PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest
items: The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel
items: Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs
items: Urban biogeography of fungal endophytes across San Francisco
items: Dynamic assessment of the effectiveness of digital game-based literacy training in beginning readers: a cluster randomised controlled trial
items: Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis
items: International fitness scale (IFIS): association with motor performance in children with obesity
items: Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato
items: Expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma
items: The tetrapod fauna of the upper Permian Naobaogou Formation of China: 10. Jimusaria monanensis sp. nov. (Dicynodontia) shows a unique epipterygoid

Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest
type: item
type: AcademicArticle
description: The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
format: application/pdf
format: text/html
creator: Vanessa Carvalho da Silva
creator: Noemi Fernandes
subject: Biodiversity
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.15762
publisher: PeerJ Inc.
rights: © 2023
abstract: The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
bibliographic citation: Carvalho da Silva et al. (2023) Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 11:e15762 https://doi.org/10.7717/peerj.15762
date submitted: 2023-04-17
date accepted: 2023-06-27
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Carvalho da Silva
  given name: Vanessa
author list: Agent
  family name: Fernandes
  given name: Noemi
doi: 10.7717/peerj.15762
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01

The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel
type: item
type: AcademicArticle
description: Objectives The study aims to understand the impact of containment policy and mobility on COVID-19 cases in Chile, Singapore, South Korea and Israel. To provide experience in epidemic prevention and control. Methods Structural equation modeling (SEM) of containment policies, mobility, and COVID-19 cases were used to test and analyze the proposed hypotheses. Results Chile, Israel and Singapore adopted containment strategies, focusing on closure measures. South Korea adopted a mitigation strategy with fewer closure measures, focusing on vaccination and severe case management. There was a significant negative relationship among containment policies, mobility, and COVID-19 cases. Conclusion To control the COVID-19 and slow down the increase of COVID-19 cases, countries can increase the stringency of containment policies when COVID-19 epidemic is more severe. Thus, countries can take measures from the following three aspects: strengthen the risk monitoring, and keep abreast of the COVID-19 risk; adjust closure measures in time and reduce mobility; and strengthen public education on COVID-19 prevention to motivate citizen to consciously adhere to preventive measures.
format: application/pdf
format: text/html
creator: Jun Jiao
creator: Leiyu Shi
creator: Manfei Yang
creator: Junyan Yang
creator: Meiheng Liu
creator: Gang Sun
subject: Global Health
subject: Health Policy
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.15769
publisher: PeerJ Inc.
rights: © 2023 Jiao et al.
abstract: Objectives The study aims to understand the impact of containment policy and mobility on COVID-19 cases in Chile, Singapore, South Korea and Israel. To provide experience in epidemic prevention and control. Methods Structural equation modeling (SEM) of containment policies, mobility, and COVID-19 cases were used to test and analyze the proposed hypotheses. Results Chile, Israel and Singapore adopted containment strategies, focusing on closure measures. South Korea adopted a mitigation strategy with fewer closure measures, focusing on vaccination and severe case management. There was a significant negative relationship among containment policies, mobility, and COVID-19 cases. Conclusion To control the COVID-19 and slow down the increase of COVID-19 cases, countries can increase the stringency of containment policies when COVID-19 epidemic is more severe. Thus, countries can take measures from the following three aspects: strengthen the risk monitoring, and keep abreast of the COVID-19 risk; adjust closure measures in time and reduce mobility; and strengthen public education on COVID-19 prevention to motivate citizen to consciously adhere to preventive measures.
bibliographic citation: Jiao et al. (2023) The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel. PeerJ 11:e15769 https://doi.org/10.7717/peerj.15769
date submitted: 2023-02-16
date accepted: 2023-06-28
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Jun
author list: Agent
  family name: Shi
  given name: Leiyu
author list: Agent
  family name: Yang
  given name: Manfei
author list: Agent
  family name: Yang
  given name: Junyan
author list: Agent
  family name: Liu
  given name: Meiheng
author list: Agent
  family name: Sun
  given name: Gang
doi: 10.7717/peerj.15769
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01
copyright: ©2023 Jiao et al.
attribution name: Jiao et al.

Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs
type: item
type: AcademicArticle
description: Acropora palmata is a foundational yet endangered Caribbean reef-building coral species. The lack of recovery after a disease outbreak and low recruitment has led to widespread use of fragmentation to restore populations. Another option is the production of sexual recruits (settlers) via assisted reproduction to improve the genetic diversity of depleted populations; however, the viability of this approach has not been tested over the long term. In 2011 and 2012, A. palmata larvae were cultured, settled, and the sexual recruits raised in an ex-situ nursery. Survival and growth were monitored over time. In 2014, these two F1 cohorts were moved to an in-situ nursery and after one year, a subset (29 colonies) was outplanted onto Cuevones Reef in the Mexican Caribbean. Growth and survival of these colonies were monitored periodically and compared to colonies that remained in the in-situ nursery. In 2019, samples were collected and analyzed for fertility and fecundity. 53% of the colonies were gravid and fecundity was 5.61 ± 1.91 oocytes and 3.04 ± 0.26 spermaries per polyp. A further 14 colonies from these two cohorts were outplanted in 2020 onto Picudas Reef and monitored during the subsequent spawning seasons. Two years after outplanting onto Picudas Reef, all colonies were alive and spawning of three of these colonies was recorded in 2022 in synchrony with the wild population. Gametes were collected from two colonies and crossed, with 15% fertilization success. Spermatozoa from wild colonies were then added and fertilization success increased to 95%. The resultant larvae followed normal development and symbiont uptake was visible within two weeks. The F2 generation was settled, maintained in an ex-situ nursery, and monitored for survival and growth. Both F1 and F2 generations followed a Type III survival curve with high initial mortality while in the ex-situ nursery and low later-stage mortality. The growth rates of these colonies increased three-fold after outplantin…
format: application/pdf
format: text/html
creator: Sandra Mendoza Quiroz
creator: Aurora Urania Beltrán-Torres
creator: Maria Victoria Grosso-Becerra
creator: Daniela Muñoz Villareal
creator: Raúl Tecalco Rentería
creator: Anastazia T. Banaszak
subject: Developmental Biology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.15813
publisher: PeerJ Inc.
rights: © 2023 Mendoza Quiroz et al.
abstract: Acropora palmata is a foundational yet endangered Caribbean reef-building coral species. The lack of recovery after a disease outbreak and low recruitment has led to widespread use of fragmentation to restore populations. Another option is the production of sexual recruits (settlers) via assisted reproduction to improve the genetic diversity of depleted populations; however, the viability of this approach has not been tested over the long term. In 2011 and 2012, A. palmata larvae were cultured, settled, and the sexual recruits raised in an ex-situ nursery. Survival and growth were monitored over time. In 2014, these two F1 cohorts were moved to an in-situ nursery and after one year, a subset (29 colonies) was outplanted onto Cuevones Reef in the Mexican Caribbean. Growth and survival of these colonies were monitored periodically and compared to colonies that remained in the in-situ nursery. In 2019, samples were collected and analyzed for fertility and fecundity. 53% of the colonies were gravid and fecundity was 5.61 ± 1.91 oocytes and 3.04 ± 0.26 spermaries per polyp. A further 14 colonies from these two cohorts were outplanted in 2020 onto Picudas Reef and monitored during the subsequent spawning seasons. Two years after outplanting onto Picudas Reef, all colonies were alive and spawning of three of these colonies was recorded in 2022 in synchrony with the wild population. Gametes were collected from two colonies and crossed, with 15% fertilization success. Spermatozoa from wild colonies were then added and fertilization success increased to 95%. The resultant larvae followed normal development and symbiont uptake was visible within two weeks. The F2 generation was settled, maintained in an ex-situ nursery, and monitored for survival and growth. Both F1 and F2 generations followed a Type III survival curve with high initial mortality while in the ex-situ nursery and low later-stage mortality. The growth rates of these colonies increased three-fold after outplantin…
bibliographic citation: Mendoza Quiroz et al. (2023) Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs. PeerJ 11:e15813 https://doi.org/10.7717/peerj.15813
date submitted: 2023-01-18
date accepted: 2023-07-07
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza Quiroz
  given name: Sandra
author list: Agent
  family name: Beltrán-Torres
  given name: Aurora Urania
author list: Agent
  family name: Grosso-Becerra
  given name: Maria Victoria
author list: Agent
  family name: Muñoz Villareal
  given name: Daniela
author list: Agent
  family name: Tecalco Rentería
  given name: Raúl
author list: Agent
  family name: Banaszak
  given name: Anastazia T.
doi: 10.7717/peerj.15813
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01
copyright: ©2023 Mendoza Quiroz et al.
attribution name: Mendoza Quiroz et al.

