PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: The weathering process of carbonatite: weathering time
items: Green synthesis of silver nanoparticles using Ocimum sanctum Linn. and its antibacterial activity against multidrug resistant Acinetobacter baumannii
items: Large-sized fossil hamsters from the late Middle Pleistocene Locality 2 of Shanyangzhai, China, and discussion on the validity of Cricetinus and C. varians (Rodentia: Cricetidae)

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

The weathering process of carbonatite: weathering time
type: item
type: AcademicArticle
description: Soil formation by rock weathering is driven by a combination of parent material, climate, organisms, topography, and time. Among these soil-forming factors, time plays a pivotal role in the weathering of carbonatite but it is a challenging factor to study quantitatively. A method for determining the weathering duration of carbonatite based on its weathering characteristics over a century-scale time period has not been clearly established. In this study, we selected abandoned carbonatite tombstones commonly found in the karst region of southwest China for investigation, using the date when the tombstones were erected as the onset of weathering. Chemical weathering indices were used to evaluate the weathering degree of different oxide contents produced by the carbonatite weathering process. In order to explore the weathering characteristics over time, the relationship between weathering duration and weathering degree was established. The results showed the following: (1) magnesium (Mg), aluminum (Al), silicon (Si), iron (Fe), titanium (Ti) are gradually enriched in the carbonatite regolith, and calcium (Ca) is gradually reduced. (2) The chemical indices of alteration (CIA), leaching coefficient (Lc), alumina-to-calcium ratio (AC) and mobiles index (Imob) can be successfully used for evaluation of the weathering degree of the carbonatite in different weathering time periods. (3) During the weathering of carbonatite, the weathering rate is a logarithmic function of time. Our research shows that over a period of more than 100 years of weathering, the carbonatite weathering process is characterized by fast weathering rates and low weathering degree in the early stages, but slow weathering rates in the later stages.
format: application/pdf
format: text/html
creator: Jin Chen
creator: Fangbing Li
creator: Xiangwei Zhao
creator: Yang Wang
creator: Limin Zhang
creator: Ling Feng
creator: Xiong Liu
creator: Lingbin Yan
creator: Lifei Yu
subject: Ecology
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.15793
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Soil formation by rock weathering is driven by a combination of parent material, climate, organisms, topography, and time. Among these soil-forming factors, time plays a pivotal role in the weathering of carbonatite but it is a challenging factor to study quantitatively. A method for determining the weathering duration of carbonatite based on its weathering characteristics over a century-scale time period has not been clearly established. In this study, we selected abandoned carbonatite tombstones commonly found in the karst region of southwest China for investigation, using the date when the tombstones were erected as the onset of weathering. Chemical weathering indices were used to evaluate the weathering degree of different oxide contents produced by the carbonatite weathering process. In order to explore the weathering characteristics over time, the relationship between weathering duration and weathering degree was established. The results showed the following: (1) magnesium (Mg), aluminum (Al), silicon (Si), iron (Fe), titanium (Ti) are gradually enriched in the carbonatite regolith, and calcium (Ca) is gradually reduced. (2) The chemical indices of alteration (CIA), leaching coefficient (Lc), alumina-to-calcium ratio (AC) and mobiles index (Imob) can be successfully used for evaluation of the weathering degree of the carbonatite in different weathering time periods. (3) During the weathering of carbonatite, the weathering rate is a logarithmic function of time. Our research shows that over a period of more than 100 years of weathering, the carbonatite weathering process is characterized by fast weathering rates and low weathering degree in the early stages, but slow weathering rates in the later stages.
bibliographic citation: Chen et al. (2023) The weathering process of carbonatite: weathering time. PeerJ 11:e15793 https://doi.org/10.7717/peerj.15793
date submitted: 2023-02-07
date accepted: 2023-07-04
issued: 2023-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jin
author list: Agent
  family name: Li
  given name: Fangbing
author list: Agent
  family name: Zhao
  given name: Xiangwei
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Zhang
  given name: Limin
author list: Agent
  family name: Feng
  given name: Ling
author list: Agent
  family name: Liu
  given name: Xiong
author list: Agent
  family name: Yan
  given name: Lingbin
author list: Agent
  family name: Yu
  given name: Lifei
doi: 10.7717/peerj.15793
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-31
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Green synthesis of silver nanoparticles using Ocimum sanctum Linn. and its antibacterial activity against multidrug resistant Acinetobacter baumannii
type: item
type: AcademicArticle
description: The biosynthesis of nanoparticles using the green route is an effective strategy in nanotechnology that provides a cost-effective and environmentally friendly alternative to physical and chemical methods. This study aims to prepare an aqueous extract of Ocimum sanctum (O. sanctum)-based silver nanoparticles (AgNPs) through the green route and test their antibacterial activity. The biosynthesized silver nanoparticles were characterised by colour change, UV spectrometric analysis, FTIR, and particle shape and size morphology by SEM and TEM images. The nanoparticles are almost spherical to oval or rod-shaped with smooth surfaces and have a mean particle size in the range of 55 nm with a zeta potential of −2.7 mV. The antibacterial activities of AgNPs evaluated against clinically isolated multidrug-resistant Acinetobacter baumannii (A. baumannii) showed that the AgNPs from O. sanctum are effective in inhibiting A. baumannii growth with a zone of inhibition of 15 mm in the agar well diffusion method and MIC and MBC of 32 µg/mL and 64 µg/mL, respectively. The SEM images of A. baumannii treated with AgNPs revealed damage and rupture in bacterial cells. The time-killing assay by spectrophotometry revealed the time- and dose-dependent killing action of AgNPs against A. baumannii, and the assay at various concentrations and time intervals indicated a statistically significant result in comparison with the positive control colistin at 2 µg/mL (P < 0.05). The cytotoxicity test using the MTT assay protocol showed that prepared nanoparticles of O. sanctum are less toxic against human cell A549. This study opens up a ray of hope to explore the further research in this area and to improve the antimicrobial activities against multidrug resistant bacteria.
