PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data
items: Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology
items: Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan
items: Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods
items: Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma
items: Promoting effect of rapamycin on osteogenic differentiation of maxillary sinus membrane stem cells
items: Structural variation and evolution of chloroplast tRNAs in green algae
items: T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia
items: High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study
items: Changes in the stoichiometry of Castanopsis fargesii along an elevation gradient in a Chinese subtropical forest

Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data
type: item
type: AcademicArticle
description: Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.
format: application/pdf
format: text/html
creator: Sofia G. Seabra
creator: Ana S.B. Rodrigues
creator: Sara E. Silva
creator: Ana Carina Neto
creator: Francisco Pina-Martins
creator: Eduardo Marabuto
creator: Vinton Thompson
creator: Michael R. Wilson
creator: Selçuk Yurtsever
creator: Antti Halkka
creator: Maria Teresa Rebelo
creator: Paulo A.V. Borges
creator: José A. Quartau
creator: Chris D. Jiggins
creator: Octávio S. Paulo
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11425
publisher: PeerJ Inc.
rights: © 2021 Seabra et al.
abstract: Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.
bibliographic citation: Seabra et al. (2021) Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data. PeerJ 9:e11425 https://doi.org/10.7717/peerj.11425
date submitted: 2020-11-30
date accepted: 2021-04-17
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Seabra
  given name: Sofia G.
author list: Agent
  family name: Rodrigues
  given name: Ana S.B.
author list: Agent
  family name: Silva
  given name: Sara E.
author list: Agent
  family name: Neto
  given name: Ana Carina
author list: Agent
  family name: Pina-Martins
  given name: Francisco
author list: Agent
  family name: Marabuto
  given name: Eduardo
author list: Agent
  family name: Thompson
  given name: Vinton
author list: Agent
  family name: Wilson
  given name: Michael R.
author list: Agent
  family name: Yurtsever
  given name: Selçuk
author list: Agent
  family name: Halkka
  given name: Antti
author list: Agent
  family name: Rebelo
  given name: Maria Teresa
author list: Agent
  family name: Borges
  given name: Paulo A.V.
author list: Agent
  family name: Quartau
  given name: José A.
author list: Agent
  family name: Jiggins
  given name: Chris D.
author list: Agent
  family name: Paulo
  given name: Octávio S.
doi: 10.7717/peerj.11425
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Seabra et al.
attribution name: Seabra et al.

Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology
type: item
type: AcademicArticle
description: Understanding landscape as a socio-ecological system where systematic interactions occur among diverse ecosystems and human society is necessary for a sustainable landscape and resource management. However, many countries with rapid economic growth, including South Korea, depend on conventional planning and policy decisions to meet increasing demands for the use of specific natural resources. Such resource-oriented planning and policy which neglect considerations for the surrounding landscape can result in conflicts of interest and regulation. We designed a landscape conservation value (LCV) map of Jeju Island, Korea to overcome rising managerial and policy issues with the provision of systematic perspectives of landscape. With a consideration for natural and human-modified characteristics of the landscape, we used landform and land cover data to create fundamental landscape types. Then, the LCV was assigned to each type by a board of landscape experts. Within a study region, we observed relatively high values in registered protected areas and unique landscapes, and areas where high and low values are aligned. The resultant LCV map can identify areas that potentially require an integrated approach to prevent adverse effects caused by a conventional approach.
format: application/pdf
format: text/html
creator: Baysok Jun
creator: Ilkwon Kim
creator: Jihoon Shin
creator: Hyuksoo Kwon
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.11449
publisher: PeerJ Inc.
rights: © 2021 Jun et al.
abstract: Understanding landscape as a socio-ecological system where systematic interactions occur among diverse ecosystems and human society is necessary for a sustainable landscape and resource management. However, many countries with rapid economic growth, including South Korea, depend on conventional planning and policy decisions to meet increasing demands for the use of specific natural resources. Such resource-oriented planning and policy which neglect considerations for the surrounding landscape can result in conflicts of interest and regulation. We designed a landscape conservation value (LCV) map of Jeju Island, Korea to overcome rising managerial and policy issues with the provision of systematic perspectives of landscape. With a consideration for natural and human-modified characteristics of the landscape, we used landform and land cover data to create fundamental landscape types. Then, the LCV was assigned to each type by a board of landscape experts. Within a study region, we observed relatively high values in registered protected areas and unique landscapes, and areas where high and low values are aligned. The resultant LCV map can identify areas that potentially require an integrated approach to prevent adverse effects caused by a conventional approach.
