PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories
items: The role of exercise in improving hyperlipidemia-renal injuries induced by a high-fat diet: a literature review
items: Clinical diagnostic value of amino acids in laryngeal squamous cell carcinomas
items: Integrating robotics into wildlife conservation: testing improvements to predator deterrents through movement
items: Tolerogenic dendritic cell reporting: Has a minimum information model made a difference?
items: Quiz-style online training tool helps to learn birdsong identification and support citizen science
items: https://peerj.com/articles/15451
items: Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous)
items: The significance of PD-1/PD-L1 imbalance in ulcerative colitis
items: Over-expression of CcMYB24, encoding a R2R3-MYB transcription factor from a high-leaf-number mutant of Cymbidium, increases the number of leaves in Arabidopsis

Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories
type: item
type: AcademicArticle
description: Ocean warming and marine heatwaves induced by climate change are impacting coral reefs globally, leading to coral bleaching and mortality. Yet, coral resistance and resilience to warming are not uniform across reef sites and corals can show inter- and intraspecific variability. To understand changes in coral health and to elucidate mechanisms of coral thermal tolerance, baseline data on the dynamics of coral holobiont performance under non-stressed conditions are needed. We monitored the seasonal dynamics of algal symbionts (family Symbiodiniaceae) hosted by corals from a chronically warmed and thermally variable reef compared to a thermally stable reef in southern Taiwan over 15 months. We assessed the genera and photochemical efficiency of Symbiodiniaceae in three coral species: Acropora nana, Pocillopora acuta, and Porites lutea. Both Durusdinium and Cladocopium were present in all coral species at both reef sites across all seasons, but general trends in their detection (based on qPCR cycle) varied between sites and among species. Photochemical efficiency (i.e., maximum quantum yield; Fv/Fm) was relatively similar between reef sites but differed consistently among species; no clear evidence of seasonal trends in Fv/Fm was found. Quantifying natural Symbiodiniaceae dynamics can help facilitate a more comprehensive interpretation of thermal tolerance response as well as plasticity potential of the coral holobiont.
format: application/pdf
format: text/html
creator: Crystal J. McRae
creator: Shashank Keshavmurthy
creator: Hung-Kai Chen
creator: Zong-Min Ye
creator: Pei-Jie Meng
creator: Sabrina L. Rosset
creator: Wen-Bin Huang
creator: Chaolun Allen Chen
creator: Tung-Yung Fan
creator: Isabelle M. Côté
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.15421
publisher: PeerJ Inc.
rights: © 2023 McRae et al.
abstract: Ocean warming and marine heatwaves induced by climate change are impacting coral reefs globally, leading to coral bleaching and mortality. Yet, coral resistance and resilience to warming are not uniform across reef sites and corals can show inter- and intraspecific variability. To understand changes in coral health and to elucidate mechanisms of coral thermal tolerance, baseline data on the dynamics of coral holobiont performance under non-stressed conditions are needed. We monitored the seasonal dynamics of algal symbionts (family Symbiodiniaceae) hosted by corals from a chronically warmed and thermally variable reef compared to a thermally stable reef in southern Taiwan over 15 months. We assessed the genera and photochemical efficiency of Symbiodiniaceae in three coral species: Acropora nana, Pocillopora acuta, and Porites lutea. Both Durusdinium and Cladocopium were present in all coral species at both reef sites across all seasons, but general trends in their detection (based on qPCR cycle) varied between sites and among species. Photochemical efficiency (i.e., maximum quantum yield; Fv/Fm) was relatively similar between reef sites but differed consistently among species; no clear evidence of seasonal trends in Fv/Fm was found. Quantifying natural Symbiodiniaceae dynamics can help facilitate a more comprehensive interpretation of thermal tolerance response as well as plasticity potential of the coral holobiont.
bibliographic citation: McRae et al. (2023) Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories. PeerJ 11:e15421 https://doi.org/10.7717/peerj.15421
date submitted: 2022-12-02
date accepted: 2023-04-25
issued: 2023-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McRae
  given name: Crystal J.
author list: Agent
  family name: Keshavmurthy
  given name: Shashank
author list: Agent
  family name: Chen
  given name: Hung-Kai
author list: Agent
  family name: Ye
  given name: Zong-Min
author list: Agent
  family name: Meng
  given name: Pei-Jie
author list: Agent
  family name: Rosset
  given name: Sabrina L.
author list: Agent
  family name: Huang
  given name: Wen-Bin
author list: Agent
  family name: Chen
  given name: Chaolun Allen
author list: Agent
  family name: Fan
  given name: Tung-Yung
author list: Agent
  family name: Côté
  given name: Isabelle M.
doi: 10.7717/peerj.15421
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-01
copyright: ©2023 McRae et al.
attribution name: McRae et al.