format: application/pdf
format: text/html
creator: Deepan Gautam
creator: Karma Gurmey Dolma
creator: Bidita Khandelwal
creator: Madhu Gupta
creator: Meghna Singh
creator: Tooba Mahboob
creator: Anil Teotia
creator: Prasad Thota
creator: Jaydeep Bhattacharya
creator: Ramesh Goyal
creator: Sonia M.R. Oliveira
creator: Maria de Lourdes Pereira
creator: Christophe Wiart
creator: Polrat Wilairatana
creator: Komgrit Eawsakul
creator: Mohammed Rahmatullah
creator: Shanmuga Sundar Saravanabhavan
creator: Veeranoot Nissapatorn
subject: Microbiology
subject: Infectious Diseases
subject: Pharmacology
description: doi:10.7717/peerj.15590
publisher: PeerJ Inc.
rights: © 2023 Gautam et al.
abstract: The biosynthesis of nanoparticles using the green route is an effective strategy in nanotechnology that provides a cost-effective and environmentally friendly alternative to physical and chemical methods. This study aims to prepare an aqueous extract of Ocimum sanctum (O. sanctum)-based silver nanoparticles (AgNPs) through the green route and test their antibacterial activity. The biosynthesized silver nanoparticles were characterised by colour change, UV spectrometric analysis, FTIR, and particle shape and size morphology by SEM and TEM images. The nanoparticles are almost spherical to oval or rod-shaped with smooth surfaces and have a mean particle size in the range of 55 nm with a zeta potential of −2.7 mV. The antibacterial activities of AgNPs evaluated against clinically isolated multidrug-resistant Acinetobacter baumannii (A. baumannii) showed that the AgNPs from O. sanctum are effective in inhibiting A. baumannii growth with a zone of inhibition of 15 mm in the agar well diffusion method and MIC and MBC of 32 µg/mL and 64 µg/mL, respectively. The SEM images of A. baumannii treated with AgNPs revealed damage and rupture in bacterial cells. The time-killing assay by spectrophotometry revealed the time- and dose-dependent killing action of AgNPs against A. baumannii, and the assay at various concentrations and time intervals indicated a statistically significant result in comparison with the positive control colistin at 2 µg/mL (P < 0.05). The cytotoxicity test using the MTT assay protocol showed that prepared nanoparticles of O. sanctum are less toxic against human cell A549. This study opens up a ray of hope to explore the further research in this area and to improve the antimicrobial activities against multidrug resistant bacteria.
bibliographic citation: Gautam et al. (2023) Green synthesis of silver nanoparticles using Ocimum sanctum Linn. and its antibacterial activity against multidrug resistant Acinetobacter baumannii. PeerJ 11:e15590 https://doi.org/10.7717/peerj.15590
date submitted: 2022-09-07
date accepted: 2023-05-29
issued: 2023-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gautam
  given name: Deepan
author list: Agent
  family name: Dolma
  given name: Karma Gurmey
author list: Agent
  family name: Khandelwal
  given name: Bidita
author list: Agent
  family name: Gupta
  given name: Madhu
author list: Agent
  family name: Singh
  given name: Meghna
author list: Agent
  family name: Mahboob
  given name: Tooba
author list: Agent
  family name: Teotia
  given name: Anil
author list: Agent
  family name: Thota
  given name: Prasad
author list: Agent
  family name: Bhattacharya
  given name: Jaydeep
author list: Agent
  family name: Goyal
  given name: Ramesh
author list: Agent
  family name: M.R. Oliveira
  given name: Sonia
author list: Agent
  family name: Pereira
  given name: Maria de Lourdes
author list: Agent
  family name: Wiart
  given name: Christophe
author list: Agent
  family name: Wilairatana
  given name: Polrat
author list: Agent
  family name: Eawsakul
  given name: Komgrit
author list: Agent
  family name: Rahmatullah
  given name: Mohammed
author list: Agent
  family name: Saravanabhavan
  given name: Shanmuga Sundar
author list: Agent
  family name: Nissapatorn
  given name: Veeranoot
doi: 10.7717/peerj.15590
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-28
copyright: ©2023 Gautam et al.
attribution name: Gautam et al.