bibliographic citation: Jun et al. (2021) Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology. PeerJ 9:e11449 https://doi.org/10.7717/peerj.11449
date submitted: 2020-11-12
date accepted: 2021-04-22
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jun
  given name: Baysok
author list: Agent
  family name: Kim
  given name: Ilkwon
author list: Agent
  family name: Shin
  given name: Jihoon
author list: Agent
  family name: Kwon
  given name: Hyuksoo
doi: 10.7717/peerj.11449
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: © 2021 Jun et al.
attribution name: Jun et al.

Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan
type: item
type: AcademicArticle
description: Understanding the anthropogenic impact of oyster farms is essential for the management and conservation of marine fishes. In Japan, Hiroshima Bay is the region with the most intense oyster farming and thus suitable to study the impact of these farms. Here, we surveyed spherical planktonic eggs of the black sea bream Acanthopagrus schlegelii, one of the most abundant fish in the Bay. Our survey was performed at fourteen stations which included places with oyster farms and historical spawning grounds. We found the highest egg densities in four stations, one with historical spawning aggregations and three with major oyster farms. Besides, surveys at the innermost part of Hiroshima Bay, where two major rivers discharge, showed a low density of eggs indicating that black sea bream avoids spawning in low salinity areas. Our study suggests that oyster farms benefit spawners of black sea bream by providing more food sources than historical spawning grounds for efficient spawning. Yet, whether oyster farms represent a full advantage for the species remains unclear, particularly because they are known to host jellyfishes that prey on eggs and limit water flow that can influence the survival of fish eggs.
format: application/pdf
format: text/html
creator: Kentaro Kawai
creator: Hiroki Fujita
creator: Gustavo Sanchez
creator: Tetsuya Umino
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.11475
publisher: PeerJ Inc.
rights: © 2021 Kawai et al.
abstract: Understanding the anthropogenic impact of oyster farms is essential for the management and conservation of marine fishes. In Japan, Hiroshima Bay is the region with the most intense oyster farming and thus suitable to study the impact of these farms. Here, we surveyed spherical planktonic eggs of the black sea bream Acanthopagrus schlegelii, one of the most abundant fish in the Bay. Our survey was performed at fourteen stations which included places with oyster farms and historical spawning grounds. We found the highest egg densities in four stations, one with historical spawning aggregations and three with major oyster farms. Besides, surveys at the innermost part of Hiroshima Bay, where two major rivers discharge, showed a low density of eggs indicating that black sea bream avoids spawning in low salinity areas. Our study suggests that oyster farms benefit spawners of black sea bream by providing more food sources than historical spawning grounds for efficient spawning. Yet, whether oyster farms represent a full advantage for the species remains unclear, particularly because they are known to host jellyfishes that prey on eggs and limit water flow that can influence the survival of fish eggs.
bibliographic citation: Kawai et al. (2021) Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan. PeerJ 9:e11475 https://doi.org/10.7717/peerj.11475
date submitted: 2021-02-08
date accepted: 2021-04-26
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kawai
  given name: Kentaro
author list: Agent
  family name: Fujita
  given name: Hiroki
author list: Agent
  family name: Sanchez
  given name: Gustavo
author list: Agent
  family name: Umino
  given name: Tetsuya
doi: 10.7717/peerj.11475
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: © 2021 Kawai et al.
attribution name: Kawai et al.

Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods
type: item
type: AcademicArticle
description: This study explores the use of a minimally invasive assessment of myocardial infarction (MI) in mice using myocardial contrast echocardiography (MCE). The technique uses existing equipment and software readily available to the average researcher. C57/BL6 mice were randomized to either MI or sham surgery and evaluated using MCE at 1- or 2-weeks post-surgery. Size-isolated microbubbles were injected via retro-orbital catheter where their non-linear characteristics were utilized to produce the two-dimensional parameters of Wash-in-Rate and the Peak Enhancement, indicative of relative myocardial perfusion and blood volume, respectively. Three-dimensional cardiac reconstructions allowed the calculation of the Percent Agent, interpreted as the vascularity of the entire myocardium. These MCE parameters were compared to conventional assessments including M-Mode, strain analysis, and 2,3,5-Triphenyltetrazolium chloride (TTC) staining. Except for the Wash-in-Rate 2-week cohort, all MCE parameters were able to differentiate sham-operated versus MI animals and correlated with TTC staining (P < 0.05). MCE parameters were also able to identify MI group animals which failed to develop infarctions as determined by TTC staining. This study provides basic validation of these MCE parameters to detect MI in mice complementary to conventional methods while providing additional hemodynamic information in vivo.
format: application/pdf
format: text/html
creator: Nicholas T. Thielen
creator: Adison A. Kleinsasser
creator: Jessica L. Freeling
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Cardiology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.11500
publisher: PeerJ Inc.
rights: © 2021 Thielen et al.
abstract: This study explores the use of a minimally invasive assessment of myocardial infarction (MI) in mice using myocardial contrast echocardiography (MCE). The technique uses existing equipment and software readily available to the average researcher. C57/BL6 mice were randomized to either MI or sham surgery and evaluated using MCE at 1- or 2-weeks post-surgery. Size-isolated microbubbles were injected via retro-orbital catheter where their non-linear characteristics were utilized to produce the two-dimensional parameters of Wash-in-Rate and the Peak Enhancement, indicative of relative myocardial perfusion and blood volume, respectively. Three-dimensional cardiac reconstructions allowed the calculation of the Percent Agent, interpreted as the vascularity of the entire myocardium. These MCE parameters were compared to conventional assessments including M-Mode, strain analysis, and 2,3,5-Triphenyltetrazolium chloride (TTC) staining. Except for the Wash-in-Rate 2-week cohort, all MCE parameters were able to differentiate sham-operated versus MI animals and correlated with TTC staining (P < 0.05). MCE parameters were also able to identify MI group animals which failed to develop infarctions as determined by TTC staining. This study provides basic validation of these MCE parameters to detect MI in mice complementary to conventional methods while providing additional hemodynamic information in vivo.
bibliographic citation: Thielen et al. (2021) Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods. PeerJ 9:e11500 https://doi.org/10.7717/peerj.11500
date submitted: 2021-01-14
date accepted: 2021-05-02
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thielen
  given name: Nicholas T.
author list: Agent
  family name: Kleinsasser
  given name: Adison A.
author list: Agent
  family name: Freeling
  given name: Jessica L.
doi: 10.7717/peerj.11500
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: © 2021 Thielen et al.
attribution name: Thielen et al.

Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma
type: item
type: AcademicArticle
description: Stage 4S neuroblastoma, as defined by the International Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs between stage 4S and stage 4 were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of the SK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in…
format: application/pdf
format: text/html
creator: Daheng Yang
creator: Xianwei Zhang
creator: Zheqian Li
creator: Fei Xu
creator: Chenjie Tang
creator: Hongbing Chen
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
subject: Pediatrics
description: doi:10.7717/peerj.11512
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Stage 4S neuroblastoma, as defined by the International Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs between stage 4S and stage 4 were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of the SK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in…
bibliographic citation: Yang et al. (2021) Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma. PeerJ 9:e11512 https://doi.org/10.7717/peerj.11512
date submitted: 2020-09-14
date accepted: 2021-05-04
