PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum
items: Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods
items: Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation
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

Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum
type: item
type: AcademicArticle
description: Background Obesity and diabetes are becoming increasingly prevalent around the world. Inflammation, oxidative stress, insulin resistance, and glucose intolerance are linked to both obesity and type 2 diabetes, and these disorders are becoming major public health issues globally. Methods This study evaluated the effects of obesity, diabetes, and hypoxia on the levels of pro- and anti-inflammatory cytokines in rats. We divided 120 Wistar rats in two groups, male and female, each including six subgroups: control (CTRL), obese (high-fat diet (HFD)), diabetic (streptozotocin (STZ)-treated), hypoxic (HYX), obese + diabetic (HFD/STZ), and obese + diabetic + hypoxic (HFD/STZ/HYX). We examined the levels of tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL10, and leptin in pancreatic tissues and serum. Results No significant difference was observed in serum levels of cholesterol, triglycerides, and low-density lipoprotein (LDL) between HYX and CTRL in either sex. However, they were significantly increased, whereas high-density lipoprotein (HDL) was significantly decreased in HFD, STZ, HFD/STZ, and HFD/STZ/HPX compared with CTRL in both sexes. The expression of Tnf-α, Il6, and Lep was significantly upregulated in all subgroups compared with CTRL in both sexes. STZ and HYX showed no significant differences in the expression of these genes between sexes, whereas Tnf-α and Il6 were upregulated in male HFD, HFD/STZ, and HFD/STZ/HYX compared with females. Protein levels showed similar patterns. Combination subgroups, either in the absence or presence of hypoxia, frequently exhibited severe necrosis of endocrine components in pancreatic lobules. The combination of obesity, diabetes, and hypoxia was associated with inflammation, which was verified at the histopathological level.
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format: text/html
creator: Sarah Albogami
creator: Aziza Hassan
creator: Sekena H. Abdel-Aziem
creator: Saqer Alotaibi
creator: Fayez Althobaiti
creator: Ahmed El-Shehawi
creator: Alaa Alnefaie
creator: Reem Abdulla Alhamed
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.13990
publisher: PeerJ Inc.
rights: © 2022 Albogami et al.
abstract: Background Obesity and diabetes are becoming increasingly prevalent around the world. Inflammation, oxidative stress, insulin resistance, and glucose intolerance are linked to both obesity and type 2 diabetes, and these disorders are becoming major public health issues globally. Methods This study evaluated the effects of obesity, diabetes, and hypoxia on the levels of pro- and anti-inflammatory cytokines in rats. We divided 120 Wistar rats in two groups, male and female, each including six subgroups: control (CTRL), obese (high-fat diet (HFD)), diabetic (streptozotocin (STZ)-treated), hypoxic (HYX), obese + diabetic (HFD/STZ), and obese + diabetic + hypoxic (HFD/STZ/HYX). We examined the levels of tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL10, and leptin in pancreatic tissues and serum. Results No significant difference was observed in serum levels of cholesterol, triglycerides, and low-density lipoprotein (LDL) between HYX and CTRL in either sex. However, they were significantly increased, whereas high-density lipoprotein (HDL) was significantly decreased in HFD, STZ, HFD/STZ, and HFD/STZ/HPX compared with CTRL in both sexes. The expression of Tnf-α, Il6, and Lep was significantly upregulated in all subgroups compared with CTRL in both sexes. STZ and HYX showed no significant differences in the expression of these genes between sexes, whereas Tnf-α and Il6 were upregulated in male HFD, HFD/STZ, and HFD/STZ/HYX compared with females. Protein levels showed similar patterns. Combination subgroups, either in the absence or presence of hypoxia, frequently exhibited severe necrosis of endocrine components in pancreatic lobules. The combination of obesity, diabetes, and hypoxia was associated with inflammation, which was verified at the histopathological level.
