PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome
items: Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance
items: Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages
items: Specific lifestyle factors and in vitro fertilization outcomes in Romanian women: a pilot study
items: First eumonostiliferous nemertean from the Nishi-Shichito Ridge, Genrokunemertes obesa gen. et sp. nov. (Eumonostilifera, Nemertea)
items: Does treating proximal cavities in primary molars non-restoratively affect intra-arch space and alignment of successor teeth negatively? A 4-year longitudinal study
items: SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells
items: Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.)
items: Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions
items: Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis

Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome
type: item
type: AcademicArticle
description: Acute kidney injury (AKI) is a frequent and serious complication of sepsis, which results in a rapid decline of kidney function. Currently, there are no curative therapies for AKI. Theacrine is a purine alkaloid and exerts significant role in regulating inflammation, oxidative stress, and mood elevation. The study aims to evaluate the biological role and potential mechanism of theacrine in septic AKI. The murine and cellular models of septic AKI were established in lipopolysaccharide (LPS)-treated C57BL/6 mice and HK-2 cells, respectively. The effect of theacrine on alleviating septic AKI was assessed after pretreatment with theacrine in vivo and in vitro. We found that theacrine treatment significantly alleviated LPS-induced kidney injury, as evidenced by decreased levels of kidney injury markers (blood urea nitrogen and creatinine), inflammatory factors (IL-1β and IL-18), and cell apoptosis in vivo and in vitro. Mechanistically, theacrine markedly repressed the activation of NOD-like receptor (NLR) pyrin domain-containing protein 3 (NLRP3)inflammasome. As expected, MCC950 (a specific inhibitor of NLRP3) treatment also decreased LPS-induced production of IL-18 and IL-1β and cell apoptosis in HK-2 cells. More important, Nigericin sodiumsalt (a NLRP3 agonist) damaged the effect of theacrine on repressing kidney injury markers (blood urea nitrogen and creatinine), pro-inflammatory cytokines (IL-18 and IL-1β), and cell apoptosis. Taken together, these results demonstrate that theacrine alleviates septic AKI, at least in part by repressing the activation of NLRP3 inflammasome.
format: application/pdf
format: text/html
creator: Maoxian Yang
creator: Peng Shen
creator: Longsheng Xu
creator: Min Kong
creator: Congcong Yu
creator: Yunchao Shi
subject: Biochemistry
subject: Cell Biology
subject: Emergency and Critical Care
subject: Nephrology
description: doi:10.7717/peerj.14109
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Acute kidney injury (AKI) is a frequent and serious complication of sepsis, which results in a rapid decline of kidney function. Currently, there are no curative therapies for AKI. Theacrine is a purine alkaloid and exerts significant role in regulating inflammation, oxidative stress, and mood elevation. The study aims to evaluate the biological role and potential mechanism of theacrine in septic AKI. The murine and cellular models of septic AKI were established in lipopolysaccharide (LPS)-treated C57BL/6 mice and HK-2 cells, respectively. The effect of theacrine on alleviating septic AKI was assessed after pretreatment with theacrine in vivo and in vitro. We found that theacrine treatment significantly alleviated LPS-induced kidney injury, as evidenced by decreased levels of kidney injury markers (blood urea nitrogen and creatinine), inflammatory factors (IL-1β and IL-18), and cell apoptosis in vivo and in vitro. Mechanistically, theacrine markedly repressed the activation of NOD-like receptor (NLR) pyrin domain-containing protein 3 (NLRP3)inflammasome. As expected, MCC950 (a specific inhibitor of NLRP3) treatment also decreased LPS-induced production of IL-18 and IL-1β and cell apoptosis in HK-2 cells. More important, Nigericin sodiumsalt (a NLRP3 agonist) damaged the effect of theacrine on repressing kidney injury markers (blood urea nitrogen and creatinine), pro-inflammatory cytokines (IL-18 and IL-1β), and cell apoptosis. Taken together, these results demonstrate that theacrine alleviates septic AKI, at least in part by repressing the activation of NLRP3 inflammasome.