The role of exercise in improving hyperlipidemia-renal injuries induced by a high-fat diet: a literature review
type: item
type: AcademicArticle
description: A diet that is high in sugar and fat is a precursor to various chronic diseases, especially hyperlipidemia. Patients with hyperlipidemia have increased levels of plasma free fatty acids and an ectopic accumulation of lipids. The kidney is one of the main organs affected by this disease and, recently, there have been more studies conducted on renal injury caused by hyperlipidemia. The main pathological mechanism is closely related to renal lipotoxicity. However, in different kidney cells, the reaction mechanism varies due to the different affinities of the lipid receptors. At present, it is believed that in addition to lipotoxicity, hyperlipidemia induced-renal injury is also closely related to oxidative stress, endoplasmic reticulum stress, and inflammatory reactions, which are the result of multiple factors. Exercise plays an important role in the prevention of various chronic diseases and recently emerging researches indicated its positive effects to renal injury caused by hyperlipidemia. However, there are few studies summarizing the effects of exercise on this disease and the specific mechanisms need to be further explored. This article summarizes the mechanisms of hyperlipidemia induced-renal injury at the cellular level and discusses the ways in which exercise may regulate it. The results provide theoretical support and novel approaches for identifying the intervention target to treat hyperlipidemia induced-renal injury.
format: application/pdf
format: text/html
creator: Jun Shunzi Chen
creator: Peng Fei Xie
creator: Hong Feng
subject: Nephrology
subject: Nursing
subject: Nutrition
subject: Obesity
subject: Sports Medicine
description: doi:10.7717/peerj.15435
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: A diet that is high in sugar and fat is a precursor to various chronic diseases, especially hyperlipidemia. Patients with hyperlipidemia have increased levels of plasma free fatty acids and an ectopic accumulation of lipids. The kidney is one of the main organs affected by this disease and, recently, there have been more studies conducted on renal injury caused by hyperlipidemia. The main pathological mechanism is closely related to renal lipotoxicity. However, in different kidney cells, the reaction mechanism varies due to the different affinities of the lipid receptors. At present, it is believed that in addition to lipotoxicity, hyperlipidemia induced-renal injury is also closely related to oxidative stress, endoplasmic reticulum stress, and inflammatory reactions, which are the result of multiple factors. Exercise plays an important role in the prevention of various chronic diseases and recently emerging researches indicated its positive effects to renal injury caused by hyperlipidemia. However, there are few studies summarizing the effects of exercise on this disease and the specific mechanisms need to be further explored. This article summarizes the mechanisms of hyperlipidemia induced-renal injury at the cellular level and discusses the ways in which exercise may regulate it. The results provide theoretical support and novel approaches for identifying the intervention target to treat hyperlipidemia induced-renal injury.
bibliographic citation: Chen et al. (2023) The role of exercise in improving hyperlipidemia-renal injuries induced by a high-fat diet: a literature review. PeerJ 11:e15435 https://doi.org/10.7717/peerj.15435
date submitted: 2023-02-14
date accepted: 2023-04-27
issued: 2023-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jun Shunzi
author list: Agent
  family name: Xie
  given name: Peng Fei
author list: Agent
  family name: Feng
  given name: Hong
doi: 10.7717/peerj.15435
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-01
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Clinical diagnostic value of amino acids in laryngeal squamous cell carcinomas
type: item
type: AcademicArticle
description: Background Early diagnosis and treatment can improve the survival rates of patients with laryngeal squamous cell carcinoma (LSCC). Therefore, it is necessary to discover new biomarkers for laryngeal cancer screening and early diagnosis. Methods We collected fasting plasma from LSCC patients and healthy volunteers, as well as cancer and para-carcinoma tissues from LSCC patients, and performed quantitative detection of amino acid levels using liquid chromatography-mass spectrometry. We used overall analysis and multivariate statistical analysis to screen out the statistically significant differential amino acids in the plasma and tissue samples, conducted receiver operating characteristic (ROC) analysis of the differential amino acids to evaluate the sensitivity and specificity of the differential amino acids, and finally determined the diagnostic value of amino acids for laryngeal cancer. Additionally, we identified amino acids in the plasma and tissue samples that are valuable for the early diagnosis of laryngeal cancer classified according to the tumor-node-metastasis (TNM) classification. Results Asparagine (Asp) and homocysteine (Hcy) were two amino acids of common significance in plasma and tissue samples, and their specificity and sensitivity analysis showed that they may be new biomarkers for the diagnosis and treatment of LSCC. According to the TNM staging system, phenylalanine (Phe) and isoleucine (Ile) were screened out in the plasma of LSCC patients at early (I and II) and advanced (III and IV) stages; ornithine hydrochloride (Orn), glutamic acid (Glu), and Glycine (Gly) were selected in the tissue. These dysregulated amino acids found in LSCC patients may be useful as clinical biomarkers for the early diagnosis and screening of LSCC.