bibliographic citation: Albogami et al. (2022) Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum. PeerJ 10:e13990 https://doi.org/10.7717/peerj.13990
date submitted: 2022-04-26
date accepted: 2022-08-11
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albogami
  given name: Sarah
author list: Agent
  family name: Hassan
  given name: Aziza
author list: Agent
  family name: Abdel-Aziem
  given name: Sekena H.
author list: Agent
  family name: Alotaibi
  given name: Saqer
author list: Agent
  family name: Althobaiti
  given name: Fayez
author list: Agent
  family name: El-Shehawi
  given name: Ahmed
author list: Agent
  family name: Alnefaie
  given name: Alaa
author list: Agent
  family name: Alhamed
  given name: Reem Abdulla
doi: 10.7717/peerj.13990
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Albogami et al.
attribution name: Albogami et al.

Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods
type: item
type: AcademicArticle
description: Background In recent years Staphylococcus epidermidis has been considered an important and frequent causative agent of health care-associated infections (HAIs), increasing the costs of hospitalization, morbidity, and mortality. Antibiotic resistance and biofilm formation are the most important obstacles in the treatment of infections caused by this microorganism. The aim of this work was to determine the most prevalent STs, as well as the antibiotic resistance profile and biofilm formation of S. epidermidis clinical isolates obtained from hospitalized patients in two hospitals in Acapulco, Guerrero in two time periods. Methods Twenty methicillin-resistant S. epidermidis strains isolated from patients with bacteremia in two hospitals in two time periods were analyzed. Identification and antibiotic susceptibility were performed using the Vitek automated system. Molecular confirmation of the identification and methicillin resistance was performed by duplex PCR of the mecA and nuc genes. Biofilm production was analyzed, and the clonal origin was determined by multilocus sequence typing (MLST). Results We identified 14 antibiotic resistance profiles as well as 13 sequence types (ST), including the new ST761. We also found that ST2 and ST23 were the most prevalent and, together with ST59, were found in both time periods. Seventeen of our clinical isolates were multidrug-resistant, but all of them were sensitive to linezolid and vancomycin, and this was not related to biofilm production. Additionally, we standardized a duplex PCR to identify methicillin-resistant S. epidermidis strains. In conclusion, S. epidermidis STs 2, 23, and 59 were found in both time periods. This study is the first report of S. epidermidis ST761. The clinical isolates obtained in this work showed a high multidrug resistance that is apparently not related to biofilm production.
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format: text/html
creator: Verónica I. Martínez-Santos
creator: David A. Torres-Añorve
creator: Gabriela Echániz-Aviles
creator: Isela Parra-Rojas
creator: Arturo Ramírez-Peralta
creator: Natividad Castro-Alarcón
subject: Microbiology
subject: Molecular Biology
subject: Hematology
subject: Infectious Diseases
description: doi:10.7717/peerj.14030
publisher: PeerJ Inc.
rights: © 2022 Martínez-Santos et al.
abstract: Background In recent years Staphylococcus epidermidis has been considered an important and frequent causative agent of health care-associated infections (HAIs), increasing the costs of hospitalization, morbidity, and mortality. Antibiotic resistance and biofilm formation are the most important obstacles in the treatment of infections caused by this microorganism. The aim of this work was to determine the most prevalent STs, as well as the antibiotic resistance profile and biofilm formation of S. epidermidis clinical isolates obtained from hospitalized patients in two hospitals in Acapulco, Guerrero in two time periods. Methods Twenty methicillin-resistant S. epidermidis strains isolated from patients with bacteremia in two hospitals in two time periods were analyzed. Identification and antibiotic susceptibility were performed using the Vitek automated system. Molecular confirmation of the identification and methicillin resistance was performed by duplex PCR of the mecA and nuc genes. Biofilm production was analyzed, and the clonal origin was determined by multilocus sequence typing (MLST). Results We identified 14 antibiotic resistance profiles as well as 13 sequence types (ST), including the new ST761. We also found that ST2 and ST23 were the most prevalent and, together with ST59, were found in both time periods. Seventeen of our clinical isolates were multidrug-resistant, but all of them were sensitive to linezolid and vancomycin, and this was not related to biofilm production. Additionally, we standardized a duplex PCR to identify methicillin-resistant S. epidermidis strains. In conclusion, S. epidermidis STs 2, 23, and 59 were found in both time periods. This study is the first report of S. epidermidis ST761. The clinical isolates obtained in this work showed a high multidrug resistance that is apparently not related to biofilm production.
