitted: 2024-05-08
date accepted: 2024-11-19
issued: 2025-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shu
  given name: Yingge
author list: Agent
  family name: Xie
  given name: Shan
author list: Agent
  family name: Fan
  given name: Hong
author list: Agent
  family name: Duan
  given name: Chun
author list: Agent
  family name: Liu
  given name: Yuansheng
author list: Agent
  family name: Chen
  given name: Zuyong
doi: 10.7717/peerj.18683
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-24
copyright: © 2025 Shu et al.
attribution name: Shu et al.

The influence of physical activity levels on lactate production during squat training using a functional electromechanical dynamometer
type: item
type: AcademicArticle
description: Objective This study aimed to determine the association between changes in lactate production and levels of physical activity in a group of healthy young adults in response to two squat training protocols. Material and methods Twenty-nine students majoring in Sports Science willingly participated in this study. Participants visited the lab four times within a two-week period, ensuring at least 48 h between visits. In each session, they completed three sets of 12 repetitions at 75% 1RM and three sets of 30 repetitions at 50% of maximum strength, with the order of protocols being randomized. Results In the regression analysis, there was a significant positive association between lactate delta changes immediately post-squat at 50% of maximum strength at session 2 with the variable “sex: women” (β: 3.02, 95% CI [−0.18–0.30], p = 0.047) and BMI (kg/m2). Age exhibited a positive association (β: 0.19, 95% CI [0.02–0.36], p = 0.032) with lactate delta changes immediately post-squat at 75% of maximum strength at session 2. There was also a significant inverse association between lactate delta changes at 10 min post-squat test exercise at 75% of maximum strength at session 1 and 2, and vigorous physical activity (−0.01, 95% CI [−0.02–0.00], p = 0.046). Conclusion In summary, this study provides valuable insights into the association between lactate production and physical activity levels in young, healthy adults undergoing different squat training protocols. These findings suggest that intense physical activity may be associated with lower lactate production, indicating greater metabolic efficiency. In addition, sex differences in metabolic responses were observed, emphasizing the importance of personalized approaches in program design.
format: application/pdf
format: text/html
creator: Indya del-Cuerpo
creator: Daniel Jerez-Mayorga
creator: Luis Javier Chirosa-Ríos
creator: Felipe Caamaño-Navarrete
creator: Pedro Delgado-Floody
subject: Anatomy and Physiology
subject: Kinesiology
subject: Metabolic Sciences
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.18215
publisher: PeerJ Inc.
rights: © 2025 del-Cuerpo et al.
abstract: Objective This study aimed to determine the association between changes in lactate production and levels of physical activity in a group of healthy young adults in response to two squat training protocols. Material and methods Twenty-nine students majoring in Sports Science willingly participated in this study. Participants visited the lab four times within a two-week period, ensuring at least 48 h between visits. In each session, they completed three sets of 12 repetitions at 75% 1RM and three sets of 30 repetitions at 50% of maximum strength, with the order of protocols being randomized. Results In the regression analysis, there was a significant positive association between lactate delta changes immediately post-squat at 50% of maximum strength at session 2 with the variable “sex: women” (β: 3.02, 95% CI [−0.18–0.30], p = 0.047) and BMI (kg/m2). Age exhibited a positive association (β: 0.19, 95% CI [0.02–0.36], p = 0.032) with lactate delta changes immediately post-squat at 75% of maximum strength at session 2. There was also a significant inverse association between lactate delta changes at 10 min post-squat test exercise at 75% of maximum strength at session 1 and 2, and vigorous physical activity (−0.01, 95% CI [−0.02–0.00], p = 0.046). Conclusion In summary, this study provides valuable insights into the association between lactate production and physical activity levels in young, healthy adults undergoing different squat training protocols. These findings suggest that intense physical activity may be associated with lower lactate production, indicating greater metabolic efficiency. In addition, sex differences in metabolic responses were observed, emphasizing the importance of personalized approaches in program design.
bibliographic citation: del-Cuerpo et al. (2025) The influence of physical activity levels on lactate production during squat training using a functional electromechanical dynamometer. PeerJ 13:e18215 https://doi.org/10.7717/peerj.18215
date submitted: 2024-04-17
date accepted: 2024-09-11
issued: 2025-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: del-Cuerpo
  given name: Indya
author list: Agent
  family name: Jerez-Mayorga
  given name: Daniel
author list: Agent
  family name: Chirosa-Ríos
  given name: Luis Javier
author list: Agent
  family name: Caamaño-Navarrete
  given name: Felipe
author list: Agent
  family name: Delgado-Floody
  given name: Pedro
doi: 10.7717/peerj.18215
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-24
copyright: ©2025 del-Cuerpo et al.
attribution name: del-Cuerpo et al.