bibliographic citation: Yang et al. (2022) Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome. PeerJ 10:e14109 https://doi.org/10.7717/peerj.14109
date submitted: 2022-02-16
date accepted: 2022-09-02
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yang
  given name: Maoxian
author list: Agent
  family name: Shen
  given name: Peng
author list: Agent
  family name: Xu
  given name: Longsheng
author list: Agent
  family name: Kong
  given name: Min
author list: Agent
  family name: Yu
  given name: Congcong
author list: Agent
  family name: Shi
  given name: Yunchao
doi: 10.7717/peerj.14109
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance
type: item
type: AcademicArticle
description: The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.
format: application/pdf
format: text/html
creator: Alexey A. Kotov
creator: Derek J. Taylor
subject: Biodiversity
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14113
publisher: PeerJ Inc.
rights: © 2022 Kotov and Taylor
abstract: The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.
bibliographic citation: Kotov et al. (2022) Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance. PeerJ 10:e14113 https://doi.org/10.7717/peerj.14113
date submitted: 2021-11-17
date accepted: 2022-09-02
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kotov
  given name: Alexey A.
author list: Agent
  family name: Taylor
  given name: Derek J.
doi: 10.7717/peerj.14113
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: © 2022 Kotov and Taylor
attribution name: Kotov and Taylor

Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages
type: item
type: AcademicArticle
description: Background Armeniaca sibirica seed kernel oil is rich in oleic acid and linoleic acid, thus holding potential value as a source of high-quality edible oils. However, some regulatory factors involved in fatty acids accumulation in A. sibirica seed kernels remain largely elusive. Thus, the aim of this study was to elucidate the regulatory mechanisms underlying fatty acids biosynthesis in A. sibirica developing seed kernels. Methods Seed kernels from six plants from a single A. sibirica clone were taken at five different developmental stages (days 30, 41, 52, 63, and 73 after anthesis). Fatty acid composition in seed kernel oil was determined by gas chromatography-mass spectrometry (GC-MS). In addition, transcriptome analysis was conducted using second-generation sequencing (SGS) and single-molecule real-time sequencing (SMRT). Results Rapid accumulation of fatty acids occurred throughout the different stages of seed kernels development, with oleic acid and linoleic acid as the main fatty acids. A total of 10,024, 9,803, 6,004, 6,719 and 9,688 unigenes were matched in the Nt, Nr, KOG, GO and KEGG databases, respectively. In the category lipid metabolism, 228 differentially expressed genes (DEGs) were annotated into 13 KEGG pathways. Specific unigenes encoding 12 key enzymes related to fatty acids biosynthesis were determined. Co-expression network analysis identified 11 transcription factors (TFs) and 13 long non-coding RNAs (lncRNAs) which putatively participate in the regulation of fatty acid biosynthesis. This study provides insights into the molecular regulatory mechanisms of fatty acids biosynthesis in A. sibirica developing seed kernels, and enabled the identification of novel candidate factors for future improvement of the production and quality of seed kernel oil by breeding.
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creator: Yueliang Wu
creator: Wenya Gao
creator: Xinli Li
creator: Shilin Sun
creator: Jian Xu
creator: Xiaoqiong Shi
creator: Huiyan Guo
subject: Agricultural Science
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.14125
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Background Armeniaca sibirica seed kernel oil is rich in oleic acid and linoleic acid, thus holding potential value as a source of high-quality edible oils. However, some regulatory factors involved in fatty acids accumulation in A. sibirica seed kernels remain largely elusive. Thus, the aim of this study was to elucidate the regulatory mechanisms underlying fatty acids biosynthesis in A. sibirica developing seed kernels. Methods Seed kernels from six plants from a single A. sibirica clone were taken at five different developmental stages (days 30, 41, 52, 63, and 73 after anthesis). Fatty acid composition in seed kernel oil was determined by gas chromatography-mass spectrometry (GC-MS). In addition, transcriptome analysis was conducted using second-generation sequencing (SGS) and single-molecule real-time sequencing (SMRT). Results Rapid accumulation of fatty acids occurred throughout the different stages of seed kernels development, with oleic acid and linoleic acid as the main fatty acids. A total of 10,024, 9,803, 6,004, 6,719 and 9,688 unigenes were matched in the Nt, Nr, KOG, GO and KEGG databases, respectively. In the category lipid metabolism, 228 differentially expressed genes (DEGs) were annotated into 13 KEGG pathways. Specific unigenes encoding 12 key enzymes related to fatty acids biosynthesis were determined. Co-expression network analysis identified 11 transcription factors (TFs) and 13 long non-coding RNAs (lncRNAs) which putatively participate in the regulation of fatty acid biosynthesis. This study provides insights into the molecular regulatory mechanisms of fatty acids biosynthesis in A. sibirica developing seed kernels, and enabled the identification of novel candidate factors for future improvement of the production and quality of seed kernel oil by breeding.
