PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Gene synthesis design: a pythonic approach
items: An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity
items: Genotypes and phenotypes in a Wolbachia-ant symbiosis
items: Negative effects of agricultural open-channel irrigation system on vertebrate populations in central Mexico
items: Occurrence and abundance of microplastics in surface water of Songkhla Lagoon
items: Association between the metabolic score for insulin resistance and prostate cancer: a cross-sectional study in Xinjiang
items: Gliding toward an understanding of the origin of flight in bats
items: Escaping the benthos with Coral Reef Arks: effects on coral translocation and fish biomass
items: Study on the inhibitory mechanism of fig leaf extract against postharvest Fusarium in melon
items: Exploring the mediating roles of physical literacy and mindfulness on psychological distress and life satisfaction among college students

Gene synthesis design: a pythonic approach
type: item
type: AcademicArticle
description: Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function.
format: application/pdf
format: text/html
creator: Yunzhuo Hu
creator: Danni Pan
creator: Fei Xu
creator: Bifang Huang
creator: Xuanyang Chen
creator: Shiqiang Lin
subject: Biochemistry
subject: Bioinformatics
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.17750
publisher: PeerJ Inc.
rights: © 2024 Hu et al.
abstract: Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function.
bibliographic citation: Hu et al. (2024) Gene synthesis design: a pythonic approach. PeerJ 12:e17750 https://doi.org/10.7717/peerj.17750
date submitted: 2024-04-21
date accepted: 2024-06-24
issued: 2024-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Yunzhuo
author list: Agent
  family name: Pan
  given name: Danni
author list: Agent
  family name: Xu
  given name: Fei
author list: Agent
  family name: Huang
  given name: Bifang
author list: Agent
  family name: Chen
  given name: Xuanyang
author list: Agent
  family name: Lin
  given name: Shiqiang
doi: 10.7717/peerj.17750
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-26
copyright: ©2024 Hu et al.
attribution name: Hu et al.

An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity
type: item
type: AcademicArticle
description: Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants’ metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.
format: application/pdf
format: text/html
creator: Exsal M. Albores-Méndez
creator: Humberto Carrasco-Vargas
creator: Samary Alaniz Monreal
creator: Rodolfo David Mayen Quinto
creator: Ernesto Diderot López García
creator: Gabriela Gutierrez Salmean
creator: Karen Medina-Quero
creator: Marco A. Vargas-Hernández
creator: Cesar Vicente Ferreira Batista
creator: Yamilé López-Hernández
creator: Robert Winkler
subject: Data Mining and Machine Learning
subject: Obesity
description: doi:10.7717/peerj.17757
publisher: PeerJ Inc.
rights: © 2024 Albores-Méndez et al.
abstract: Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants’ metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.
bibliographic citation: Albores-Méndez et al. (2024) An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity. PeerJ 12:e17757 https://doi.org/10.7717/peerj.17757
date submitted: 2024-04-16
date accepted: 2024-06-25
issued: 2024-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albores-Méndez
  given name: Exsal M.
author list: Agent
  family name: Carrasco-Vargas
  given name: Humberto
author list: Agent
  family name: Alaniz Monreal
  given name: Samary
author list: Agent
  family name: Mayen Quinto
  given name: Rodolfo David
author list: Agent
  family name: López García
  given name: Ernesto Diderot
author list: Agent
  family name: Gutierrez Salmean
  given name: Gabriela
author list: Agent
  family name: Medina-Quero
  given name: Karen
author list: Agent
  family name: Vargas-Hernández
  given name: Marco A.
author list: Agent
  family name: Ferreira Batista
  given name: Cesar Vicente
author list: Agent
  family name: López-Hernández
  given name: Yamilé
author list: Agent
  family name: Winkler
  given name: Robert
doi: 10.7717/peerj.17757
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-26
copyright: ©2024 Albores-Méndez et al.
attribution name: Albores-Méndez et al.