Analysing head and trunk motion in the judo osoto-gari technique: relationship to sweeping-leg velocity
type: item
type: AcademicArticle
description: Background Osoto-gari is a leg throw technique that primarily relies on the hip extension to initiate the sweeping motion of the leg. A high sweep contact velocity is a crucial factor in efficiently executing this technique. While some literature emphasises whole-body coordination in the leg-sweeping action, the roles of trunk and head motion remain unclear. This study investigates head and trunk movements (including the pelvic and upper torso) contributing to higher leg-sweep velocities when executing the judo osoto-gari. Methods Kinematic data were collected from 17 male black-belt judokas using a motion capture system (250 Hz). Pearson product-moment correlation and stepwise linear regression were used to identify kinematic variables linked to the sweeping-leg velocity at sweep contact (SC). Results Six out of twenty-four variables correlated with sweeping-leg velocity at SC. A stepwise regression model (adjusted R2 = 0.53, p = 0.009) predicted sweeping-leg velocity based on head-tilt angle at maximum sweeping-leg height (MSH) and SC, head-tilt angular velocity at MSH, and trunk-tilt angular velocity at MSH. Conclusions The findings of this study indicate that (1) increasing the forward angle of the head aids the visual system in rapidly processing spatial information about the target position, thus facilitating the execution of the leg sweep, and (2) a greater forward-tilt rotation of the head, which leads to rapid trunk rotation, is conducive to enhancing sweeping-leg velocity.
format: application/pdf
format: text/html
creator: Lingjun Liu
creator: Tatsuya Deguchi
creator: Mitsuhisa Shiokawa
creator: Kazuto Hamaguchi
creator: Masahiro Shinya
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.18862
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Osoto-gari is a leg throw technique that primarily relies on the hip extension to initiate the sweeping motion of the leg. A high sweep contact velocity is a crucial factor in efficiently executing this technique. While some literature emphasises whole-body coordination in the leg-sweeping action, the roles of trunk and head motion remain unclear. This study investigates head and trunk movements (including the pelvic and upper torso) contributing to higher leg-sweep velocities when executing the judo osoto-gari. Methods Kinematic data were collected from 17 male black-belt judokas using a motion capture system (250 Hz). Pearson product-moment correlation and stepwise linear regression were used to identify kinematic variables linked to the sweeping-leg velocity at sweep contact (SC). Results Six out of twenty-four variables correlated with sweeping-leg velocity at SC. A stepwise regression model (adjusted R2 = 0.53, p = 0.009) predicted sweeping-leg velocity based on head-tilt angle at maximum sweeping-leg height (MSH) and SC, head-tilt angular velocity at MSH, and trunk-tilt angular velocity at MSH. Conclusions The findings of this study indicate that (1) increasing the forward angle of the head aids the visual system in rapidly processing spatial information about the target position, thus facilitating the execution of the leg sweep, and (2) a greater forward-tilt rotation of the head, which leads to rapid trunk rotation, is conducive to enhancing sweeping-leg velocity.
bibliographic citation: Liu et al. (2025) Analysing head and trunk motion in the judo osoto-gari technique: relationship to sweeping-leg velocity. PeerJ 13:e18862 https://doi.org/10.7717/peerj.18862
date submitted: 2024-10-04
date accepted: 2024-12-23
issued: 2025-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lingjun
author list: Agent
  family name: Deguchi
  given name: Tatsuya
author list: Agent
  family name: Shiokawa
  given name: Mitsuhisa
author list: Agent
  family name: Hamaguchi
  given name: Kazuto
author list: Agent
  family name: Shinya
  given name: Masahiro
doi: 10.7717/peerj.18862
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-23
copyright: © 2025 Liu et al.
attribution name: Liu et al.