Urban biogeography of fungal endophytes across San Francisco
type: item
type: AcademicArticle
description: In natural and agricultural systems, the plant microbiome–the microbial organisms associated with plant tissues and rhizosphere soils–has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue …
format: application/pdf
format: text/html
creator: Emma Gibson
creator: Naupaka B. Zimmerman
subject: Biogeography
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.15454
publisher: PeerJ Inc.
rights: © 2023 Gibson and Zimmerman
abstract: In natural and agricultural systems, the plant microbiome–the microbial organisms associated with plant tissues and rhizosphere soils–has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue …
bibliographic citation: Gibson et al. (2023) Urban biogeography of fungal endophytes across San Francisco. PeerJ 11:e15454 https://doi.org/10.7717/peerj.15454
date submitted: 2022-03-18
date accepted: 2023-05-03
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gibson
  given name: Emma
author list: Agent
  family name: Zimmerman
  given name: Naupaka B.
doi: 10.7717/peerj.15454
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: ©2023 Gibson and Zimmerman
attribution name: Gibson and Zimmerman

Dynamic assessment of the effectiveness of digital game-based literacy training in beginning readers: a cluster randomised controlled trial
type: item
type: AcademicArticle
description: In this article, we report on a study evaluating the effectiveness of a digital game-based learning (DGBL) tool for beginning readers of Dutch, employing active (math game) and passive (no game) control conditions. This classroom-level randomized controlled trial included 247 first graders from 16 classrooms in the Netherlands and the Dutch-speaking part of Belgium. The intervention consisted of 10 to 15 min of daily playing during school time for a period of up to 7 weeks. Our outcome measures included reading fluency, phonological skills, as well as purpose built in-game proficiency levels to measure written lexical decision and letter speech sound association. After an average of 28 playing sessions, the literacy game improved letter knowledge at a scale generalizable for all children in the classroom compared to the two control conditions. In addition to a small classroom wide benefit in terms of reading fluency, we furthermore discovered that children who scored high on phonological awareness prior to training were more fluent readers after extensive exposure to the reading game. This study is among the first to exploit game generated data for the evaluation of DGBL for literacy interventions.
format: application/pdf
format: text/html
creator: Toivo Glatz
creator: Wim Tops
creator: Elisabeth Borleffs
creator: Ulla Richardson
creator: Natasha Maurits
creator: Annemie Desoete
creator: Ben Maassen
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15499
publisher: PeerJ Inc.
rights: © 2023 Glatz et al.
abstract: In this article, we report on a study evaluating the effectiveness of a digital game-based learning (DGBL) tool for beginning readers of Dutch, employing active (math game) and passive (no game) control conditions. This classroom-level randomized controlled trial included 247 first graders from 16 classrooms in the Netherlands and the Dutch-speaking part of Belgium. The intervention consisted of 10 to 15 min of daily playing during school time for a period of up to 7 weeks. Our outcome measures included reading fluency, phonological skills, as well as purpose built in-game proficiency levels to measure written lexical decision and letter speech sound association. After an average of 28 playing sessions, the literacy game improved letter knowledge at a scale generalizable for all children in the classroom compared to the two control conditions. In addition to a small classroom wide benefit in terms of reading fluency, we furthermore discovered that children who scored high on phonological awareness prior to training were more fluent readers after extensive exposure to the reading game. This study is among the first to exploit game generated data for the evaluation of DGBL for literacy interventions.