format: application/pdf
format: text/html
creator: Shousen Hu
creator: Chang Zhao
creator: Zi’an Wang
creator: Zeyun Li
creator: Xiangzhen Kong
subject: Oncology
subject: Metabolic Sciences
description: doi:10.7717/peerj.15469
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Early diagnosis and treatment can improve the survival rates of patients with laryngeal squamous cell carcinoma (LSCC). Therefore, it is necessary to discover new biomarkers for laryngeal cancer screening and early diagnosis. Methods We collected fasting plasma from LSCC patients and healthy volunteers, as well as cancer and para-carcinoma tissues from LSCC patients, and performed quantitative detection of amino acid levels using liquid chromatography-mass spectrometry. We used overall analysis and multivariate statistical analysis to screen out the statistically significant differential amino acids in the plasma and tissue samples, conducted receiver operating characteristic (ROC) analysis of the differential amino acids to evaluate the sensitivity and specificity of the differential amino acids, and finally determined the diagnostic value of amino acids for laryngeal cancer. Additionally, we identified amino acids in the plasma and tissue samples that are valuable for the early diagnosis of laryngeal cancer classified according to the tumor-node-metastasis (TNM) classification. Results Asparagine (Asp) and homocysteine (Hcy) were two amino acids of common significance in plasma and tissue samples, and their specificity and sensitivity analysis showed that they may be new biomarkers for the diagnosis and treatment of LSCC. According to the TNM staging system, phenylalanine (Phe) and isoleucine (Ile) were screened out in the plasma of LSCC patients at early (I and II) and advanced (III and IV) stages; ornithine hydrochloride (Orn), glutamic acid (Glu), and Glycine (Gly) were selected in the tissue. These dysregulated amino acids found in LSCC patients may be useful as clinical biomarkers for the early diagnosis and screening of LSCC.
bibliographic citation: Hu et al. (2023) Clinical diagnostic value of amino acids in laryngeal squamous cell carcinomas. PeerJ 11:e15469 https://doi.org/10.7717/peerj.15469
date submitted: 2023-01-20
date accepted: 2023-05-05
issued: 2023-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Shousen
author list: Agent
  family name: Zhao
  given name: Chang
author list: Agent
  family name: Wang
  given name: Zi’an
author list: Agent
  family name: Li
  given name: Zeyun
author list: Agent
  family name: Kong
  given name: Xiangzhen
doi: 10.7717/peerj.15469
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-01
copyright: © 2023 Hu et al.
attribution name: Hu et al.

Integrating robotics into wildlife conservation: testing improvements to predator deterrents through movement
type: item
type: AcademicArticle
description: Background Agricultural and pastoral landscapes can provide important habitat for wildlife conservation, but sharing these landscapes with wildlife can create conflict that is costly and requires managing. Livestock predation is a good example of the challenges involving coexistence with wildlife across shared landscapes. Integrating new technology into agricultural practices could help minimize human-wildlife conflict. In this study, we used concepts from the fields of robotics (i.e., automated movement and adaptiveness) and agricultural practices (i.e., managing livestock risk to predation) to explore how integration of these concepts could aid the development of more effective predator deterrents. Methods We used a colony of captive coyotes as a model system, and simulated predation events with meat baits inside and outside of protected zones. Inside the protected zones we used a remote-controlled vehicle with a state-of-the art, commercially available predator deterrent (i.e., Foxlight) mounted on the top and used this to test three treatments: (1) light only (i.e., without movement or adaptiveness), (2) predetermined movement (i.e., with movement and without adaptiveness), and (3) adaptive movement (i.e., with both movement and adaptiveness). We measured the time it took for coyotes to eat the baits and analyzed the data with a time-to-event survival strategy. Results Survival of baits was consistently higher inside the protected zone, and the three movement treatments incrementally increased survival time over baseline except for the light only treatment in the nonprotected zone. Incorporating predetermined movement essentially doubled the efficacy of the light only treatment both inside and outside the protected zone. Incorporating adaptive movement exponentially increased survival time both inside and outside the protected zone. Our findings provide compelling evidence that incorporating existing robotics capabilities (predetermined and adaptive movement) co…
format: application/pdf
format: text/html
creator: Stewart W. Breck
creator: Jeffrey T. Schultz
creator: David Prause
creator: Cameron Krebs
creator: Anthony J. Giordano
creator: Byron Boots
subject: Agricultural Science
subject: Animal Behavior
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.15491
publisher: PeerJ Inc.
rights: © 2023 Breck et al.
abstract: Background Agricultural and pastoral landscapes can provide important habitat for wildlife conservation, but sharing these landscapes with wildlife can create conflict that is costly and requires managing. Livestock predation is a good example of the challenges involving coexistence with wildlife across shared landscapes. Integrating new technology into agricultural practices could help minimize human-wildlife conflict. In this study, we used concepts from the fields of robotics (i.e., automated movement and adaptiveness) and agricultural practices (i.e., managing livestock risk to predation) to explore how integration of these concepts could aid the development of more effective predator deterrents. Methods We used a colony of captive coyotes as a model system, and simulated predation events with meat baits inside and outside of protected zones. Inside the protected zones we used a remote-controlled vehicle with a state-of-the art, commercially available predator deterrent (i.e., Foxlight) mounted on the top and used this to test three treatments: (1) light only (i.e., without movement or adaptiveness), (2) predetermined movement (i.e., with movement and without adaptiveness), and (3) adaptive movement (i.e., with both movement and adaptiveness). We measured the time it took for coyotes to eat the baits and analyzed the data with a time-to-event survival strategy. Results Survival of baits was consistently higher inside the protected zone, and the three movement treatments incrementally increased survival time over baseline except for the light only treatment in the nonprotected zone. Incorporating predetermined movement essentially doubled the efficacy of the light only treatment both inside and outside the protected zone. Incorporating adaptive movement exponentially increased survival time both inside and outside the protected zone. Our findings provide compelling evidence that incorporating existing robotics capabilities (predetermined and adaptive movement) co…
bibliographic citation: Breck et al. (2023) Integrating robotics into wildlife conservation: testing improvements to predator deterrents through movement. PeerJ 11:e15491 https://doi.org/10.7717/peerj.15491
date submitted: 2023-01-11
date accepted: 2023-05-10
issued: 2023-06-01
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Breck
  given name: Stewart W.