Genotypes and phenotypes in a Wolbachia-ant symbiosis
type: item
type: AcademicArticle
description: The fitness effects of overt parasites, and host resistance to them, are well documented. Most symbionts, however, are more covert and their interactions with their hosts are less well understood. Wolbachia, an intracellular symbiont of insects, is particularly interesting because it is thought to be unaffected by the host immune response and to have fitness effects mostly focussed on sex ratio manipulation. Here, we use quantitative PCR to investigate whether host genotype affects Wolbachia infection density in the leaf-cutting ant Acromyrmex echinatior, and whether Wolbachia infection density may affect host morphology or caste determination. We found significant differences between host colonies in the density of Wolbachia infections, and also smaller intracolonial differences in infection density between host patrilines. However, the density of Wolbachia infections did not appear to affect the morphology of adult queens or likelihood of ants developing as queens. The results suggest that both host genotype and environment influence the host-Wolbachia relationship, but that Wolbachia infections carry little or no physiological effect on the development of larvae in this system.
format: application/pdf
format: text/html
creator: Crystal L. Frost
creator: Rowena Mitchell
creator: Judith Elizabeth Smith
creator: William O.H. Hughes
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.17781
publisher: PeerJ Inc.
rights: © 2024 Frost et al.
abstract: The fitness effects of overt parasites, and host resistance to them, are well documented. Most symbionts, however, are more covert and their interactions with their hosts are less well understood. Wolbachia, an intracellular symbiont of insects, is particularly interesting because it is thought to be unaffected by the host immune response and to have fitness effects mostly focussed on sex ratio manipulation. Here, we use quantitative PCR to investigate whether host genotype affects Wolbachia infection density in the leaf-cutting ant Acromyrmex echinatior, and whether Wolbachia infection density may affect host morphology or caste determination. We found significant differences between host colonies in the density of Wolbachia infections, and also smaller intracolonial differences in infection density between host patrilines. However, the density of Wolbachia infections did not appear to affect the morphology of adult queens or likelihood of ants developing as queens. The results suggest that both host genotype and environment influence the host-Wolbachia relationship, but that Wolbachia infections carry little or no physiological effect on the development of larvae in this system.
bibliographic citation: Frost et al. (2024) Genotypes and phenotypes in a Wolbachia-ant symbiosis. PeerJ 12:e17781 https://doi.org/10.7717/peerj.17781
date submitted: 2018-03-27
date accepted: 2024-06-30
issued: 2024-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frost
  given name: Crystal L.
author list: Agent
  family name: Mitchell
  given name: Rowena
author list: Agent
  family name: Smith
  given name: Judith Elizabeth
author list: Agent
  family name: Hughes
  given name: William O.H.
doi: 10.7717/peerj.17781
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-26
copyright: ©2024 Frost et al.
attribution name: Frost et al.

Negative effects of agricultural open-channel irrigation system on vertebrate populations in central Mexico
type: item
type: AcademicArticle
description: Linear infrastructures such as agricultural irrigation channels produce physical changes and negative impacts to habitats, wildlife populations, communities, and ecosystems. Open irrigation channels act as a pitfall for wildlife and can affect vertebrates of all sizes. Nonetheless, small channels have received relatively little attention by conservation biologists. The objective of this study was to analyze vertebrate species richness and mortality in relation to different sections of an irrigation channel system and the surrounding landscape characteristics. For two years, we conducted monthly surveys along an open-channel irrigation system to estimate its effect on vertebrates through records of dead and alive individuals. We examined the spatial relation of species richness and mortality with transects using a canonical correspondence analysis and chi-squared tests to determine possible variations in the different structures of the channel and seasonality. Further, a landscape diversity index was used to analyze the importance of surrounding habitat structure and composition on these parameters. Most vertebrates (61%) were found dead, small mammals and reptiles were the most affected. Our results indicate that mortality of small vertebrates varies depending on species, structures of the open-channel agricultural irrigation system (i.e., concrete channel and floodgates), seasonality (i.e., wet, and dry), and landscape heterogeneity (i.e., high, medium, and low landscape diversity). The open-channel irrigation system is a threat to populations of small vertebrates in anthropized landscapes, conservation efforts should be directed at protecting water bodies and restructuring the open-channel agricultural irrigation system to avoid mortality of species such as small rodents (M. mexicanus) and reptiles (C. triseriatus, B. imbricata, and Thamnophis spp.).
format: application/pdf
format: text/html
creator: Yuriana Gómez-Ortiz
creator: Hublester Domínguez-Vega
creator: Leroy Soria-Díaz
creator: Tamara Rubio-Blanco
creator: Claudia C. Astudillo-Sánchez
creator: Victor Mundo
creator: Armando Sunny
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.17818
publisher: PeerJ Inc.
rights: © 2024 Gómez-Ortiz et al.