bibliographic citation: Wu et al. (2022) Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages. PeerJ 10:e14125 https://doi.org/10.7717/peerj.14125
date submitted: 2022-06-13
date accepted: 2022-09-06
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Yueliang
author list: Agent
  family name: Gao
  given name: Wenya
author list: Agent
  family name: Li
  given name: Xinli
author list: Agent
  family name: Sun
  given name: Shilin
author list: Agent
  family name: Xu
  given name: Jian
author list: Agent
  family name: Shi
  given name: Xiaoqiong
author list: Agent
  family name: Guo
  given name: Huiyan
doi: 10.7717/peerj.14125
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Wu et al.
attribution name: Wu et al.

Specific lifestyle factors and in vitro fertilization outcomes in Romanian women: a pilot study
type: item
type: AcademicArticle
description: Background Infertility is an important health concern worldwide. Although lifestyle habits and behaviors have been widely reported as predictors of IVF outcomes by previous studies, they have not been reported for Romanian women undergoing IVF. In this regard, our pilot study aimed to begin to address the data gap by assessing lifestyle predictors of in vitro fertilization (IVF) outcomes in Romanian women. Study design Our pilot study included 35 participants who completed a first IVF cycle at a single infertility center. We evaluated individual self-reported lifestyle habits and behaviors as predictors of IVF outcomes, and employed principal component analysis (PCA) to characterize multiple lifestyle habits and behaviors into personal care product (PCP) use, and healthy diet and physical activity patterns as predictors of IVF outcomes. Results Our PCA analysis showed that greater use of PCPs was associated with lower probabilities of pregnancy (RR: 0.92, 95% CI [0.87–0.98]) and live birth (RR: 0.94, 95% CI [0.88–1.01]) while, the healthy dietary habits and physical activity were associated with a higher likelihood of pregnancy, although without statistical significance (RR: 1.10, 95% CI [0.93–1.30]). Conclusions In this pilot study we identified associations between IVF outcomes among Romanian women and certain lifestyle habits and behaviors including stress, diet and physical activity, and certain PCP use. We also estimated the joint effects of multiple lifestyle factors using PCA and found that PCP use, healthy dietary habits and physical activity were associated with IVF outcomes.
format: application/pdf
format: text/html
creator: Iulia A. Neamtiu
creator: Mihai Surcel
creator: Thoin F. Begum
creator: Eugen S. Gurzau
creator: Ioana Berindan-Neagoe
creator: Cornelia Braicu
creator: Ioana Rotar
creator: Daniel Muresan
creator: Michael S. Bloom
subject: Global Health
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Environmental Health
description: doi:10.7717/peerj.14189
publisher: PeerJ Inc.
rights: © 2022 Neamtiu et al.