author list: Agent
  family name: Schultz
  given name: Jeffrey T.
author list: Agent
  family name: Prause
  given name: David
author list: Agent
  family name: Krebs
  given name: Cameron
author list: Agent
  family name: Giordano
  given name: Anthony J.
author list: Agent
  family name: Boots
  given name: Byron
doi: 10.7717/peerj.15491
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-01
copyright: © 2023 Breck et al.
attribution name: Breck et al.

Tolerogenic dendritic cell reporting: Has a minimum information model made a difference?
type: item
type: AcademicArticle
description: Minimum information models are reporting frameworks that describe the essential information that needs to be provided in a publication, so that the work can be repeated or compared to other work. In 2016, Minimum Information about Tolerogenic Antigen-Presenting cells (MITAP) was created to standardize the reporting on tolerogenic antigen-presenting cells, including tolerogenic dendritic cells (tolDCs). tolDCs is a generic term for dendritic cells that have the ability to (re-)establish immune tolerance; they have been developed as a cell therapy for autoimmune diseases or for the prevention of transplant rejection. Because protocols to generate these therapeutic cells vary widely, MITAP was deemed to be a pivotal reporting tool by and for the tolDC community. In this paper, we explored the impact that MITAP has had on the tolDC field. We did this by examining a subset of the available literature on tolDCs. Our analysis shows that MITAP is used in only the minority of relevant papers (14%), but where it is used the amount of metadata available is slightly increased over where it is not. From this, we conclude that MITAP has been a partial success, but that much more needs to be done if standardized reporting is to become common within the discipline.
format: application/pdf
format: text/html
creator: Ayesha Sahar
creator: Ioana Nicorescu
creator: Gabrielle Barran
creator: Megan Paterson
creator: Catharien M.U. Hilkens
creator: Phillip Lord
subject: Bioinformatics
subject: Immunology
subject: Translational Medicine
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.15352
publisher: PeerJ Inc.
rights: © 2023 Sahar et al.
abstract: Minimum information models are reporting frameworks that describe the essential information that needs to be provided in a publication, so that the work can be repeated or compared to other work. In 2016, Minimum Information about Tolerogenic Antigen-Presenting cells (MITAP) was created to standardize the reporting on tolerogenic antigen-presenting cells, including tolerogenic dendritic cells (tolDCs). tolDCs is a generic term for dendritic cells that have the ability to (re-)establish immune tolerance; they have been developed as a cell therapy for autoimmune diseases or for the prevention of transplant rejection. Because protocols to generate these therapeutic cells vary widely, MITAP was deemed to be a pivotal reporting tool by and for the tolDC community. In this paper, we explored the impact that MITAP has had on the tolDC field. We did this by examining a subset of the available literature on tolDCs. Our analysis shows that MITAP is used in only the minority of relevant papers (14%), but where it is used the amount of metadata available is slightly increased over where it is not. From this, we conclude that MITAP has been a partial success, but that much more needs to be done if standardized reporting is to become common within the discipline.
bibliographic citation: Sahar et al. (2023) Tolerogenic dendritic cell reporting: Has a minimum information model made a difference?. PeerJ 11:e15352 https://doi.org/10.7717/peerj.15352
date submitted: 2022-12-23
date accepted: 2023-04-13
issued: 2023-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sahar
  given name: Ayesha
author list: Agent
  family name: Nicorescu
  given name: Ioana
author list: Agent
  family name: Barran
  given name: Gabrielle
author list: Agent
  family name: Paterson
  given name: Megan
author list: Agent
  family name: Hilkens
  given name: Catharien M.U.
author list: Agent
  family name: Lord
  given name: Phillip
doi: 10.7717/peerj.15352
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-31
copyright: ©2023 Sahar et al.
attribution name: Sahar et al.