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Daheng
author list: Agent
  family name: Zhang
  given name: Xianwei
author list: Agent
  family name: Li
  given name: Zheqian
author list: Agent
  family name: Xu
  given name: Fei
author list: Agent
  family name: Tang
  given name: Chenjie
author list: Agent
  family name: Chen
  given name: Hongbing
doi: 10.7717/peerj.11512
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Promoting effect of rapamycin on osteogenic differentiation of maxillary sinus membrane stem cells
type: item
type: AcademicArticle
description: Background Stem cells located in the maxillary sinus membrane can differentiate into osteocytes. Our study aimed to evaluate the effect of rapamycin (RAPA) on the osteogenic differentiation of maxillary sinus membrane stem cells (MSMSCs). Methods Colony-forming unit assay, immunophenotype identification assay, and multi-differentiation assay confirmed characteristics of MSMSCs obtained from SD rats. Transmission electron microscopy (TEM) and flow cytometry (FCM) identified the initial autophagic level of MSMSCs induced by RAPA. Real-time quantitative PCR (qPCR) evaluated subsequent autophagic levels and osteogenic differentiation. Alkaline phosphatase (ALP) activity assay and alizarin red staining (ARS) evaluated subsequent osteogenic differentiation. We performed a histological examination to clarify in vivo osteogenesis with ectopic bone mass from BALB/c nude mice. Results MSMSCs possessed an active proliferation and multi-differentiation capacity, showing a phenotype of mesenchymal stem cells. The autophagic level increased with increasing RAPA (0, 10, 100, 1,000 nM) and decreased over time. ALP activity and calcium nodules forming in four RAPA-treated groups on three-time points (7, 14, 21 d) showed significant differences. Col1a1, Runx2, and Spp1 expressed most in 100 nM RAPA group on 7 and 14 d. Osteogenesis-related genes except for Ibsp expression between four groups tended to be consistent on 21 d. 100 nM and 10 nM RAPA-treated groups showed more bone formation in vivo. Conclusion RAPA can promote osteogenic differentiation of MSMSCs, indicating a possible relationship between osteogenic differentiation and autophagy.
format: application/pdf
format: text/html
creator: Yanjun Lin
creator: Min Zhang
creator: Lin Zhou
creator: Xuxi Chen
creator: Jiang Chen
creator: Dong Wu
subject: Cell Biology
subject: Molecular Biology
subject: Dentistry
subject: Orthopedics
subject: Otorhinolaryngology
description: doi:10.7717/peerj.11513
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Background Stem cells located in the maxillary sinus membrane can differentiate into osteocytes. Our study aimed to evaluate the effect of rapamycin (RAPA) on the osteogenic differentiation of maxillary sinus membrane stem cells (MSMSCs). Methods Colony-forming unit assay, immunophenotype identification assay, and multi-differentiation assay confirmed characteristics of MSMSCs obtained from SD rats. Transmission electron microscopy (TEM) and flow cytometry (FCM) identified the initial autophagic level of MSMSCs induced by RAPA. Real-time quantitative PCR (qPCR) evaluated subsequent autophagic levels and osteogenic differentiation. Alkaline phosphatase (ALP) activity assay and alizarin red staining (ARS) evaluated subsequent osteogenic differentiation. We performed a histological examination to clarify in vivo osteogenesis with ectopic bone mass from BALB/c nude mice. Results MSMSCs possessed an active proliferation and multi-differentiation capacity, showing a phenotype of mesenchymal stem cells. The autophagic level increased with increasing RAPA (0, 10, 100, 1,000 nM) and decreased over time. ALP activity and calcium nodules forming in four RAPA-treated groups on three-time points (7, 14, 21 d) showed significant differences. Col1a1, Runx2, and Spp1 expressed most in 100 nM RAPA group on 7 and 14 d. Osteogenesis-related genes except for Ibsp expression between four groups tended to be consistent on 21 d. 100 nM and 10 nM RAPA-treated groups showed more bone formation in vivo. Conclusion RAPA can promote osteogenic differentiation of MSMSCs, indicating a possible relationship between osteogenic differentiation and autophagy.
bibliographic citation: Lin et al. (2021) Promoting effect of rapamycin on osteogenic differentiation of maxillary sinus membrane stem cells. PeerJ 9:e11513 https://doi.org/10.7717/peerj.11513
date submitted: 2020-06-22
date accepted: 2021-05-04
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Yanjun
author list: Agent
  family name: Zhang
  given name: Min
author list: Agent
  family name: Zhou
  given name: Lin
author list: Agent
  family name: Chen
  given name: Xuxi
author list: Agent
  family name: Chen
  given name: Jiang
author list: Agent
  family name: Wu
  given name: Dong
doi: 10.7717/peerj.11513
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Lin et al.
attribution name: Lin et al.