abstract: Linear infrastructures such as agricultural irrigation channels produce physical changes and negative impacts to habitats, wildlife populations, communities, and ecosystems. Open irrigation channels act as a pitfall for wildlife and can affect vertebrates of all sizes. Nonetheless, small channels have received relatively little attention by conservation biologists. The objective of this study was to analyze vertebrate species richness and mortality in relation to different sections of an irrigation channel system and the surrounding landscape characteristics. For two years, we conducted monthly surveys along an open-channel irrigation system to estimate its effect on vertebrates through records of dead and alive individuals. We examined the spatial relation of species richness and mortality with transects using a canonical correspondence analysis and chi-squared tests to determine possible variations in the different structures of the channel and seasonality. Further, a landscape diversity index was used to analyze the importance of surrounding habitat structure and composition on these parameters. Most vertebrates (61%) were found dead, small mammals and reptiles were the most affected. Our results indicate that mortality of small vertebrates varies depending on species, structures of the open-channel agricultural irrigation system (i.e., concrete channel and floodgates), seasonality (i.e., wet, and dry), and landscape heterogeneity (i.e., high, medium, and low landscape diversity). The open-channel irrigation system is a threat to populations of small vertebrates in anthropized landscapes, conservation efforts should be directed at protecting water bodies and restructuring the open-channel agricultural irrigation system to avoid mortality of species such as small rodents (M. mexicanus) and reptiles (C. triseriatus, B. imbricata, and Thamnophis spp.).
bibliographic citation: Gómez-Ortiz et al. (2024) Negative effects of agricultural open-channel irrigation system on vertebrate populations in central Mexico. PeerJ 12:e17818 https://doi.org/10.7717/peerj.17818
date submitted: 2023-12-04
date accepted: 2024-07-05
issued: 2024-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gómez-Ortiz
  given name: Yuriana
author list: Agent
  family name: Domínguez-Vega
  given name: Hublester
author list: Agent
  family name: Soria-Díaz
  given name: Leroy
author list: Agent
  family name: Rubio-Blanco
  given name: Tamara
author list: Agent
  family name: Astudillo-Sánchez
  given name: Claudia C.
author list: Agent
  family name: Mundo
  given name: Victor
author list: Agent
  family name: Sunny
  given name: Armando
doi: 10.7717/peerj.17818
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-26
copyright: ©2024 Gómez-Ortiz et al.
attribution name: Gómez-Ortiz et al.

Occurrence and abundance of microplastics in surface water of Songkhla Lagoon
type: item
type: AcademicArticle
description: Background Microplastic (MP) pollution is now a global critical issue and has been the subject of considerable worry for multiple various types of habitats, notably in lagoons which are coastal areas connected to the ocean. MPs are of concern, particularly because floating MP in surface water can be ingested by a number of marine organisms. There are several lagoons along Southeast Asia’s coastline, but Songkhla Lagoon is Thailand’s only exit with a rich biodiversity. To date, there has been little research undertaken on MP in this lagoon, so there is a pressing need to learn more about the presence of MP in the lagoon’s water. Methods We investigate MPs in the surface water of Songkhla Lagoon, Thailand. Sampling took place at ten stations in the lagoon during the wet season in December 2022 and the dry season in February 2023. Samples were digested with hydrogen peroxide to remove organic matter followed by density separation using saturated sodium chloride. MPs were visually examined under a stereo microscope to describe and determine the shape, size, and color. Polymer type was identified using a micro Fourier transform infrared (FTIR) spectrometer. Moreover, the in-situ of water quality of the surface water was measured using a multi-parameter probe. A Mann-Whitney U test was performed to investigate the variations in MP levels and water quality parameters between the wet and dry seasons. Correlation analysis (Spearman rho) was used to determine the significance of correlations between MP and water quality (p < 0.05). Results MPs were detected at all ten of the sites sampled. The most abundant MPs were small size class (<500 µm, primarily consisting of fibers). Five types of polymers were seen in surface water, including polyethylene terephthalate, rayon, polypropylene, polyester, and poly (ethylene:propylene). Rayon and polyester were the dominant polymers. Additionally, the most dominant color of MPs in the wet and dry season was black and blue, respectively. …
format: application/pdf
format: text/html
creator: Siriporn Pradit
creator: Prakrit Noppradit
creator: Kittiwara Sornplang
creator: Preyanuch Jitkaew
creator: Thanakorn Jiwarungrueangkul
creator: Dudsadee Muenhor
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.17822
publisher: PeerJ Inc.