bibliographic citation: Glatz et al. (2023) Dynamic assessment of the effectiveness of digital game-based literacy training in beginning readers: a cluster randomised controlled trial. PeerJ 11:e15499 https://doi.org/10.7717/peerj.15499
date submitted: 2017-11-18
date accepted: 2023-05-12
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glatz
  given name: Toivo
author list: Agent
  family name: Tops
  given name: Wim
author list: Agent
  family name: Borleffs
  given name: Elisabeth
author list: Agent
  family name: Richardson
  given name: Ulla
author list: Agent
  family name: Maurits
  given name: Natasha
author list: Agent
  family name: Desoete
  given name: Annemie
author list: Agent
  family name: Maassen
  given name: Ben
doi: 10.7717/peerj.15499
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: © 2023 Glatz et al.
attribution name: Glatz et al.

Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis
type: item
type: AcademicArticle
description: Background and Objective Colorectal cancer (CRC) is a malignant tumor that affects the digestive system. With the increased of modernization of society, the incidence of colorectal cancer has increased throughout the world. As a transcription factor, ELK1 has been widely studied in colorectal cancer. However, there are still many unknown factors regarding its specific mechanism of action.This study explored the role of ELK1 and its downstream pathway in CRC pathogenesis. Methods Based on clinical samples, this study examined miR-31-5p expression in CRC cells and its impact on malignant behaviors (migration, invasion, apoptosis) and autophagy. The promoter sequence of miR-31-5p was obtained from the UCSC database, and ELK1 was identified as its transcription factor. In ELK1-knockdown CRC cells, miR-31-5p was overexpressed, and its response in malignant behaviors and autophagy was analyzed. The target gene CDIP1 was predicted and verified using a dual-luciferase assay. The influence of CDIP1 on malignant behavior in CRC cells was assessed, and CDIP1 siRNA was used as a rescue treatment for miR-31-5p inhibition. The role of ELK1/miR-31-5p in tumor growth was validated in vivo. Results miR-31-5p expression was upregulated in the colorectal cancer tissues and cells. The knockdown of miR-31-5p markedly inhibited cancer cells’ malignant behaviors and mediated autophagy. ELK1 was confirmed to bind with the miR-31-5p promoter and enhance miR-31-5p transcription. miR-31-5p was found to bind with the CDIP1 3’UTR and inhibit CDIP1 expression. CDIP1 siRNA partially rescued the effects of miR-31-5p knockdown on cell metastatic ability, autophagy, and apoptosis. Based on the in vivo experiments, results showed that the ELK1/miR-31-5p axis positively regulated tumor growth in nude mice. Conclusion Our findings indicate that ELK1 regulates the progression of colorectal cancer via an miR-31-5p/CDIP1 axis, and the ELK1/miR-31-5p/CDIP1 axis could be a therapeutic target for colorectal …
format: application/pdf
format: text/html
creator: Guoqiang Yan
creator: Lei Wang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Histology
description: doi:10.7717/peerj.15602
publisher: PeerJ Inc.
rights: © 2023 Yan and Lei
abstract: Background and Objective Colorectal cancer (CRC) is a malignant tumor that affects the digestive system. With the increased of modernization of society, the incidence of colorectal cancer has increased throughout the world. As a transcription factor, ELK1 has been widely studied in colorectal cancer. However, there are still many unknown factors regarding its specific mechanism of action.This study explored the role of ELK1 and its downstream pathway in CRC pathogenesis. Methods Based on clinical samples, this study examined miR-31-5p expression in CRC cells and its impact on malignant behaviors (migration, invasion, apoptosis) and autophagy. The promoter sequence of miR-31-5p was obtained from the UCSC database, and ELK1 was identified as its transcription factor. In ELK1-knockdown CRC cells, miR-31-5p was overexpressed, and its response in malignant behaviors and autophagy was