Structural variation and evolution of chloroplast tRNAs in green algae
type: item
type: AcademicArticle
description: As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast.
format: application/pdf
format: text/html
creator: Fangbing Qi
creator: Yajing Zhao
creator: Ningbo Zhao
creator: Kai Wang
creator: Zhonghu Li
creator: Yingjuan Wang
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
subject: Data Science
description: doi:10.7717/peerj.11524
publisher: PeerJ Inc.
rights: © 2021 Qi et al.
abstract: As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast.
bibliographic citation: Qi et al. (2021) Structural variation and evolution of chloroplast tRNAs in green algae. PeerJ 9:e11524 https://doi.org/10.7717/peerj.11524
date submitted: 2021-01-27
date accepted: 2021-05-05
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Fangbing
author list: Agent
  family name: Zhao
  given name: Yajing
author list: Agent
  family name: Zhao
  given name: Ningbo
author list: Agent
  family name: Wang
  given name: Kai
author list: Agent
  family name: Li
  given name: Zhonghu
author list: Agent
  family name: Wang
  given name: Yingjuan
doi: 10.7717/peerj.11524
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Qi et al.
attribution name: Qi et al.

T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia
type: item
type: AcademicArticle
description: Background The CCT complex is an important mediator of microtubule assembly and intracellular protein folding. Owing to its high expression in spermatids, CCT knockdown can disrupt spermatogenesis. In the present report, we therefore evaluated the in vivo functionality of the testis-specific CCT complex component CCT6B using a murine knockout model system. Methods A CRISPR/Cas9 approach was used to generate Cct6b−/− mice, after which candidate gene expression in these animals was evaluated via qPCR and Western blotting. Testicular and epididymal phenotypes were assessed through histological and immunofluorescent staining assays, while a computer-assisted sperm analyzer was employed to assess semen quality. Results Cct6b−/− mice were successfully generated, and exhibited no differences in development, fertility, appearance, testis weight, or sperm counts relative to control littermates. In addition, no differences in spermatogenesis were detected when comparingCct6b+/+ and Cct6b−/− testes. However, when progressive motility was analyzed, the ratio of normal sperm was significantly decreased in Cct6b−/− male mice, with nuclear base bending being the primary detected abnormality. In addition, slight decreases in Cct4 and Cct7 expression were detected. Conclusion These data indicated that CCT6B is an important regulator of murine spermatogenesis, with the loss of this protein resulting in CCT complex dysfunction, providing a foundation for further studies.
format: application/pdf
format: text/html
creator: Peiyin Yang
creator: Wenjing Tang
creator: Huiling Li
creator: Rong Hua
creator: Yan Yuan
creator: Yue Zhang
creator: Yunfei Zhu
creator: Yiqiang Cui
creator: Jiahao Sha
subject: Biochemistry
subject: Developmental Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.11545
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background The CCT complex is an important mediator of microtubule assembly and intracellular protein folding. Owing to its high expression in spermatids, CCT knockdown can disrupt spermatogenesis. In the present report, we therefore evaluated the in vivo functionality of the testis-specific CCT complex component CCT6B using a murine knockout model system. Methods A CRISPR/Cas9 approach was used to generate Cct6b−/− mice, after which candidate gene expression in these animals was evaluated via qPCR and Western blotting. Testicular and epididymal phenotypes were assessed through histological and immunofluorescent staining assays, while a computer-assisted sperm analyzer was employed to assess semen quality. Results Cct6b−/− mice were successfully generated, and exhibited no differences in development, fertility, appearance, testis weight, or sperm counts relative to control littermates. In addition, no differences in spermatogenesis were detected when comparingCct6b+/+ and Cct6b−/− testes. However, when progressive motility was analyzed, the ratio of normal sperm was significantly decreased in Cct6b−/− male mice, with nuclear base bending being the primary detected abnormality. In addition, slight decreases in Cct4 and Cct7 expression were detected. Conclusion These data indicated that CCT6B is an important regulator of murine spermatogenesis, with the loss of this protein resulting in CCT complex dysfunction, providing a foundation for further studies.
bibliographic citation: Yang et al. (2021) T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia. PeerJ 9:e11545 https://doi.org/10.7717/peerj.11545
date submitted: 2021-02-18
date accepted: 2021-05-11
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Peiyin
author list: Agent
  family name: Tang
  given name: Wenjing
author list: Agent
  family name: Li
  given name: Huiling
author list: Agent
  family name: Hua
  given name: Rong
author list: Agent
  family name: Yuan
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Zhu
  given name: Yunfei
author list: Agent
  family name: Cui
  given name: Yiqiang
author list: Agent
  family name: Sha
  given name: Jiahao
doi: 10.7717/peerj.11545
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Yang et al.
attribution name: Yang et al.