rights: © 2024 Pradit et al.
abstract: Background Microplastic (MP) pollution is now a global critical issue and has been the subject of considerable worry for multiple various types of habitats, notably in lagoons which are coastal areas connected to the ocean. MPs are of concern, particularly because floating MP in surface water can be ingested by a number of marine organisms. There are several lagoons along Southeast Asia’s coastline, but Songkhla Lagoon is Thailand’s only exit with a rich biodiversity. To date, there has been little research undertaken on MP in this lagoon, so there is a pressing need to learn more about the presence of MP in the lagoon’s water. Methods We investigate MPs in the surface water of Songkhla Lagoon, Thailand. Sampling took place at ten stations in the lagoon during the wet season in December 2022 and the dry season in February 2023. Samples were digested with hydrogen peroxide to remove organic matter followed by density separation using saturated sodium chloride. MPs were visually examined under a stereo microscope to describe and determine the shape, size, and color. Polymer type was identified using a micro Fourier transform infrared (FTIR) spectrometer. Moreover, the in-situ of water quality of the surface water was measured using a multi-parameter probe. A Mann-Whitney U test was performed to investigate the variations in MP levels and water quality parameters between the wet and dry seasons. Correlation analysis (Spearman rho) was used to determine the significance of correlations between MP and water quality (p < 0.05). Results MPs were detected at all ten of the sites sampled. The most abundant MPs were small size class (<500 µm, primarily consisting of fibers). Five types of polymers were seen in surface water, including polyethylene terephthalate, rayon, polypropylene, polyester, and poly (ethylene:propylene). Rayon and polyester were the dominant polymers. Additionally, the most dominant color of MPs in the wet and dry season was black and blue, respectively. …
bibliographic citation: Pradit et al. (2024) Occurrence and abundance of microplastics in surface water of Songkhla Lagoon. PeerJ 12:e17822 https://doi.org/10.7717/peerj.17822
date submitted: 2024-01-02
date accepted: 2024-07-07
issued: 2024-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pradit
  given name: Siriporn
author list: Agent
  family name: Noppradit
  given name: Prakrit
author list: Agent
  family name: Sornplang
  given name: Kittiwara
author list: Agent
  family name: Jitkaew
  given name: Preyanuch
author list: Agent
  family name: Jiwarungrueangkul
  given name: Thanakorn
author list: Agent
  family name: Muenhor
  given name: Dudsadee
doi: 10.7717/peerj.17822
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-26
copyright: © 2024 Pradit et al.
attribution name: Pradit et al.

Association between the metabolic score for insulin resistance and prostate cancer: a cross-sectional study in Xinjiang
type: item
type: AcademicArticle
description: Background Insulin resistance is associated with the development and progression of various cancers. However, the epidemiological evidence for the association between insulin resistance and prostate cancer is still limited. Objectives To investigate the associations between insulin resistance and prostate cancer prevalence. Methods A total of 451 patients who were pathologically diagnosed with prostate cancer in the First Affiliated Hospital of Xinjiang Medical University were selected as the case population; 1,863 participants who conducted physical examinations during the same period were selected as the control population. The metabolic score for insulin resistance (METS-IR) was calculated as a substitute indicator for evaluating insulin resistance. The Chi-square test and Mann-Whitney U test were performed to compare the basic information of the case population and control population. Univariate and multivariate logistic regression analyses to define factors that may influence prostate cancer prevalence. The generalized additive model (GAM) was applied to fit the relationship between METS-IR and prostate cancer. Interaction tests based on generalized additive model (GAM) and contour plots were also carried out to analyze the interaction effect of each factor with METS-IR on prostate cancer. Results METS-IR as both a continuous and categorical variable suggested that METS-IR was negatively associated with prostate cancer prevalence. Smoothed curves fitted by generalized additive model (GAM) displayed a nonlinear correlation between METS-IR and prostate cancer prevalence (P < 0.001), and presented that METS-IR was negatively associated with the odds ratio (OR) of prostate cancer. The interaction based on the generalized additive model (GAM) revealed that METS-IR interacted with low-density lipoprotein cholesterol (LDL-c) to influence the prostate cancer prevalence (P = 0.004). Contour plots showed that the highest prevalence probability of prostate cancer was achi…
format: application/pdf
format: text/html
creator: Jinru Wang
creator: Aireti Apizi
creator: Ning Tao
creator: Hengqing An
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.17827