The bacterial composition signatures of perianal abscess and origin of infecting microbes
type: item
type: AcademicArticle
description: Background Perianal abscess is a common anal condition primarily caused by bacterial infections, yet the precise origins of these infecting bacteria remain unclear. Understanding the distinct microbial signatures associated with periaabscesses is crucial for provide fresh ideas for disease prevention. Materials and Methods Samples of anal skin, feces, and abscesses were collected from a cohort of 75 patients diagnosed with perianal abscesses. The microbial composition at each site was analyzed using 16S rRNA gene sequencing to characterize the bacterial communities present. Results Analysis using MaAslin2 revealed distinct bacterial compositional signatures among the anal skin, feces, and abscess samples. Alpha diversity analysis indicated significant differences in bacterial diversity between abscesses, anal skin, and feces, with abscesses showing lower diversity compared to higher richness in feces. Biomarker analysis highlighted key taxa such as Bacteroides and Escherichia-Shisgella in fecal samples, and Staphylococcus and Corynebacterium in anal skin samples. The analysis of abscess samples suggested that the bacterial composition may originate from the skin, feces, and potentially other sources.
format: application/pdf
format: text/html
creator: Song Han
creator: Wenya Su
creator: Kefeng Fan
creator: Zhen Xu
creator: Hai Xu
creator: Mingyu Wang
creator: Ling Li
creator: Wenlong Shen
subject: Bioinformatics
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18855
publisher: PeerJ Inc.
rights: © 2025 Han et al.
abstract: Background Perianal abscess is a common anal condition primarily caused by bacterial infections, yet the precise origins of these infecting bacteria remain unclear. Understanding the distinct microbial signatures associated with periaabscesses is crucial for provide fresh ideas for disease prevention. Materials and Methods Samples of anal skin, feces, and abscesses were collected from a cohort of 75 patients diagnosed with perianal abscesses. The microbial composition at each site was analyzed using 16S rRNA gene sequencing to characterize the bacterial communities present. Results Analysis using MaAslin2 revealed distinct bacterial compositional signatures among the anal skin, feces, and abscess samples. Alpha diversity analysis indicated significant differences in bacterial diversity between abscesses, anal skin, and feces, with abscesses showing lower diversity compared to higher richness in feces. Biomarker analysis highlighted key taxa such as Bacteroides and Escherichia-Shisgella in fecal samples, and Staphylococcus and Corynebacterium in anal skin samples. The analysis of abscess samples suggested that the bacterial composition may originate from the skin, feces, and potentially other sources.
bibliographic citation: Han et al. (2025) The bacterial composition signatures of perianal abscess and origin of infecting microbes. PeerJ 13:e18855 https://doi.org/10.7717/peerj.18855
date submitted: 2024-09-19
date accepted: 2024-12-20
issued: 2025-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Song
author list: Agent
  family name: Su
  given name: Wenya
author list: Agent
  family name: Fan
  given name: Kefeng
author list: Agent
  family name: Xu
  given name: Zhen
author list: Agent
  family name: Xu
  given name: Hai
author list: Agent
  family name: Wang
  given name: Mingyu
author list: Agent
  family name: Li
  given name: Ling
author list: Agent
  family name: Shen
  given name: Wenlong
doi: 10.7717/peerj.18855
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-23
copyright: © 2025 Han et al.
attribution name: Han et al.

Evolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus Euplotes (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits
type: item
type: AcademicArticle
description: The genus Euplotes, a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus Euplotes, with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea. Our analysis revealed significant variations in the V4 region secondary structure, particularly in helix E23_8, across different clades of Euplotes. Reconstruction of the ancestral state indicated a transition from a simpler (Type I) to a more complex (Type II) secondary structure, with several species showing a reversal to Type I especially species in clade VI, suggesting of reverse evolution. In addition, our study identified cryptic species within Euplotes based on differences in the secondary structure of the V4 region, particularly evident in clade VI, where CBC analysis highlighted differences in E. minuta compared to E. vannus and E. crassus. These results highlight the utility of molecular data in refining species boundaries and evolutionary patterns within the genus Euplotes.