analyzed. The target gene CDIP1 was predicted and verified using a dual-luciferase assay. The influence of CDIP1 on malignant behavior in CRC cells was assessed, and CDIP1 siRNA was used as a rescue treatment for miR-31-5p inhibition. The role of ELK1/miR-31-5p in tumor growth was validated in vivo. Results miR-31-5p expression was upregulated in the colorectal cancer tissues and cells. The knockdown of miR-31-5p markedly inhibited cancer cells’ malignant behaviors and mediated autophagy. ELK1 was confirmed to bind with the miR-31-5p promoter and enhance miR-31-5p transcription. miR-31-5p was found to bind with the CDIP1 3’UTR and inhibit CDIP1 expression. CDIP1 siRNA partially rescued the effects of miR-31-5p knockdown on cell metastatic ability, autophagy, and apoptosis. Based on the in vivo experiments, results showed that the ELK1/miR-31-5p axis positively regulated tumor growth in nude mice. Conclusion Our findings indicate that ELK1 regulates the progression of colorectal cancer via an miR-31-5p/CDIP1 axis, and the ELK1/miR-31-5p/CDIP1 axis could be a therapeutic target for colorectal …
bibliographic citation: Yan et al. (2023) Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis. PeerJ 11:e15602 https://doi.org/10.7717/peerj.15602
date submitted: 2023-03-23
date accepted: 2023-05-30
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Guoqiang
author list: Agent
  family name: Wang
  given name: Lei
doi: 10.7717/peerj.15602
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: ©2023 Yan and Lei
attribution name: Yan and Lei

International fitness scale (IFIS): association with motor performance in children with obesity
type: item
type: AcademicArticle
description: Background Overweight and obesity are defined as abnormal or excessive fat accumulation that presents a risk to health; and compared with their normal-weight peers, these individuals tend to have a lower level of self-confidence, and consequently lower physical activity adherence. Due to these self-perceived barriers, the aim of our study was to evaluate the efficacy of an online training program on self-reported physical fitness (SRPF) in children with obesity (OB). Methods A total of 32 children with OB carried out physical fitness (PF) tests and were asked to complete the International Fitness Enjoyment Scale (IFIS) questionnaire. The physical fitness tests were the Standing Broad Jump (SBJ), the 6-Min Walking Test (6MWT) and the 4 × 10 m sprint test. Children participated in a 3-weekly 60-min training session through Zoom platform. Before the beginning of the training protocol, OB children were compared with normal weight (NW) ones for PF batteries and the IFIS questionnaire. Changes in performances after the training were assessed by paired Student t and Wilcoxon tests. Results After the online training program children increased their performance in 6MWT (mean difference (MD) = 54.93; p < 0.0001) in SBJ (MD = 10.00; p = 0.0001) and in 4 × 10 m sprint test (MD = −0.78; p < 0.0001). No differences were found in children’s physical fitness perception. Discussion Our study highlighted how a structured online training program can lead to improvements in PF of children with OB. Instead, the lack of differences in SRPF after the training suggests interesting questions to be explored on the aspects linked to self-perception. Therefore, even if our training protocol could not directly improve SRPF in children with obesity, the enhancement of their PF could be a starting point for achieving this result with a longer training period and consequently improve PA participation for children with OB.
format: application/pdf
format: text/html
creator: Mariangela Valentina Puci
creator: Caterina Cavallo
creator: Alessandro Gatti
creator: Vittoria Carnevale Pellino
creator: Daniela Lucini
creator: Valeria Calcaterra
creator: Gianvincenzo Zuccotti
creator: Nicola Lovecchio
creator: Matteo Vandoni
subject: Kinesiology
subject: Pediatrics
subject: Public Health
subject: Obesity
subject: Sports Medicine
description: doi:10.7717/peerj.15765
publisher: PeerJ Inc.
rights: © 2023 Puci et al.