Large-sized fossil hamsters from the late Middle Pleistocene Locality 2 of Shanyangzhai, China, and discussion on the validity of Cricetinus and C. varians (Rodentia: Cricetidae)
type: item
type: AcademicArticle
description: A detailed morphological description and comparative study were conducted on numerous large-sized hamster remains collected from the late Middle Pleistocene Locality 2 of Shanyangzhai (Syz 2), Hebei Province, China. The comparisons reveal that these fossils are highly similar to the extant Tscherskia triton in size and morphology, including the small degree of alternating between the main opposite cusps on M1-3, the presence of axioloph on M3, and mesolophids on m1-2 that are present but seldom reach the lingual margin of the teeth, among other features. However, minor differences between the two still exist. Consequently, all these fossils are designated as a chronosubspecies of the extant species, T. triton varians comb. nov. The skull and molar morphologies of Cricetinus varians and T. triton were meticulously compared to resolve the long-standing debate regarding the validity of Cricetinus Zdansky, 1928 and C. varians Zdansky, 1928. The findings indicate that the differences between the two are slight; as a result, C. varians can only be considered a chronosubspecies of T. triton, i.e., T. triton varians comb. nov., and Cricetinus should be recognized as a junior synonym of Tscherskia. We tentatively propose that, among the seven species once referred to Cricetinus, C. europaeus, C. gritzai, C. janossyi, and C. koufosi should be reassigned to Tscherskia, while C. beremendensis should be transferred to Allocricetus, and C. mesolophidos to Neocricetodon. Excluding Tscherskia sp. from the Late Pliocene Youhe fauna, there are no reliable Tscherskia fossils in China earlier than the Middle Pleistocene. Based on the current evidence, Tscherskia may have originated from Neocricetodon during the Early Pliocene in Europe and subsequently spread to Asia. T. triton is its sole surviving representative, which now exclusively inhabits East Asia.
format: application/pdf
format: text/html
creator: Kun Xie
creator: Yunxiang Zhang
creator: Yongxiang Li
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.15604
publisher: PeerJ Inc.
rights: © 2023 Xie et al.
abstract: A detailed morphological description and comparative study were conducted on numerous large-sized hamster remains collected from the late Middle Pleistocene Locality 2 of Shanyangzhai (Syz 2), Hebei Province, China. The comparisons reveal that these fossils are highly similar to the extant Tscherskia triton in size and morphology, including the small degree of alternating between the main opposite cusps on M1-3, the presence of axioloph on M3, and mesolophids on m1-2 that are present but seldom reach the lingual margin of the teeth, among other features. However, minor differences between the two still exist. Consequently, all these fossils are designated as a chronosubspecies of the extant species, T. triton varians comb. nov. The skull and molar morphologies of Cricetinus varians and T. triton were meticulously compared to resolve the long-standing debate regarding the validity of Cricetinus Zdansky, 1928 and C. varians Zdansky, 1928. The findings indicate that the differences between the two are slight; as a result, C. varians can only be considered a chronosubspecies of T. triton, i.e., T. triton varians comb. nov., and Cricetinus should be recognized as a junior synonym of Tscherskia. We tentatively propose that, among the seven species once referred to Cricetinus, C. europaeus, C. gritzai, C. janossyi, and C. koufosi should be reassigned to Tscherskia, while C. beremendensis should be transferred to Allocricetus, and C. mesolophidos to Neocricetodon. Excluding Tscherskia sp. from the Late Pliocene Youhe fauna, there are no reliable Tscherskia fossils in China earlier than the Middle Pleistocene. Based on the current evidence, Tscherskia may have originated from Neocricetodon during the Early Pliocene in Europe and subsequently spread to Asia. T. triton is its sole surviving representative, which now exclusively inhabits East Asia.
bibliographic citation: Xie et al. (2023) Large-sized fossil hamsters from the late Middle Pleistocene Locality 2 of Shanyangzhai, China, and discussion on the validity of Cricetinus and C. varians (Rodentia: Cricetidae). PeerJ 11:e15604 https://doi.org/10.7717/peerj.15604
date submitted: 2023-01-07
date accepted: 2023-05-31
issued: 2023-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Kun
author list: Agent
  family name: Zhang
  given name: Yunxiang
author list: Agent
  family name: Li
  given name: Yongxiang
doi: 10.7717/peerj.15604
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-28
copyright: © 2023 Xie et al.
attribution name: Xie et al.

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