abstract: Background Infertility is an important health concern worldwide. Although lifestyle habits and behaviors have been widely reported as predictors of IVF outcomes by previous studies, they have not been reported for Romanian women undergoing IVF. In this regard, our pilot study aimed to begin to address the data gap by assessing lifestyle predictors of in vitro fertilization (IVF) outcomes in Romanian women. Study design Our pilot study included 35 participants who completed a first IVF cycle at a single infertility center. We evaluated individual self-reported lifestyle habits and behaviors as predictors of IVF outcomes, and employed principal component analysis (PCA) to characterize multiple lifestyle habits and behaviors into personal care product (PCP) use, and healthy diet and physical activity patterns as predictors of IVF outcomes. Results Our PCA analysis showed that greater use of PCPs was associated with lower probabilities of pregnancy (RR: 0.92, 95% CI [0.87–0.98]) and live birth (RR: 0.94, 95% CI [0.88–1.01]) while, the healthy dietary habits and physical activity were associated with a higher likelihood of pregnancy, although without statistical significance (RR: 1.10, 95% CI [0.93–1.30]). Conclusions In this pilot study we identified associations between IVF outcomes among Romanian women and certain lifestyle habits and behaviors including stress, diet and physical activity, and certain PCP use. We also estimated the joint effects of multiple lifestyle factors using PCA and found that PCP use, healthy dietary habits and physical activity were associated with IVF outcomes.
bibliographic citation: Neamtiu et al. (2022) Specific lifestyle factors and in vitro fertilization outcomes in Romanian women: a pilot study. PeerJ 10:e14189 https://doi.org/10.7717/peerj.14189
date submitted: 2022-07-11
date accepted: 2022-09-14
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Neamtiu
  given name: Iulia A.
author list: Agent
  family name: Surcel
  given name: Mihai
author list: Agent
  family name: Begum
  given name: Thoin F.
author list: Agent
  family name: Gurzau
  given name: Eugen S.
author list: Agent
  family name: Berindan-Neagoe
  given name: Ioana
author list: Agent
  family name: Braicu
  given name: Cornelia
author list: Agent
  family name: Rotar
  given name: Ioana
author list: Agent
  family name: Muresan
  given name: Daniel
author list: Agent
  family name: Bloom
  given name: Michael S.
doi: 10.7717/peerj.14189
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: © 2022 Neamtiu et al.
attribution name: Neamtiu et al.

First eumonostiliferous nemertean from the Nishi-Shichito Ridge, Genrokunemertes obesa gen. et sp. nov. (Eumonostilifera, Nemertea)
type: item
type: AcademicArticle
description: Nemerteans are mostly marine, benthic invertebrates, inhabiting intertidal to hadal zones. Recently, they have been recognized from deep sea with environmental DNA (eDNA) metabarcoding of sediment samples whereas any records from the locations and/or the water depth have not been documented in nemertean taxonomic publications to date. It suggests that there are major gaps between deep-sea nemertean fauna observed with eDNA and taxonomic knowledge. During a research expedition in 2021, we obtained a single specimen of eumonostiliferous nemertean from the southern part of Genroku Seamount Chain, the Nishi-Shichito Ridge, where any nemertean species have never been reported. Subsequent morphological and molecular examination reveal that the species is placed in a new genus and herein described as Genrokunemertes obesa gen. et sp. nov. It resembles shallow-water-dwelling Kurilonemertes and Typhloerstedia, but differs from the former in lacking eyes and the latter in possessing well-developed cephalic glands and lacking accessory nerves of lateral nerve cords. In terms of genetic distances based on partial sequences of the cytochrome c oxidase subunit I gene, G. obesa gen. et sp. nov. is closest to Monostilifera sp. Owase collected from Japan, which is characterized by large four eyes; the COI distance is higher than commonly observed interspecific divergences in eumonostiliferans.
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creator: Natsumi Hookabe
creator: Keita Koeda
creator: Yoshihiro Fujiwara
creator: Shinji Tsuchida
creator: Rei Ueshima
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13857
publisher: PeerJ Inc.
rights: © 2022 Hookabe et al.