abstract: Background Overweight and obesity are defined as abnormal or excessive fat accumulation that presents a risk to health; and compared with their normal-weight peers, these individuals tend to have a lower level of self-confidence, and consequently lower physical activity adherence. Due to these self-perceived barriers, the aim of our study was to evaluate the efficacy of an online training program on self-reported physical fitness (SRPF) in children with obesity (OB). Methods A total of 32 children with OB carried out physical fitness (PF) tests and were asked to complete the International Fitness Enjoyment Scale (IFIS) questionnaire. The physical fitness tests were the Standing Broad Jump (SBJ), the 6-Min Walking Test (6MWT) and the 4 × 10 m sprint test. Children participated in a 3-weekly 60-min training session through Zoom platform. Before the beginning of the training protocol, OB children were compared with normal weight (NW) ones for PF batteries and the IFIS questionnaire. Changes in performances after the training were assessed by paired Student t and Wilcoxon tests. Results After the online training program children increased their performance in 6MWT (mean difference (MD) = 54.93; p < 0.0001) in SBJ (MD = 10.00; p = 0.0001) and in 4 × 10 m sprint test (MD = −0.78; p < 0.0001). No differences were found in children’s physical fitness perception. Discussion Our study highlighted how a structured online training program can lead to improvements in PF of children with OB. Instead, the lack of differences in SRPF after the training suggests interesting questions to be explored on the aspects linked to self-perception. Therefore, even if our training protocol could not directly improve SRPF in children with obesity, the enhancement of their PF could be a starting point for achieving this result with a longer training period and consequently improve PA participation for children with OB.
bibliographic citation: Puci et al. (2023) International fitness scale (IFIS): association with motor performance in children with obesity. PeerJ 11:e15765 https://doi.org/10.7717/peerj.15765
date submitted: 2023-03-31
date accepted: 2023-06-27
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puci
  given name: Mariangela Valentina
author list: Agent
  family name: Cavallo
  given name: Caterina
author list: Agent
  family name: Gatti
  given name: Alessandro
author list: Agent
  family name: Carnevale Pellino
  given name: Vittoria
author list: Agent
  family name: Lucini
  given name: Daniela
author list: Agent
  family name: Calcaterra
  given name: Valeria
author list: Agent
  family name: Zuccotti
  given name: Gianvincenzo
author list: Agent
  family name: Lovecchio
  given name: Nicola
author list: Agent
  family name: Vandoni
  given name: Matteo
doi: 10.7717/peerj.15765
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: © 2023 Puci et al.
attribution name: Puci et al.

Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato
type: item
type: AcademicArticle
description: CRISPR/Cas9-mediated genome editing technology has been widely used for the study of gene function in crops, but the differences between species have led to widely varying genome editing efficiencies. The present study utilized a potato hairy root genetic transformation system and incorporated a rapid assay with GFP as a screening marker. The results clearly demonstrated that salt and osmotic stress induced by NaCl (10 to 50 mM) and mannitol (50 to 200 mM) treatments significantly increased the positive rates of genetic transformation mediated by A. rhizogenes and the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato. However, it was observed that the regeneration of potato roots was partially inhibited as a result. The analysis of CRISPR/Cas9-mediated mutation types revealed that chimeras accounted for the largest proportion, ranging from 62.50% to 100%. Moreover, the application of salt and osmotic stress resulted in an increased probability of null mutations in potato. Notably, the highest rate of null mutations, reaching 37.5%, was observed at a NaCl concentration of 10 mM. Three potential off-target sites were sequenced and no off-targeting was found. In conclusion, the application of appropriate salt and osmotic stress significantly improved the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato, with no observed off-target effects. However, there was a trade-off as the regeneration of potato roots was partially inhibited. Overall, these findings present a new and convenient approach to enhance the genome editing efficiency of the CRISPR/Cas9-mediated gene editing system in potato.
format: application/pdf
format: text/html
creator: Mingwang Ye
creator: Mengfan Yao
creator: Canhui Li
creator: Ming Gong
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15771
publisher: PeerJ Inc.
rights: © 2023 Ye et al.
abstract: CRISPR/Cas9-mediated genome editing technology has been widely used for the study of gene function in crops, but the differences between species have led to widely varying genome editing efficiencies. The present study utilized a potato hairy root genetic transformation system and incorporated a rapid assay with GFP as a screening marker. The results clearly demonstrated that salt and osmotic stress induced by NaCl (10 to 50 mM) and mannitol (50 to 200 mM) treatments significantly increased the positive rates of genetic transformation mediated by A. rhizogenes and the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato. However, it was observed that the regeneration of potato roots was partially inhibited as a result. The analysis of CRISPR/Cas9-mediated mutation types revealed that chimeras accounted for the largest proportion, ranging from 62.50% to 100%. Moreover, the application of salt and osmotic stress resulted in an increased probability of null mutations in potato. Notably, the highest rate of null mutations, reaching 37.5%, was observed at a NaCl concentration of 10 mM. Three potential off-target sites were sequenced and no off-targeting was found. In conclusion, the application of appropriate salt and osmotic stress significantly improved the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato, with no observed off-target effects. However, there was a trade-off as the regeneration of potato roots was partially inhibited. Overall, these findings present a new and convenient approach to enhance the genome editing efficiency of the CRISPR/Cas9-mediated gene editing system in potato.