format: application/pdf
format: text/html
creator: Ratih Kusuma Wardani
creator: Ragib Ahsan
creator: Mann Kyoon Shin
subject: Biodiversity
subject: Bioinformatics
subject: Evolutionary Studies
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.18852
publisher: PeerJ Inc.
rights: © 2025 Wardani et al.
abstract: The genus Euplotes, a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus Euplotes, with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea. Our analysis revealed significant variations in the V4 region secondary structure, particularly in helix E23_8, across different clades of Euplotes. Reconstruction of the ancestral state indicated a transition from a simpler (Type I) to a more complex (Type II) secondary structure, with several species showing a reversal to Type I especially species in clade VI, suggesting of reverse evolution. In addition, our study identified cryptic species within Euplotes based on differences in the secondary structure of the V4 region, particularly evident in clade VI, where CBC analysis highlighted differences in E. minuta compared to E. vannus and E. crassus. These results highlight the utility of molecular data in refining species boundaries and evolutionary patterns within the genus Euplotes.
bibliographic citation: Wardani et al. (2025) Evolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus Euplotes (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits. PeerJ 13:e18852 https://doi.org/10.7717/peerj.18852
date submitted: 2024-04-16
date accepted: 2024-12-20
issued: 2025-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wardani
  given name: Ratih Kusuma
author list: Agent
  family name: Ahsan
  given name: Ragib
author list: Agent
  family name: Shin
  given name: Mann Kyoon
doi: 10.7717/peerj.18852
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-23
copyright: © 2025 Wardani et al.
attribution name: Wardani et al.

Re-evaluation of mastodon material from Oregon and Washington, USA, Alberta, Canada, and Hidalgo and Jalisco, Mexico
type: item
type: AcademicArticle
description: The presence of at least two contemporaneous Pleistocene mastodon taxa in North America (Mammut americanum and M. pacificus) invites re-examination of specimens at the geographic margins of each species in order to determine range boundaries, overlaps, and fluctuations. Third molars from Oregon in the United States, as well as from Hidalgo and Jalisco in Mexico, were found to be morphologically consistent with M. pacificus. Washington in the United States includes a number of specimens that could not be confidently assigned to either taxon. Alberta in Canada was found to have some specimens that were consistent with M. pacificus, but others that were identified as M. americanum. The Alberta specimen referred to M. pacificus is the same tooth found to have a Pliocene divergence time from M. americanum based on mitochondrial genome data from a previous study, suggesting a deep divergence time between the two taxa. The apparent presence of both mastodon taxa in close geographic proximity has interesting paleobiogeographic implications. It is not yet clear if both taxa were present simultaneously in a given location; if not, it suggests fluctuating ranges that may reflect shifting climates and/or biomes over time. Alternatively, if both taxa were simultaneously present in the same place, it may suggest a high degree of niche partitioning in mammutids. Additional accurately dated specimens will be required to resolve this question.
format: application/pdf
format: text/html
creator: Alton C. Dooley
creator: Chris Widga
creator: Brittney E. Stoneburg
creator: Christopher Jass
creator: Victor M. Bravo-Cuevas
creator: Andrew Boehm
creator: Eric Scott
creator: Andrew T. McDonald
creator: Mark Volmut
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.18848
publisher: PeerJ Inc.
rights: © 2025 Dooley Jr et al.
abstract: The presence of at least two contemporaneous Pleistocene mastodon taxa in North America (Mammut americanum and M. pacificus) invites re-examination of specimens at the geographic margins of each species in order to determine range boundaries, overlaps, and fluctuations. Third molars from Oregon in the United States, as well as from Hidalgo and Jalisco in Mexico, were found to be morphologically consistent with M. pacificus. Washington in the United States includes a number of specimens that could not be confidently assigned to either taxon. Alberta in Canada was found to have some specimens that were consistent with M. pacificus, but others that were identified as M. americanum. The Alberta specimen referred to M. pacificus is the same tooth found to have a Pliocene divergence time from M. americanum based on mitochondrial genome data from a previous study, suggesting a deep divergence time between the two taxa. The apparent presence of both mastodon taxa in close geographic proximity has interesting paleobiogeographic implications. It is not yet clear if both taxa were present simultaneously in a given location; if not, it suggests fluctuating ranges that may reflect shifting climates and/or biomes over time. Alternatively, if both taxa were simultaneously present in the same place, it may suggest a high degree of niche partitioning in mammutids. Additional accurately dated specimens will be required to resolve this question.