High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) is the third most common cancer all around the world, and it seriously threats human health. PHF19 has been proved to be closely related to the prognosis of patients in a variety of malignant tumors, but the effect of PHF19 on the prognosis evaluation of CRC patients has not been confirmed. Methods In our study, we used GEO, TCGA database and IHC to verify the PHF19 expression in CRC samples. Survival analysis of PHF19 based on TCGA, GEO series, and our own CRC sample were performed. Cox regression was performed to reveal the relationship between PHF19 and prognosis. Co-expression was performed to find genes related to PHF19 expression. GO/KEGG enrichment analysis and GSEA analysis were used to confirm the most relevant signal pathway to PHF19. Next, cell experiments were performed to verify the effect of PHF19 on the proliferation, invasion and metastasis of CRC. Then, Western blot was used to verify the protein expression of the above two phenotypes. Finally, tumor formation experiments in nude mice were used to verify the role of PHF19 of tumor proliferation in vivo. Results We found that PHF19 was significantly over-expressed in tumors compared with normal tissues. Kaplan–Meier (K–M) analysis indicated that high PHF19 in CRC associated with poor overall survival (OS) in CRC patients. Clinical correlation analysis showed that high expression of PHF19 was closely related to t umor progression in CRC patients, especially infiltration and metastasis. Bioinformatics revealed that PHF19 might affect tumor malignant phenotype by regulating the cell cycle in CRC. CCK-8 and clonal formation experiment showed that the proliferative ability of tumor cells was promoted. Flow cytometry showed that the cell cycle accelerated the transition from G1 to S phase. Western blot found that Cyclin D1, CDK4, and CDK6 expression were up-regulated. Transwell and wound-healing experiment found that invasive and migratory abilities was promoted after the…
format: application/pdf
format: text/html
creator: Pengfei Li
creator: Jie Sun
creator: Yuanyuan Ruan
creator: Lujun Song
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Histology
description: doi:10.7717/peerj.11551
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Colorectal cancer (CRC) is the third most common cancer all around the world, and it seriously threats human health. PHF19 has been proved to be closely related to the prognosis of patients in a variety of malignant tumors, but the effect of PHF19 on the prognosis evaluation of CRC patients has not been confirmed. Methods In our study, we used GEO, TCGA database and IHC to verify the PHF19 expression in CRC samples. Survival analysis of PHF19 based on TCGA, GEO series, and our own CRC sample were performed. Cox regression was performed to reveal the relationship between PHF19 and prognosis. Co-expression was performed to find genes related to PHF19 expression. GO/KEGG enrichment analysis and GSEA analysis were used to confirm the most relevant signal pathway to PHF19. Next, cell experiments were performed to verify the effect of PHF19 on the proliferation, invasion and metastasis of CRC. Then, Western blot was used to verify the protein expression of the above two phenotypes. Finally, tumor formation experiments in nude mice were used to verify the role of PHF19 of tumor proliferation in vivo. Results We found that PHF19 was significantly over-expressed in tumors compared with normal tissues. Kaplan–Meier (K–M) analysis indicated that high PHF19 in CRC associated with poor overall survival (OS) in CRC patients. Clinical correlation analysis showed that high expression of PHF19 was closely related to t umor progression in CRC patients, especially infiltration and metastasis. Bioinformatics revealed that PHF19 might affect tumor malignant phenotype by regulating the cell cycle in CRC. CCK-8 and clonal formation experiment showed that the proliferative ability of tumor cells was promoted. Flow cytometry showed that the cell cycle accelerated the transition from G1 to S phase. Western blot found that Cyclin D1, CDK4, and CDK6 expression were up-regulated. Transwell and wound-healing experiment found that invasive and migratory abilities was promoted after the…
bibliographic citation: Li et al. (2021) High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study. PeerJ 9:e11551 https://doi.org/10.7717/peerj.11551
date submitted: 2020-12-29
date accepted: 2021-05-11
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Pengfei
author list: Agent
  family name: Sun
  given name: Jie
author list: Agent
  family name: Ruan
  given name: Yuanyuan
author list: Agent
  family name: Song
  given name: Lujun
doi: 10.7717/peerj.11551
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: © 2021 Li et al.