Quiz-style online training tool helps to learn birdsong identification and support citizen science
type: item
type: AcademicArticle
description: Citizen science is an important approach to monitoring for biodiversity conservation because it allows for data acquisition or analysis on a scale that is not possible for researchers alone. In citizen science projects, the use of online training is increasing to improve such skills. However, the effectiveness of quiz-style online training, assumed to be efficient to enhance participants’ skills, has not been evaluated adequately on species identification for citizen science biodiversity monitoring projects. Memory mechanisms in adaptive learning were hypothesized to guide the development of quiz-based online training tools for learning birdsong identification and for improving interest in birds and natural environments. To examine the hypothesis, we developed a quiz-style online training tool called TORI-TORE. We experimentally applied TORI-TORE in Fukushima, Japan, and examined its effectiveness for bird identification training using test scores and questionnaires to determine participants’ attitudes in a randomized control trial. We obtained the following key results: (1) TORI-TORE had positive effects on test scores and trainees’ attitudes toward birds. (2) Adaptive training, in which questions focused preferentially on unmastered bird species based on the answer history of individual trainees inspired by adaptive learning, unexpectedly led to lower scores and satisfaction in TORI-TORE. (3) Focusing on species that are relatively easy to remember, short lag times between training and testing, and long question intervals positively affected scores. While there is room for improvement, we expect TORI-TORE to contribute to online capacity building and to increase interest in natural environments.
format: application/pdf
format: text/html
creator: Yui Ogawa
creator: Keita Fukasawa
creator: Akira Yoshioka
creator: Nao Kumada
creator: Akio Takenaka
creator: Taiichi Ito
subject: Biodiversity
subject: Conservation Biology
subject: Science and Medical Education
subject: Human-Computer Interaction
subject: Data Science
description: doi:10.7717/peerj.15387
publisher: PeerJ Inc.
rights: © 2023 Ogawa et al.
abstract: Citizen science is an important approach to monitoring for biodiversity conservation because it allows for data acquisition or analysis on a scale that is not possible for researchers alone. In citizen science projects, the use of online training is increasing to improve such skills. However, the effectiveness of quiz-style online training, assumed to be efficient to enhance participants’ skills, has not been evaluated adequately on species identification for citizen science biodiversity monitoring projects. Memory mechanisms in adaptive learning were hypothesized to guide the development of quiz-based online training tools for learning birdsong identification and for improving interest in birds and natural environments. To examine the hypothesis, we developed a quiz-style online training tool called TORI-TORE. We experimentally applied TORI-TORE in Fukushima, Japan, and examined its effectiveness for bird identification training using test scores and questionnaires to determine participants’ attitudes in a randomized control trial. We obtained the following key results: (1) TORI-TORE had positive effects on test scores and trainees’ attitudes toward birds. (2) Adaptive training, in which questions focused preferentially on unmastered bird species based on the answer history of individual trainees inspired by adaptive learning, unexpectedly led to lower scores and satisfaction in TORI-TORE. (3) Focusing on species that are relatively easy to remember, short lag times between training and testing, and long question intervals positively affected scores. While there is room for improvement, we expect TORI-TORE to contribute to online capacity building and to increase interest in natural environments.
bibliographic citation: Ogawa et al. (2023) Quiz-style online training tool helps to learn birdsong identification and support citizen science. PeerJ 11:e15387 https://doi.org/10.7717/peerj.15387
date submitted: 2022-11-17
date accepted: 2023-04-19
issued: 2023-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ogawa
  given name: Yui
author list: Agent
  family name: Fukasawa
  given name: Keita
author list: Agent
  family name: Yoshioka
  given name: Akira
author list: Agent
  family name: Kumada
  given name: Nao
author list: Agent
  family name: Takenaka
  given name: Akio
author list: Agent
  family name: Ito
  given name: Taiichi
doi: 10.7717/peerj.15387
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-31
copyright: ©2023 Ogawa et al.
attribution name: Ogawa et al.

https://peerj.com/articles/15451
type: item
type: AcademicArticle
title: Ontogenetic progression of individual head size in the larvae of the beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): catch-up growth within stages and per-stage growth rate changes across stages
description: The ontogenetic progression of insect larval head size has received much attention due to its fundamental and practical importance. However, although previous studies have analyzed the population mean head size, such an approach may not be appropriate for developmental studies of larval head sizes when the trajectory of individual head size growth is correlated with pre-molt head size and developmental stage. Additionally, there is covariation between the head and body sizes; however, few studies have compared the ontogenetic progression of individual head sizes with that of individual body sizes. In this investigation, the per-stage growth rates (PSGRs) for head width (HW) and cubic-rooted body mass at the beginning of each instar (body size, BS) were assessed in Trypoxylus dichotomus. Linear models were used to test the size- and instar-dependence of the ontogenetic progression of individual HW and BS. The individual PSGRs of the HW (iPSGRH) and BS (iPSGRB) were then compared. In addition, the allometric relationship between HW and BS was examined. The iPSGRH was negatively correlated with the pre-molt HW at every instar (i.e., head catch-up growth). Furthermore, the mean iPSGRH at L2 was relatively higher than that at L1 when the pre-molt HW was used as covariate in the analysis (i.e., instar-effect), whereas the mean iPSGRH decreased ontogenetically. The iPSGRB showed catch-up growth and instar-effects similar to those of iPSGRH; however, iPSGRH was found to be lower than iPSGRB. Due to the differences between the PSGRs for the larval head and body, the larval head size showed negative ontogenetic allometry against body size.