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background Insulin resistance is associated with the development and progression of various cancers. However, the epidemiological evidence for the association between insulin resistance and prostate cancer is still limited. Objectives To investigate the associations between insulin resistance and prostate cancer prevalence. Methods A total of 451 patients who were pathologically diagnosed with prostate cancer in the First Affiliated Hospital of Xinjiang Medical University were selected as the case population; 1,863 participants who conducted physical examinations during the same period were selected as the control population. The metabolic score for insulin resistance (METS-IR) was calculated as a substitute indicator for evaluating insulin resistance. The Chi-square test and Mann-Whitney U test were performed to compare the basic information of the case population and control population. Univariate and multivariate logistic regression analyses to define factors that may influence prostate cancer prevalence. The generalized additive model (GAM) was applied to fit the relationship between METS-IR and prostate cancer. Interaction tests based on generalized additive model (GAM) and contour plots were also carried out to analyze the interaction effect of each factor with METS-IR on prostate cancer. Results METS-IR as both a continuous and categorical variable suggested that METS-IR was negatively associated with prostate cancer prevalence. Smoothed curves fitted by generalized additive model (GAM) displayed a nonlinear correlation between METS-IR and prostate cancer prevalence (P < 0.001), and presented that METS-IR was negatively associated with the odds ratio (OR) of prostate cancer. The interaction based on the generalized additive model (GAM) revealed that METS-IR interacted with low-density lipoprotein cholesterol (LDL-c) to influence the prostate cancer prevalence (P = 0.004). Contour plots showed that the highest prevalence probability of prostate cancer was achi…
bibliographic citation: Wang et al. (2024) Association between the metabolic score for insulin resistance and prostate cancer: a cross-sectional study in Xinjiang. PeerJ 12:e17827 https://doi.org/10.7717/peerj.17827
date submitted: 2024-04-22
date accepted: 2024-07-08
issued: 2024-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jinru
author list: Agent
  family name: Apizi
  given name: Aireti
author list: Agent
  family name: Tao
  given name: Ning
author list: Agent
  family name: An
  given name: Hengqing
doi: 10.7717/peerj.17827
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-26
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Gliding toward an understanding of the origin of flight in bats
type: item
type: AcademicArticle
description: Bats are the only mammals capable of powered flight and have correspondingly specialized body plans, particularly in their limb morphology. The origin of bat flight is still not fully understood due to an uninformative fossil record but, from the perspective of a functional transition, it is widely hypothesized that bats evolved from gliding ancestors. Here, we test predictions of the gliding-to-flying hypothesis of the origin of bat flight by using phylogenetic comparative methods to model the evolution of forelimb and hindlimb traits on a dataset spanning four extinct bats and 231 extant mammals with diverse locomotor modes. Our results reveal that gliders exhibit adaptive trait optima (1) toward relatively elongate forelimbs that are intermediate between those of bats and non-gliding arborealists, and (2) toward relatively narrower but not longer hindlimbs that are intermediate between those of non-gliders and bats. We propose an adaptive landscape based on limb length and width optimal trends derived from our modeling analyses. Our results support a hypothetical evolutionary pathway wherein glider-like postcranial morphology precedes a bat-like morphology adapted to powered-flight, setting a foundation for future developmental, biomechanical, and evolutionary research to test this idea.
format: application/pdf
format: text/html
creator: Abigail E. Burtner
creator: David M. Grossnickle
creator: Sharlene E. Santana
creator: Chris J. Law
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17824
publisher: PeerJ Inc.
rights: © 2024 Burtner et al.
abstract: Bats are the only mammals capable of powered flight and have correspondingly specialized body plans, particularly in their limb morphology. The origin of bat flight is still not fully understood due to an uninformative fossil record but, from the perspective of a functional transition, it is widely hypothesized that bats evolved from gliding ancestors. Here, we test predictions of the gliding-to-flying hypothesis of the origin of bat flight by using phylogenetic comparative methods to model the evolution of forelimb and hindlimb traits on a dataset spanning four extinct bats and 231 extant mammals with diverse locomotor modes. Our results reveal that gliders exhibit adaptive trait optima (1) toward relatively elongate forelimbs that are intermediate between those of bats and non-gliding arborealists, and (2) toward relatively narrower but not longer hindlimbs that are intermediate between those of non-gliders and bats. We propose an adaptive landscape based on limb length and width optimal trends derived from our modeling analyses. Our results support a hypothetical evolutionary pathway wherein glider-like postcranial morphology precedes a bat-like morphology adapted to powered-flight, setting a foundation for future developmental, biomechanical, and evolutionary research to test this idea.