attribution name: Li et al.

Changes in the stoichiometry of Castanopsis fargesii along an elevation gradient in a Chinese subtropical forest
type: item
type: AcademicArticle
description: Elevation is important for determining the nutrient biogeochemical cycle in forest ecosystems. Changes in the ecological stoichiometry of nutrients along an elevation gradient can be used to predict how an element cycle responds in the midst of global climate change. We investigated changes in concentrations of and relationships between nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) in the leaves and roots of the dominant tree species, Castanopsis fargesii, along an elevation gradient (from 500 to 1,000 m above mean sea level) in a subtropical natural forest in China. We analyzed correlations between C. fargesii’s above-ground biomass and stoichiometry with environmental factors. We also analyzed the soil and plant stoichiometry of this C. fargesii population. Our results showed that leaf N decreased while leaf K and Ca increased at higher elevations. Meanwhile, leaf P showed no relationship with elevation. The leaf N:P indicated that C. fargesii was limited by N. Elevation gradients contributed 46.40% of the total variance of ecological stoichiometry when assessing environmental factors. Our research may provide a theoretical basis for the biogeochemical cycle along with better forest management and fertilization for this C. fargesii population.
format: application/pdf
format: text/html
creator: Danping Liu
creator: Dexiang Zheng
creator: Yaoyao Xu
creator: Yifei Chen
creator: Hesong Wang
creator: Ku Wang
creator: Xiaoli Liao
creator: Changxiong Chen
creator: Jiangjiang Xia
creator: Shaofei Jin
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.11553
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Elevation is important for determining the nutrient biogeochemical cycle in forest ecosystems. Changes in the ecological stoichiometry of nutrients along an elevation gradient can be used to predict how an element cycle responds in the midst of global climate change. We investigated changes in concentrations of and relationships between nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) in the leaves and roots of the dominant tree species, Castanopsis fargesii, along an elevation gradient (from 500 to 1,000 m above mean sea level) in a subtropical natural forest in China. We analyzed correlations between C. fargesii’s above-ground biomass and stoichiometry with environmental factors. We also analyzed the soil and plant stoichiometry of this C. fargesii population. Our results showed that leaf N decreased while leaf K and Ca increased at higher elevations. Meanwhile, leaf P showed no relationship with elevation. The leaf N:P indicated that C. fargesii was limited by N. Elevation gradients contributed 46.40% of the total variance of ecological stoichiometry when assessing environmental factors. Our research may provide a theoretical basis for the biogeochemical cycle along with better forest management and fertilization for this C. fargesii population.
bibliographic citation: Liu et al. (2021) Changes in the stoichiometry of Castanopsis fargesii along an elevation gradient in a Chinese subtropical forest. PeerJ 9:e11553 https://doi.org/10.7717/peerj.11553
date submitted: 2020-09-16
date accepted: 2021-05-11
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Danping
author list: Agent
  family name: Zheng
  given name: Dexiang
author list: Agent
  family name: Xu
  given name: Yaoyao
author list: Agent
  family name: Chen
  given name: Yifei
author list: Agent
  family name: Wang
  given name: Hesong
author list: Agent
  family name: Wang
  given name: Ku
author list: Agent
  family name: Liao
  given name: Xiaoli
author list: Agent
  family name: Chen
  given name: Changxiong
author list: Agent
  family name: Xia
  given name: Jiangjiang
author list: Agent
  family name: Jin
  given name: Shaofei
doi: 10.7717/peerj.11553
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Liu et al.
attribution name: Liu et al.

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