format: application/pdf
format: text/html
creator: Sugihiko Hoshizaki
subject: Developmental Biology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.15451
publisher: PeerJ Inc.
rights: © 2023 Hoshizaki
abstract: The ontogenetic progression of insect larval head size has received much attention due to its fundamental and practical importance. However, although previous studies have analyzed the population mean head size, such an approach may not be appropriate for developmental studies of larval head sizes when the trajectory of individual head size growth is correlated with pre-molt head size and developmental stage. Additionally, there is covariation between the head and body sizes; however, few studies have compared the ontogenetic progression of individual head sizes with that of individual body sizes. In this investigation, the per-stage growth rates (PSGRs) for head width (HW) and cubic-rooted body mass at the beginning of each instar (body size, BS) were assessed in Trypoxylus dichotomus. Linear models were used to test the size- and instar-dependence of the ontogenetic progression of individual HW and BS. The individual PSGRs of the HW (iPSGRH) and BS (iPSGRB) were then compared. In addition, the allometric relationship between HW and BS was examined. The iPSGRH was negatively correlated with the pre-molt HW at every instar (i.e., head catch-up growth). Furthermore, the mean iPSGRH at L2 was relatively higher than that at L1 when the pre-molt HW was used as covariate in the analysis (i.e., instar-effect), whereas the mean iPSGRH decreased ontogenetically. The iPSGRB showed catch-up growth and instar-effects similar to those of iPSGRH; however, iPSGRH was found to be lower than iPSGRB. Due to the differences between the PSGRs for the larval head and body, the larval head size showed negative ontogenetic allometry against body size.
bibliographic citation: Hoshizaki (2023) Ontogenetic progression of individual head size in the larvae of the beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): catch-up growth within stages and per-stage growth rate changes across stages. PeerJ 11:e15451 https://doi.org/10.7717/peerj.15451
date submitted: 2022-07-20
date accepted: 2023-05-03
issued: 2023-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoshizaki
  given name: Sugihiko
doi: 10.7717/peerj.15451
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-31
copyright: © 2023 Hoshizaki
attribution name: Hoshizaki

Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous)
type: item
type: AcademicArticle
description: Isolated spinosaurid teeth are relatively well represented in the Lower Cretaceous Wealden Supergroup of southern England, UK. Until recently it was assumed that these teeth were referable to Baryonyx, the type species (B. walkeri) and specimen of which is from the Barremian Upper Weald Clay Formation of Surrey. British spinosaurid teeth are known from formations that span much of the c. 25 Ma depositional history of the Wealden Supergroup, and recent works suggest that British spinosaurids were more taxonomically diverse than previously thought. On the basis of both arguments, it is appropriate to doubt the hypothesis that isolated teeth from outside the Upper Weald Clay Formation are referable to Baryonyx. Here, we use phylogenetic, discriminant and cluster analyses to test whether an isolated spinosaurid tooth (HASMG G369a, consisting of a crown and part of the root) from a non-Weald Clay Formation unit can be referred to Baryonyx. HASMG G369a was recovered from an uncertain Lower Cretaceous locality in East Sussex but is probably from a Valanginian exposure of the Hastings Group and among the oldest spinosaurid material known from the UK. Spinosaurid affinities are both quantitatively and qualitatively supported, and HASMG G369a does not associate with Baryonyx in any analysis. This supports recent reinterpretations of the diversity of spinosaurid in the Early Cretaceous of Britain, which appears to have been populated by multiple spinosaurid lineages in a manner comparable to coeval Iberian deposits. This work also reviews the British and global records of early spinosaurids (known mainly from dental specimens), and revisits evidence for post-Cenomanian spinosaurid persistence.
format: application/pdf
format: text/html
creator: Chris T. Barker
creator: Darren Naish
creator: Neil J. Gostling
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15453
publisher: PeerJ Inc.
rights: © 2023 Barker et al.
abstract: Isolated spinosaurid teeth are relatively well represented in the Lower Cretaceous Wealden Supergroup of southern England, UK. Until recently it was assumed that these teeth were referable to Baryonyx, the type species (B. walkeri) and specimen of which is from the Barremian Upper Weald Clay Formation of Surrey. British spinosaurid teeth are known from formations that span much of the c. 25 Ma depositional history of the Wealden Supergroup, and recent works suggest that British spinosaurids were more taxonomically diverse than previously thought. On the basis of both arguments, it is appropriate to doubt the hypothesis that isolated teeth from outside the Upper Weald Clay Formation are referable to Baryonyx. Here, we use phylogenetic, discriminant and cluster analyses to test whether an isolated spinosaurid tooth (HASMG G369a, consisting of a crown and part of the root) from a non-Weald Clay Formation unit can be referred to Baryonyx. HASMG G369a was recovered from an uncertain Lower Cretaceous locality in East Sussex but is probably from a Valanginian exposure of the Hastings Group and among the oldest spinosaurid material known from the UK. Spinosaurid affinities are both quantitatively and qualitatively supported, and HASMG G369a does not associate with Baryonyx in any analysis. This supports recent reinterpretations of the diversity of spinosaurid in the Early Cretaceous of Britain, which appears to have been populated by multiple spinosaurid lineages in a manner comparable to coeval Iberian deposits. This work also reviews the British and global records of early spinosaurids (known mainly from dental specimens), and revisits evidence for post-Cenomanian spinosaurid persistence.