bibliographic citation: Ye et al. (2023) Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato. PeerJ 11:e15771 https://doi.org/10.7717/peerj.15771
date submitted: 2023-04-19
date accepted: 2023-06-28
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Mingwang
author list: Agent
  family name: Yao
  given name: Mengfan
author list: Agent
  family name: Li
  given name: Canhui
author list: Agent
  family name: Gong
  given name: Ming
doi: 10.7717/peerj.15771
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: © 2023 Ye et al.
attribution name: Ye et al.

Expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma
type: item
type: AcademicArticle
description: Objective To investigate the expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma and adjacent tissues. Methods The expression of COX-2 and NUCB1 and their effects on prognosis were predicted using bioinformatics. Immunohistochemistry was used to identify the expression of two molecules in 56 cases of colorectal adenocarcinoma and the surrounding tissues. The expression of two molecules and their association with clinicopathological variables were examined using the chi-square test. The association between COX-2 and NUCB1 was investigated using the Spearman correlation test. Results The STRING database revealed that COX-2 and NUCB1 were strongly linked. According to the UALCAN and HPA database, COX-2 was upregulated while NUCB1 was downregulated in colorectal adenocarcinoma, both at the protein and gene levels. The OS times for COX-2 and NUCB1 high expression, however, exhibited the same patterns. The rate of positive COX-2 immunohistochemical staining in cancer tissues was 69.64% (39/56), which was significantly higher than the rate in healthy tissues 28.57% (16/56). NUCB1 was expressed positively in cancer tissues at a rate of 64.29% (36/56) compared to just 19.64% (11/56) in neighboring tissues. The positive expression levels of COX-2 and NUCB1 were both closely related to clinical stage, differentiation degree, and lymphatic metastases (P < 0.05). In colorectal cancer, COX-2 and NUCB1 expression were significantly correlated (rs = 0.6312, P < 0.001). Conclusion Both COX-2 and NUCB1 are overexpressed and significantly associated in colorectal adenocarcinoma.
format: application/pdf
format: text/html
creator: Yuanyuan Zhang
creator: Gai Zhang
creator: Jinghua Zhong
creator: An Li
creator: Yanyang Wu
creator: Zhenli Guo
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.15774
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Objective To investigate the expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma and adjacent tissues. Methods The expression of COX-2 and NUCB1 and their effects on prognosis were predicted using bioinformatics. Immunohistochemistry was used to identify the expression of two molecules in 56 cases of colorectal adenocarcinoma and the surrounding tissues. The expression of two molecules and their association with clinicopathological variables were examined using the chi-square test. The association between COX-2 and NUCB1 was investigated using the Spearman correlation test. Results The STRING database revealed that COX-2 and NUCB1 were strongly linked. According to the UALCAN and HPA database, COX-2 was upregulated while NUCB1 was downregulated in colorectal adenocarcinoma, both at the protein and gene levels. The OS times for COX-2 and NUCB1 high expression, however, exhibited the same patterns. The rate of positive COX-2 immunohistochemical staining in cancer tissues was 69.64% (39/56), which was significantly higher than the rate in healthy tissues 28.57% (16/56). NUCB1 was expressed positively in cancer tissues at a rate of 64.29% (36/56) compared to just 19.64% (11/56) in neighboring tissues. The positive expression levels of COX-2 and NUCB1 were both closely related to clinical stage, differentiation degree, and lymphatic metastases (P < 0.05). In colorectal cancer, COX-2 and NUCB1 expression were significantly correlated (rs = 0.6312, P < 0.001). Conclusion Both COX-2 and NUCB1 are overexpressed and significantly associated in colorectal adenocarcinoma.
bibliographic citation: Zhang et al. (2023) Expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma. PeerJ 11:e15774 https://doi.org/10.7717/peerj.15774
date submitted: 2023-05-29
date accepted: 2023-06-29
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yuanyuan
author list: Agent
  family name: Zhang
  given name: Gai
author list: Agent
  family name: Zhong
  given name: Jinghua
author list: Agent
  family name: Li
  given name: An
author list: Agent
  family name: Wu
  given name: Yanyang
author list: Agent
  family name: Guo
  given name: Zhenli
doi: 10.7717/peerj.15774
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: © 2023 Zhang et al.
attribution name: Zhang et al.