bibliographic citation: Dooley et al. (2025) Re-evaluation of mastodon material from Oregon and Washington, USA, Alberta, Canada, and Hidalgo and Jalisco, Mexico. PeerJ 13:e18848 https://doi.org/10.7717/peerj.18848
date submitted: 2023-12-29
date accepted: 2024-12-19
issued: 2025-01-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dooley
  given name: Alton C.
author list: Agent
  family name: Widga
  given name: Chris
author list: Agent
  family name: Stoneburg
  given name: Brittney E.
author list: Agent
  family name: Jass
  given name: Christopher
author list: Agent
  family name: Bravo-Cuevas
  given name: Victor M.
author list: Agent
  family name: Boehm
  given name: Andrew
author list: Agent
  family name: Scott
  given name: Eric
author list: Agent
  family name: McDonald
  given name: Andrew T.
author list: Agent
  family name: Volmut
  given name: Mark
doi: 10.7717/peerj.18848
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-23
copyright: © 2025 Dooley Jr et al.
attribution name: Dooley Jr et al.

Deep water vetulicolians from the lower Cambrian of China
type: item
type: AcademicArticle
description: Vetulicolians are an enigmatic phylum of extinct Cambrian marine invertebrates. They are particularly diverse in the Chengjiang Biota of China, but representatives have been recovered from other Fossil-Lagerstätten (Cambrian Stage 3-Drumian). These organisms are characterized by a bipartite body, which is split into an anterior section and a posterior segmented section connected by a narrow constriction. Here we report new material of the genus Pomatrum from the Cambrian Balang Biota (Series 2, Stage 4) of Hunan, southern China. This is the first discovery of this vetulicolian outside of the Chengjiang Biota (Series 2, Stage 3) and the first report of vetulicolians from the Balang Biota. This finding not only suggests that this group had a wider spatial and temporal distribution than previously known, but also adds information to the overall biodiversity of the Balang Biota—one of the most important Stage 4 fossil deposits known from Gondwana.
format: application/pdf
format: text/html
creator: Shuhan Ma
creator: Julien Kimmig
creator: James D. Schiffbauer
creator: Ruibo Li
creator: Shanchi Peng
creator: Xianfeng Yang
subject: Ecology
subject: Ecosystem Science
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.18864
publisher: PeerJ Inc.
rights: © 2025 Ma et al.
abstract: Vetulicolians are an enigmatic phylum of extinct Cambrian marine invertebrates. They are particularly diverse in the Chengjiang Biota of China, but representatives have been recovered from other Fossil-Lagerstätten (Cambrian Stage 3-Drumian). These organisms are characterized by a bipartite body, which is split into an anterior section and a posterior segmented section connected by a narrow constriction. Here we report new material of the genus Pomatrum from the Cambrian Balang Biota (Series 2, Stage 4) of Hunan, southern China. This is the first discovery of this vetulicolian outside of the Chengjiang Biota (Series 2, Stage 3) and the first report of vetulicolians from the Balang Biota. This finding not only suggests that this group had a wider spatial and temporal distribution than previously known, but also adds information to the overall biodiversity of the Balang Biota—one of the most important Stage 4 fossil deposits known from Gondwana.
bibliographic citation: Ma et al. (2025) Deep water vetulicolians from the lower Cambrian of China. PeerJ 13:e18864 https://doi.org/10.7717/peerj.18864
date submitted: 2024-10-03
date accepted: 2024-12-23
issued: 2025-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Shuhan
author list: Agent
  family name: Kimmig
  given name: Julien
author list: Agent
  family name: Schiffbauer
  given name: James D.
author list: Agent
  family name: Li
  given name: Ruibo
author list: Agent
  family name: Peng
  given name: Shanchi
author list: Agent
  family name: Yang
  given name: Xianfeng
doi: 10.7717/peerj.18864
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-22
copyright: © 2025 Ma et al.
attribution name: Ma et al.

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