bibliographic citation: Burtner et al. (2024) Gliding toward an understanding of the origin of flight in bats. PeerJ 12:e17824 https://doi.org/10.7717/peerj.17824
date submitted: 2024-02-28
date accepted: 2024-07-08
issued: 2024-07-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burtner
  given name: Abigail E.
author list: Agent
  family name: M. Grossnickle
  given name: David
author list: Agent
  family name: Santana
  given name: Sharlene E.
author list: Agent
  family name: Law
  given name: Chris J.
doi: 10.7717/peerj.17824
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-25
copyright: © 2024 Burtner et al.
attribution name: Burtner et al.

Escaping the benthos with Coral Reef Arks: effects on coral translocation and fish biomass
type: item
type: AcademicArticle
description: Anthropogenic stressors like overfishing, land based runoff, and increasing temperatures cause the degradation of coral reefs, leading to the loss of corals and other calcifiers, increases in competitive fleshy algae, and increases in microbial pathogen abundance and hypoxia. To test the hypothesis that corals would be healthier by moving them off the benthos, a common garden experiment was conducted in which corals were translocated to midwater geodesic spheres (hereafter called Coral Reef Arks or Arks). Coral fragments translocated to the Arks survived significantly longer than equivalent coral fragments translocated to Control sites (i.e., benthos at the same depth). Over time, average living coral surface area and volume were higher on the Arks than the Control sites. The abundance and biomass of fish were also generally higher on the Arks compared to the Control sites, with more piscivorous fish on the Arks. The addition of Autonomous Reef Monitoring Structures (ARMS), which served as habitat for sessile and motile reef-associated organisms, also generally significantly increased fish associated with the Arks. Overall, the Arks increased translocated coral survivorship and growth, and exhibited knock-on effects such as higher fish abundance.
format: application/pdf
format: text/html
creator: Jessica Carilli
creator: Jason Baer
creator: Jenna Marie Aquino
creator: Mark Little
creator: Bart Chadwick
creator: Forest Rohwer
creator: Gunther Rosen
creator: Anneke van der Geer
creator: Andrés Sánchez-Quinto
creator: Ashton Ballard
creator: Aaron C. Hartmann
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.17640
publisher: PeerJ Inc.
rights: © 2024
abstract: Anthropogenic stressors like overfishing, land based runoff, and increasing temperatures cause the degradation of coral reefs, leading to the loss of corals and other calcifiers, increases in competitive fleshy algae, and increases in microbial pathogen abundance and hypoxia. To test the hypothesis that corals would be healthier by moving them off the benthos, a common garden experiment was conducted in which corals were translocated to midwater geodesic spheres (hereafter called Coral Reef Arks or Arks). Coral fragments translocated to the Arks survived significantly longer than equivalent coral fragments translocated to Control sites (i.e., benthos at the same depth). Over time, average living coral surface area and volume were higher on the Arks than the Control sites. The abundance and biomass of fish were also generally higher on the Arks compared to the Control sites, with more piscivorous fish on the Arks. The addition of Autonomous Reef Monitoring Structures (ARMS), which served as habitat for sessile and motile reef-associated organisms, also generally significantly increased fish associated with the Arks. Overall, the Arks increased translocated coral survivorship and growth, and exhibited knock-on effects such as higher fish abundance.
bibliographic citation: Carilli et al. (2024) Escaping the benthos with Coral Reef Arks: effects on coral translocation and fish biomass. PeerJ 12:e17640 https://doi.org/10.7717/peerj.17640
date submitted: 2024-01-11
date accepted: 2024-06-06
issued: 2024-07-25
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Carilli
  given name: Jessica
author list: Agent
  family name: Baer
  given name: Jason
author list: Agent
  family name: Aquino
  given name: Jenna Marie
author list: Agent
  family name: Little
  given name: Mark
author list: Agent
  family name: Chadwick
  given name: Bart
author list: Agent
  family name: Rohwer
  given name: Forest
author list: Agent
  family name: Rosen
  given name: Gunther
author list: Agent
  family name: van der Geer
  given name: Anneke
author list: Agent
  family name: Sánchez-Quinto
  given name: Andrés
author list: Agent
  family name: Ballard
  given name: Ashton
author list: Agent
  family name: Hartmann
  given name: Aaron C.