The tetrapod fauna of the upper Permian Naobaogou Formation of China: 10. Jimusaria monanensis sp. nov. (Dicynodontia) shows a unique epipterygoid
type: item
type: AcademicArticle
description: Jimusaria is the first reported Chinese dicynodont, previously only known from Xinjiang. Here we refer two specimens from the Naobaogou Formation, Nei Mongol, China to Jimusaria based on the following features: squamosal separated from supraoccipital by tabular, tabular contacting opisthotic, sharp and thin lateral dentary shelf expanding anteriorly into a thick swelling, nasals fused as single element, rod-like medial bar formed by footplate of epipterygoid connecting to the parabasisphenoid and periotic medially. A new species, J. monanensis, is named based on the diagnostic characters on these two specimens such as distinct caniniform buttress lacking posteroventral furrow, naso-frontal suture forming an anterior directed sharp angle, and converging ventral ridges on posterior portion of anterior pterygoid rami. In Jimusaria, the epipterygoid posteromedially contacts the parabasisphenoid and the periotic as a rod-like bar, a unique morphology unknown in any other dicynodonts. This structure probably increases the stability of the palatal complex. A similar structure might also appear in other dicynodonts as a cartilage connection. The new occurrence of Jimusaria increases the diversity of the tetrapod assemblage from the Naobaogou Formation, and further strengthens the connection between the tetrapod faunas from Nei Mongol and Xinjiang. Based on the current record, Jimusaria is one of the few tetrapod genera which survived in the end-Permian mass extinction.
format: application/pdf
format: text/html
creator: Yu-Tai Shi
creator: Jun Liu
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15783
publisher: PeerJ Inc.
rights: © 2023 Shi and Liu
abstract: Jimusaria is the first reported Chinese dicynodont, previously only known from Xinjiang. Here we refer two specimens from the Naobaogou Formation, Nei Mongol, China to Jimusaria based on the following features: squamosal separated from supraoccipital by tabular, tabular contacting opisthotic, sharp and thin lateral dentary shelf expanding anteriorly into a thick swelling, nasals fused as single element, rod-like medial bar formed by footplate of epipterygoid connecting to the parabasisphenoid and periotic medially. A new species, J. monanensis, is named based on the diagnostic characters on these two specimens such as distinct caniniform buttress lacking posteroventral furrow, naso-frontal suture forming an anterior directed sharp angle, and converging ventral ridges on posterior portion of anterior pterygoid rami. In Jimusaria, the epipterygoid posteromedially contacts the parabasisphenoid and the periotic as a rod-like bar, a unique morphology unknown in any other dicynodonts. This structure probably increases the stability of the palatal complex. A similar structure might also appear in other dicynodonts as a cartilage connection. The new occurrence of Jimusaria increases the diversity of the tetrapod assemblage from the Naobaogou Formation, and further strengthens the connection between the tetrapod faunas from Nei Mongol and Xinjiang. Based on the current record, Jimusaria is one of the few tetrapod genera which survived in the end-Permian mass extinction.
bibliographic citation: Shi et al. (2023) The tetrapod fauna of the upper Permian Naobaogou Formation of China: 10. Jimusaria monanensis sp. nov. (Dicynodontia) shows a unique epipterygoid. PeerJ 11:e15783 https://doi.org/10.7717/peerj.15783
date submitted: 2023-05-19
date accepted: 2023-07-03
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yu-Tai
author list: Agent
  family name: Liu
  given name: Jun
doi: 10.7717/peerj.15783
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: © 2023 Shi and Liu
attribution name: Shi and Liu

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