bibliographic citation: Barker et al. (2023) Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous). PeerJ 11:e15453 https://doi.org/10.7717/peerj.15453
date submitted: 2023-03-01
date accepted: 2023-05-03
issued: 2023-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barker
  given name: Chris T.
author list: Agent
  family name: Naish
  given name: Darren
author list: Agent
  family name: Gostling
  given name: Neil J.
doi: 10.7717/peerj.15453
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-31
copyright: ©2023 Barker et al.
attribution name: Barker et al.

The significance of PD-1/PD-L1 imbalance in ulcerative colitis
type: item
type: AcademicArticle
description: Objectives To investigate the expression and significance of programmed cell death protein 1 (PD-1) and programmed cell death ligand-1 (PD-L1) in the mucosal tissues and peripheral blood of patients with ulcerative colitis (UC). Methods Eighty patients with UC were recruited from January 2021 to August 2022 from the Shanxi Province People’s Hospital. PD-1 and PD-L1 expression was assessed by immunohistochemistry in mucosal tissues. An enzyme-linked immunosorbent assay was used to measure soluble PD-1 and PD-L1 levels in peripheral blood serum, and the membrane-bound forms of PD-1 (mPD-1), (T-helper cell) Th1 and Th17, in peripheral blood were determined by flow cytometry. Result PD-1 expression was observed only in the monocytes of the mucosal lamina propria of UC patients, while PD-L1 was mainly located in both epithelial cells and monocytes on the cell membrane. The expression level of PD-1/PD-L1 in the monocytes and epithelial cells of mucosal lamina propria increased with disease activity (P < 0.05). The percentages of PD-1/T and PD-1/CD4+T in the peripheral blood of moderate UC patients (PD-1/T 12.83 ± 6.15% and PD-1/CD4+T 19.67 ± 9.95%) and severe UC patients (PD-1/T 14.29 ± 5.71% and PD-1/CD4+T 21.63 ± 11.44%) were higher than in mild UC patients (PD-1/T 8.17 ± 2.80% and PD-1/CD4+T 12.44 ± 4.73%; P < 0.05). There were no significant differences in PD-1/CD8+T cells between mild and severe UC patients (P > 0.05). There was a statistically significant difference in the expression level of sPD-L1 between the UC groups and healthy controls, and the expression level of sPD-L1 increased with disease severity (P < 0.05); however, there was no statistically significant difference in sPD-1 expression levels between the UC groups and healthy controls (P > 0.05). The correlation coefficients between Th1 and sPD-L1, PD-1/T, PD-1/CD4+T and PD-1/CD8+T were 0.427, 0.589, 0.486, and 0.329, respectively (P < 0.001). The correlation coefficients between Th17 and sPD-L1, PD-1/T,…
format: application/pdf
format: text/html
creator: Wei Shi
creator: Yu Zhang
creator: Chonghua Hao
creator: Xiaofeng Guo
creator: Qin Yang
creator: Junfang Du
creator: Yabin Hou
creator: Gaigai Cao
creator: Jingru Li
creator: Haijiao Wang
creator: Wei Fang
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Pathology
subject: Medical Genetics
description: doi:10.7717/peerj.15481
publisher: PeerJ Inc.
rights: © 2023 Shi et al.