abstract: Nemerteans are mostly marine, benthic invertebrates, inhabiting intertidal to hadal zones. Recently, they have been recognized from deep sea with environmental DNA (eDNA) metabarcoding of sediment samples whereas any records from the locations and/or the water depth have not been documented in nemertean taxonomic publications to date. It suggests that there are major gaps between deep-sea nemertean fauna observed with eDNA and taxonomic knowledge. During a research expedition in 2021, we obtained a single specimen of eumonostiliferous nemertean from the southern part of Genroku Seamount Chain, the Nishi-Shichito Ridge, where any nemertean species have never been reported. Subsequent morphological and molecular examination reveal that the species is placed in a new genus and herein described as Genrokunemertes obesa gen. et sp. nov. It resembles shallow-water-dwelling Kurilonemertes and Typhloerstedia, but differs from the former in lacking eyes and the latter in possessing well-developed cephalic glands and lacking accessory nerves of lateral nerve cords. In terms of genetic distances based on partial sequences of the cytochrome c oxidase subunit I gene, G. obesa gen. et sp. nov. is closest to Monostilifera sp. Owase collected from Japan, which is characterized by large four eyes; the COI distance is higher than commonly observed interspecific divergences in eumonostiliferans.
bibliographic citation: Hookabe et al. (2022) First eumonostiliferous nemertean from the Nishi-Shichito Ridge, Genrokunemertes obesa gen. et sp. nov. (Eumonostilifera, Nemertea). PeerJ 10:e13857 https://doi.org/10.7717/peerj.13857
date submitted: 2022-04-19
date accepted: 2022-07-17
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hookabe
  given name: Natsumi
author list: Agent
  family name: Koeda
  given name: Keita
author list: Agent
  family name: Fujiwara
  given name: Yoshihiro
author list: Agent
  family name: Tsuchida
  given name: Shinji
author list: Agent
  family name: Ueshima
  given name: Rei
doi: 10.7717/peerj.13857
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Hookabe et al.
attribution name: Hookabe et al.

Does treating proximal cavities in primary molars non-restoratively affect intra-arch space and alignment of successor teeth negatively? A 4-year longitudinal study
type: item
type: AcademicArticle
description: Background Removing plaque with toothbrush and toothpaste from proximal cavities in primary molars without restoring them follows sound cariological principles. But does this treatment affect space for and alignment of their permanent successors negatively? Hypothesis There is no difference in impaction and displacement of the premolars, as well as in the D+E space in quadrants with three different statuses of the proximal surface of primary molars over a 4-year period. Methods A total of 936 quadrants (466 maxillary and 470 mandibular quadrants) in 233 children were assessed. Treatment of cavities in the proximal surfaces of the primary molars consisted of amalgam and ART restorations using high-viscosity glass-ionomer cement, and cleaning of open large- and medium-sized cavities with toothbrush and toothpaste (UCT) under supervision for 220 days per year over 3 years. Dental casts were made at baseline, and after two, three, and 4 years. The D+E spaces were measured digitally. Status of the proximal surface of the primary molars was assessed by two calibrated examiners, and quadrants were grouped into normal anatomy, defective restoration, and proximal cavity. ANCOVA, ANOVA and LSD tests were applied. Results There was a statistically significant difference between groups (p <= 0.001) and between evaluation times (p < 0.001), for the D+E space in both the maxilla and mandible. A sex difference related to the D+E space in the maxilla was found (p = 0.007). For boys, quadrants in the maxilla of the group ‘proximal cavity’ showed a significant shorter D+E space when compared to quadrants of the group ‘normal anatomy’ at the 3- and 4-year evaluation time. For girls the difference between the two groups was only present at the 3-year evaluation time. There was no significant difference between the D+E space in quadrants with defective restorations and those with normal anatomy in the mandible and in the maxilla. Displacement and impaction of the premolars showed no sig…
format: application/pdf
format: text/html
creator: Rafael T. Gomide
creator: Jo E. Frencken
creator: Jorge Faber
creator: Anne Marie Kuijpers-Jagtman
subject: Dentistry
subject: Global Health
subject: Health Policy
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.14008
publisher: PeerJ Inc.
rights: © 2022 Gomide et al.