doi: 10.7717/peerj.17640
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-25

Study on the inhibitory mechanism of fig leaf extract against postharvest Fusarium in melon
type: item
type: AcademicArticle
description: The objective of this study was to explore the fungistatic mechanism of fig leaf extract against Fusarium and to provide a theoretical basis for the development of new plant-derived fungicides. Methods The fungistaticity of fig leaf extract were analyzed by the ring of inhibition method. Fusarium equiseti was selected as the target for analyzing its fungistatic mechanism in terms of mycelial morphology, ultrastructure, cell membrane permeability, membrane plasma peroxidation, reactive oxygen species (ROS) content and changes in the activity of protective enzymes. The effect of this extract was verified in melon, and its components were determined by metabolite analysis using ultraperformance liquid chromatography‒mass spectrometry (UPLC‒MS). Results Fig leaf extract had an obvious inhibitory effect on Fusarium, and the difference was significant (P < 0.05) or highly significant (P < 0.01). Scanning and transmission electron microscopy revealed that F. equiseti hyphae exhibited obvious folding, twisting and puckering phenomena, resulting in an increase in the cytoplasmic leakage of spores, interstitial plasma, and the concentration of the nucleus, which seriously damaged the integrity of the fungal cell membrane. This phenomenon was confirmed by propidium iodide (PI) and fluorescein diacetate (FAD) staining, cell membrane permeability and malondialdehyde (MDA) content. Fig leaf extract also induced the mycelium to produce excessive H2O2,which led to lipid peroxidation of the cell membrane, promoted the accumulation of MDA, accelerated protein hydrolysis, induced an increase in antioxidant enzyme activity, and disrupted the balance of ROS metabolism; these findings showed that fungal growth was inhibited, which was verified in melons. A total of 1,540 secondary metabolites were detected by broad-targeted metabolomics, among which the fungistatic active substances flavonoids (15.45%), phenolic acids (15%), and alkaloids (10.71%) accounted for a high percentage and the …
format: application/pdf
format: text/html
creator: Jun Yao
creator: Xinli Geng
creator: Heyun Zheng
creator: Zhiwei Wang
creator: Cuihuan Zhang
creator: Jing Li
creator: Zaituna Maimaiti
creator: Yong Qin
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Mycology
description: doi:10.7717/peerj.17654
publisher: PeerJ Inc.
rights: © 2024 Yao et al.
abstract: The objective of this study was to explore the fungistatic mechanism of fig leaf extract against Fusarium and to provide a theoretical basis for the development of new plant-derived fungicides. Methods The fungistaticity of fig leaf extract were analyzed by the ring of inhibition method. Fusarium equiseti was selected as the target for analyzing its fungistatic mechanism in terms of mycelial morphology, ultrastructure, cell membrane permeability, membrane plasma peroxidation, reactive oxygen species (ROS) content and changes in the activity of protective enzymes. The effect of this extract was verified in melon, and its components were determined by metabolite analysis using ultraperformance liquid chromatography‒mass spectrometry (UPLC‒MS). Results Fig leaf extract had an obvious inhibitory effect on Fusarium, and the difference was significant (P < 0.05) or highly significant (P < 0.01). Scanning and transmission electron microscopy revealed that F. equiseti hyphae exhibited obvious folding, twisting and puckering phenomena, resulting in an increase in the cytoplasmic leakage of spores, interstitial plasma, and the concentration of the nucleus, which seriously damaged the integrity of the fungal cell membrane. This phenomenon was confirmed by propidium iodide (PI) and fluorescein diacetate (FAD) staining, cell membrane permeability and malondialdehyde (MDA) content. Fig leaf extract also induced the mycelium to produce excessive H2O2,which led to lipid peroxidation of the cell membrane, promoted the accumulation of MDA, accelerated protein hydrolysis, induced an increase in antioxidant enzyme activity, and disrupted the balance of ROS metabolism; these findings showed that fungal growth was inhibited, which was verified in melons. A total of 1,540 secondary metabolites were detected by broad-targeted metabolomics, among which the fungistatic active substances flavonoids (15.45%), phenolic acids (15%), and alkaloids (10.71%) accounted for a high percentage and the …
bibliographic citation: Yao et al. (2024) Study on the inhibitory mechanism of fig leaf extract against postharvest Fusarium in melon. PeerJ 12:e17654 https://doi.org/10.7717/peerj.17654
date submitted: 2024-01-30
date accepted: 2024-06-07
issued: 2024-07-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Jun
author list: Agent
  family name: Geng
  given name: Xinli
author list: Agent
  family name: Zheng
  given name: Heyun
author list: Agent
  family name: Wang
  given name: Zhiwei
author list: Agent
  family name: Zhang
  given name: Cuihuan
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Maimaiti
  given name: Zaituna
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.17654
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-25
copyright: © 2024 Yao et al.
attribution name: Yao et al.