abstract: Objectives To investigate the expression and significance of programmed cell death protein 1 (PD-1) and programmed cell death ligand-1 (PD-L1) in the mucosal tissues and peripheral blood of patients with ulcerative colitis (UC). Methods Eighty patients with UC were recruited from January 2021 to August 2022 from the Shanxi Province People’s Hospital. PD-1 and PD-L1 expression was assessed by immunohistochemistry in mucosal tissues. An enzyme-linked immunosorbent assay was used to measure soluble PD-1 and PD-L1 levels in peripheral blood serum, and the membrane-bound forms of PD-1 (mPD-1), (T-helper cell) Th1 and Th17, in peripheral blood were determined by flow cytometry. Result PD-1 expression was observed only in the monocytes of the mucosal lamina propria of UC patients, while PD-L1 was mainly located in both epithelial cells and monocytes on the cell membrane. The expression level of PD-1/PD-L1 in the monocytes and epithelial cells of mucosal lamina propria increased with disease activity (P < 0.05). The percentages of PD-1/T and PD-1/CD4+T in the peripheral blood of moderate UC patients (PD-1/T 12.83 ± 6.15% and PD-1/CD4+T 19.67 ± 9.95%) and severe UC patients (PD-1/T 14.29 ± 5.71% and PD-1/CD4+T 21.63 ± 11.44%) were higher than in mild UC patients (PD-1/T 8.17 ± 2.80% and PD-1/CD4+T 12.44 ± 4.73%; P < 0.05). There were no significant differences in PD-1/CD8+T cells between mild and severe UC patients (P > 0.05). There was a statistically significant difference in the expression level of sPD-L1 between the UC groups and healthy controls, and the expression level of sPD-L1 increased with disease severity (P < 0.05); however, there was no statistically significant difference in sPD-1 expression levels between the UC groups and healthy controls (P > 0.05). The correlation coefficients between Th1 and sPD-L1, PD-1/T, PD-1/CD4+T and PD-1/CD8+T were 0.427, 0.589, 0.486, and 0.329, respectively (P < 0.001). The correlation coefficients between Th17 and sPD-L1, PD-1/T,…
bibliographic citation: Shi et al. (2023) The significance of PD-1/PD-L1 imbalance in ulcerative colitis. PeerJ 11:e15481 https://doi.org/10.7717/peerj.15481
date submitted: 2022-12-05
date accepted: 2023-05-09
issued: 2023-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Hao
  given name: Chonghua
author list: Agent
  family name: Guo
  given name: Xiaofeng
author list: Agent
  family name: Yang
  given name: Qin
author list: Agent
  family name: Du
  given name: Junfang
author list: Agent
  family name: Hou
  given name: Yabin
author list: Agent
  family name: Cao
  given name: Gaigai
author list: Agent
  family name: Li
  given name: Jingru
author list: Agent
  family name: Wang
  given name: Haijiao
author list: Agent
  family name: Fang
  given name: Wei
doi: 10.7717/peerj.15481
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-31
copyright: © 2023 Shi et al.
attribution name: Shi et al.

Over-expression of CcMYB24, encoding a R2R3-MYB transcription factor from a high-leaf-number mutant of Cymbidium, increases the number of leaves in Arabidopsis
type: item
type: AcademicArticle
description: Ornamental foliage plants have long been cultivated for their attractive leaves. Variation in leaf traits of ornamental foliage plants is one of the goals in breeding. MYB transcription factors regulate many aspects of leaf development, and thus influence morphological traits of leaves. However, little is known about the function of MYB transcription factors in leaf development of Cymbidium, one of the most economically important ornamental plants in the world. In the present study, a MYB transcription factor, CcMYB24, was identified and the corresponding gene cloned from a new orchid mutant, TRIR-2, which produces more leaves than control plants. The CcMYB24 showed a higher expression level in ‘TRIR-2’ than in control plants, and the protein was located in the nucleus. The sequence of CcMYB24 showed a high similarity with RAX2-like genes which belong to the R2R3-MYB gene family in other Cymbidium plants. Overexpression of CcMYB24 resulted in a phenotype with an increased number of leaves, elevated chlorophyll content, and decreased contents of carotenoids and flavonoids in Arabidopsis. These results provide functional evidence for the role of CcMYB24 in promoting the production of leaves in ‘TRIR-2’. Understanding the role of CcMYB24 in Cymbidium will be beneficial for the molecular breeding of ornamental foliage plants.
format: application/pdf
format: text/html
creator: Gengyun Li
creator: Longjie Cheng
creator: Zhilin Li
creator: Yiran Zhao
creator: Yuying Wang
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15490
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Ornamental foliage plants have long been cultivated for their attractive leaves. Variation in leaf traits of ornamental foliage plants is one of the goals in breeding. MYB transcription factors regulate many aspects of leaf development, and thus influence morphological traits of leaves. However, little is known about the function of MYB transcription factors in leaf development of Cymbidium, one of the most economically important ornamental plants in the world. In the present study, a MYB transcription factor, CcMYB24, was identified and the corresponding gene cloned from a new orchid mutant, TRIR-2, which produces more leaves than control plants. The CcMYB24 showed a higher expression level in ‘TRIR-2’ than in control plants, and the protein was located in the nucleus. The sequence of CcMYB24 showed a high similarity with RAX2-like genes which belong to the R2R3-MYB gene family in other Cymbidium plants. Overexpression of CcMYB24 resulted in a phenotype with an increased number of leaves, elevated chlorophyll content, and decreased contents of carotenoids and flavonoids in Arabidopsis. These results provide functional evidence for the role of CcMYB24 in promoting the production of leaves in ‘TRIR-2’. Understanding the role of CcMYB24 in Cymbidium will be beneficial for the molecular breeding of ornamental foliage plants.
bibliographic citation: Li et al. (2023) Over-expression of CcMYB24, encoding a R2R3-MYB transcription factor from a high-leaf-number mutant of Cymbidium, increases the number of leaves in Arabidopsis. PeerJ 11:e15490 https://doi.org/10.7717/peerj.15490
date submitted: 2023-02-01
date accepted: 2023-05-10
issued: 2023-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Gengyun
author list: Agent
  family name: Cheng
  given name: Longjie
author list: Agent
  family name: Li
  given name: Zhilin
author list: Agent
  family name: Zhao
  given name: Yiran
author list: Agent
  family name: Wang
  given name: Yuying
doi: 10.7717/peerj.15490
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-31
copyright: © 2023 Li et al.
attribution name: Li et al.

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