abstract: Background Removing plaque with toothbrush and toothpaste from proximal cavities in primary molars without restoring them follows sound cariological principles. But does this treatment affect space for and alignment of their permanent successors negatively? Hypothesis There is no difference in impaction and displacement of the premolars, as well as in the D+E space in quadrants with three different statuses of the proximal surface of primary molars over a 4-year period. Methods A total of 936 quadrants (466 maxillary and 470 mandibular quadrants) in 233 children were assessed. Treatment of cavities in the proximal surfaces of the primary molars consisted of amalgam and ART restorations using high-viscosity glass-ionomer cement, and cleaning of open large- and medium-sized cavities with toothbrush and toothpaste (UCT) under supervision for 220 days per year over 3 years. Dental casts were made at baseline, and after two, three, and 4 years. The D+E spaces were measured digitally. Status of the proximal surface of the primary molars was assessed by two calibrated examiners, and quadrants were grouped into normal anatomy, defective restoration, and proximal cavity. ANCOVA, ANOVA and LSD tests were applied. Results There was a statistically significant difference between groups (p <= 0.001) and between evaluation times (p < 0.001), for the D+E space in both the maxilla and mandible. A sex difference related to the D+E space in the maxilla was found (p = 0.007). For boys, quadrants in the maxilla of the group ‘proximal cavity’ showed a significant shorter D+E space when compared to quadrants of the group ‘normal anatomy’ at the 3- and 4-year evaluation time. For girls the difference between the two groups was only present at the 3-year evaluation time. There was no significant difference between the D+E space in quadrants with defective restorations and those with normal anatomy in the mandible and in the maxilla. Displacement and impaction of the premolars showed no sig…
bibliographic citation: Gomide et al. (2022) Does treating proximal cavities in primary molars non-restoratively affect intra-arch space and alignment of successor teeth negatively? A 4-year longitudinal study. PeerJ 10:e14008 https://doi.org/10.7717/peerj.14008
date submitted: 2022-05-11
date accepted: 2022-08-14
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gomide
  given name: Rafael T.
author list: Agent
  family name: Frencken
  given name: Jo E.
author list: Agent
  family name: Faber
  given name: Jorge
author list: Agent
  family name: Kuijpers-Jagtman
  given name: Anne Marie
doi: 10.7717/peerj.14008
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Gomide et al.
attribution name: Gomide et al.

SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells
type: item
type: AcademicArticle
description: Background RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis. Methods We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis. Conclusions We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.
format: application/pdf
format: text/html
creator: Junjie Zhou
creator: Wenhao Chen
creator: Qianwen He
creator: Dong Chen
creator: Chunguang Li
creator: Congqing Jiang
creator: Zhao Ding
creator: Qun Qian
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.14084
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis. Methods We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis. Conclusions We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.
bibliographic citation: Zhou et al. (2022) SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells. PeerJ 10:e14084 https://doi.org/10.7717/peerj.14084
date submitted: 2022-05-13
date accepted: 2022-08-29
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Junjie
author list: Agent
  family name: Chen
  given name: Wenhao
author list: Agent
  family name: He
  given name: Qianwen
author list: Agent
  family name: Chen
  given name: Dong
author list: Agent
  family name: Li
  given name: Chunguang
author list: Agent
  family name: Jiang
  given name: Congqing
author list: Agent
  family name: Ding
  given name: Zhao
author list: Agent
  family name: Qian
  given name: Qun
doi: 10.7717/peerj.14084
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Zhou et al.
attribution name: Zhou et al.

Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.)
type: item
type: AcademicArticle
description: Background DNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet. Methods Using the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns. Results Fifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.
format: application/pdf
format: text/html
creator: Tianjie Li
creator: Xiaoyu Wang
creator: Dinakaran Elango
creator: Weihua Zhang
creator: Min Li
creator: Fan Zhang
creator: Qi Pan
creator: Ying Wu
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14087
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background DNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet. Methods Using the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns. Results Fifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.
bibliographic citation: Li et al. (2022) Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.). PeerJ 10:e14087 https://doi.org/10.7717/peerj.14087
date submitted: 2022-07-06
date accepted: 2022-08-29
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Tianjie
author list: Agent
  family name: Wang
  given name: Xiaoyu
author list: Agent
  family name: Elango
  given name: Dinakaran
author list: Agent
  family name: Zhang
  given name: Weihua
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Zhang
  given name: Fan
author list: Agent
  family name: Pan
  given name: Qi
author list: Agent
  family name: Wu
  given name: Ying
doi: 10.7717/peerj.14087
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Li et al.
attribution name: Li et al.

Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions
type: item
type: AcademicArticle
description: Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
format: application/pdf
format: text/html
creator: Xiaolan Zhang
creator: Xuan Shan
creator: Hongdan Fu
creator: Zhouping Sun
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14088
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
bibliographic citation: Zhang et al. (2022) Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions. PeerJ 10:e14088 https://doi.org/10.7717/peerj.14088
date submitted: 2022-05-20
date accepted: 2022-08-29
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaolan
author list: Agent
  family name: Shan
  given name: Xuan
author list: Agent
  family name: Fu
  given name: Hongdan
author list: Agent
  family name: Sun
  given name: Zhouping
doi: 10.7717/peerj.14088
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis
type: item
type: AcademicArticle
description: Anthocyanin is a natural pigment that has a functional role in plants to attract pollinating insects and is important in stress response. Foxtail millet (Setaria italica) is known as a nutritional crop with high resistance to drought and barren. However, the molecular mechanism regulating anthocyanin accumulation and the relationship between anthocyanin and the stress resistance of foxtail millet remains obscure. In this study, we screened hundreds of germplasm resources and obtained several varieties with purple plants in foxtail millet. By studying the purple-leaved B100 variety and the control variety, Yugu1 with green leaves, we found that B100 could accumulate a large amount of anthocyanin in the leaf epiderma, and B100 had stronger stress tolerance. Further transcriptome analysis revealed the differences in gene expression patterns between the two varieties. We identified nine genes encoding enzymes related to anthocyanin biosynthesis using quantitative PCR validation that showed significantly higher expression levels in B100 than Yugu1. The results of this study lay the foundation for the analysis of the molecular mechanism of anthocyanin accumulation in foxtail millet, and provided genetic resources for the molecular breeding of crops with high anthocyanin content.
format: application/pdf
format: text/html
creator: Yaofei Zhao
creator: Yaqiong Li
creator: Xiaoxi Zhen
creator: Jinli Zhang
creator: Qianxiang Zhang
creator: Zhaowen Liu
creator: Shupei Hou
creator: Yuanhuai Han
creator: Bin Zhang
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.14099
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Anthocyanin is a natural pigment that has a functional role in plants to attract pollinating insects and is important in stress response. Foxtail millet (Setaria italica) is known as a nutritional crop with high resistance to drought and barren. However, the molecular mechanism regulating anthocyanin accumulation and the relationship between anthocyanin and the stress resistance of foxtail millet remains obscure. In this study, we screened hundreds of germplasm resources and obtained several varieties with purple plants in foxtail millet. By studying the purple-leaved B100 variety and the control variety, Yugu1 with green leaves, we found that B100 could accumulate a large amount of anthocyanin in the leaf epiderma, and B100 had stronger stress tolerance. Further transcriptome analysis revealed the differences in gene expression patterns between the two varieties. We identified nine genes encoding enzymes related to anthocyanin biosynthesis using quantitative PCR validation that showed significantly higher expression levels in B100 than Yugu1. The results of this study lay the foundation for the analysis of the molecular mechanism of anthocyanin accumulation in foxtail millet, and provided genetic resources for the molecular breeding of crops with high anthocyanin content.
bibliographic citation: Zhao et al. (2022) Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis. PeerJ 10:e14099 https://doi.org/10.7717/peerj.14099
date submitted: 2022-02-25
date accepted: 2022-08-31
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yaofei
author list: Agent
  family name: Li
  given name: Yaqiong
author list: Agent
  family name: Zhen
  given name: Xiaoxi
author list: Agent
  family name: Zhang
  given name: Jinli
author list: Agent
  family name: Zhang
  given name: Qianxiang
author list: Agent
  family name: Liu
  given name: Zhaowen
author list: Agent
  family name: Hou
  given name: Shupei
author list: Agent
  family name: Han
  given name: Yuanhuai
author list: Agent
  family name: Zhang
  given name: Bin
doi: 10.7717/peerj.14099
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Zhao et al.
attribution name: Zhao et al.

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