Exploring the mediating roles of physical literacy and mindfulness on psychological distress and life satisfaction among college students
type: item
type: AcademicArticle
description: Background Psychological distress has been a growing challenge to healthy living worldwide. Special attention has been concentrated on examining the cost of psychological distress on the life satisfaction of college students who are vulnerable groups coping with the challenge. The purpose of this study is to explore the roles of physical literacy (PL) and mindfulness in mediating the impact of psychological distress on life satisfaction among college students in China. Methods A sample of 653 students from six universities across three cities in China participated in an online survey, which included measures of PL, mindfulness, life satisfaction, as well as stress, anxiety, and depression levels. Structural equation modeling (SEM) was implemented to analyze the survey data. Results The findings of the SEM analysis demonstrated an acceptable model fit (X2/df = 3.63, CFI = 0.951, TLI = 0.940, RMSEA = 0.068, 90% CI = [0.060, 0.075], SRMR = 0.051) with a large effect size (R2 = 0.36) for life satisfaction, indicating that 36% of the variation in life satisfaction could be explained by the model. In addition, significant partial-mediation effects of PL and mindfulness were observed in the relationship between psychological distress and life satisfaction. These findings provide empirical support for the notion that interventions targeting PL and mindfulness practices may effectively enhance well-being and alleviate psychological distress among college students. Furthermore, this study suggests that integrating PL and mindfulness components into physical education and activity programs could be beneficial in meeting individuals’ holistic health needs.
format: application/pdf
format: text/html
creator: Wencong Kan
creator: Fan Huang
creator: Menglin Xu
creator: Xiangyun Shi
creator: Zengyin Yan
creator: Mehmet Türegün
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.17741
publisher: PeerJ Inc.
rights: © 2024 Kan et al.
abstract: Background Psychological distress has been a growing challenge to healthy living worldwide. Special attention has been concentrated on examining the cost of psychological distress on the life satisfaction of college students who are vulnerable groups coping with the challenge. The purpose of this study is to explore the roles of physical literacy (PL) and mindfulness in mediating the impact of psychological distress on life satisfaction among college students in China. Methods A sample of 653 students from six universities across three cities in China participated in an online survey, which included measures of PL, mindfulness, life satisfaction, as well as stress, anxiety, and depression levels. Structural equation modeling (SEM) was implemented to analyze the survey data. Results The findings of the SEM analysis demonstrated an acceptable model fit (X2/df = 3.63, CFI = 0.951, TLI = 0.940, RMSEA = 0.068, 90% CI = [0.060, 0.075], SRMR = 0.051) with a large effect size (R2 = 0.36) for life satisfaction, indicating that 36% of the variation in life satisfaction could be explained by the model. In addition, significant partial-mediation effects of PL and mindfulness were observed in the relationship between psychological distress and life satisfaction. These findings provide empirical support for the notion that interventions targeting PL and mindfulness practices may effectively enhance well-being and alleviate psychological distress among college students. Furthermore, this study suggests that integrating PL and mindfulness components into physical education and activity programs could be beneficial in meeting individuals’ holistic health needs.
bibliographic citation: Kan et al. (2024) Exploring the mediating roles of physical literacy and mindfulness on psychological distress and life satisfaction among college students. PeerJ 12:e17741 https://doi.org/10.7717/peerj.17741
date submitted: 2024-03-29
date accepted: 2024-06-24
issued: 2024-07-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kan
  given name: Wencong
author list: Agent
  family name: Huang
  given name: Fan
author list: Agent
  family name: Xu
  given name: Menglin
author list: Agent
  family name: Shi
  given name: Xiangyun
author list: Agent
  family name: Yan
  given name: Zengyin
author list: Agent
  family name: Türegün
  given name: Mehmet
doi: 10.7717/peerj.17741
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-25
copyright: ©2024 Kan et al.
attribution name: Kan et al.

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