bibliographic citation: Martínez-Santos et al. (2022) Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods. PeerJ 10:e14030 https://doi.org/10.7717/peerj.14030
date submitted: 2022-04-11
date accepted: 2022-08-16
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Santos
  given name: Verónica I.
author list: Agent
  family name: Torres-Añorve
  given name: David A.
author list: Agent
  family name: Echániz-Aviles
  given name: Gabriela
author list: Agent
  family name: Parra-Rojas
  given name: Isela
author list: Agent
  family name: Ramírez-Peralta
  given name: Arturo
author list: Agent
  family name: Castro-Alarcón
  given name: Natividad
doi: 10.7717/peerj.14030
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: © 2022 Martínez-Santos et al.
attribution name: Martínez-Santos et al.

Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation
type: item
type: AcademicArticle
description: The recording of hand kinematics during product manipulation is challenging, and certain degrees of freedom such as distal interphalangeal (DIP) joints are difficult to record owing to limitations of the motion capture systems used. DIP joint kinematics could be estimated by taking advantage of its kinematic linkage with proximal interphalangeal (PIP) and metacarpophalangeal joints. This work analyses this linkage both in free motion conditions and during the performance of 26 activities of daily living. We have studied the appropriateness of different types of linear regressions (several combinations of independent variables and constant coefficients) and sets of data (free motion and manipulation data) to obtain equations to estimate DIP joints kinematics both in free motion and manipulation conditions. Errors that arise when estimating DIP joint angles assuming linear relationships using the equations obtained both from free motion data and from manipulation data are compared for each activity of daily living performed. Estimation using manipulation condition equations implies a lower mean absolute error per task (from 5.87° to 13.67°) than using the free motion ones (from 9° to 17.87°), but it fails to provide accurate estimations when passive extension of DIP joints occurs while PIP is flexed. This work provides evidence showing that estimating DIP joint angles is only recommended when studying free motion or grasps where both joints are highly flexed and when using linear relationships that consider only PIP joint angles.
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format: text/html
creator: Alba Roda-Sales
creator: Joaquín L. Sancho-Bru
creator: Margarita Vergara
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.14051
publisher: PeerJ Inc.
rights: © 2022 Roda-Sales et al.
abstract: The recording of hand kinematics during product manipulation is challenging, and certain degrees of freedom such as distal interphalangeal (DIP) joints are difficult to record owing to limitations of the motion capture systems used. DIP joint kinematics could be estimated by taking advantage of its kinematic linkage with proximal interphalangeal (PIP) and metacarpophalangeal joints. This work analyses this linkage both in free motion conditions and during the performance of 26 activities of daily living. We have studied the appropriateness of different types of linear regressions (several combinations of independent variables and constant coefficients) and sets of data (free motion and manipulation data) to obtain equations to estimate DIP joints kinematics both in free motion and manipulation conditions. Errors that arise when estimating DIP joint angles assuming linear relationships using the equations obtained both from free motion data and from manipulation data are compared for each activity of daily living performed. Estimation using manipulation condition equations implies a lower mean absolute error per task (from 5.87° to 13.67°) than using the free motion ones (from 9° to 17.87°), but it fails to provide accurate estimations when passive extension of DIP joints occurs while PIP is flexed. This work provides evidence showing that estimating DIP joint angles is only recommended when studying free motion or grasps where both joints are highly flexed and when using linear relationships that consider only PIP joint angles.
bibliographic citation: Roda-Sales et al. (2022) Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation. PeerJ 10:e14051 https://doi.org/10.7717/peerj.14051
date submitted: 2022-04-22
date accepted: 2022-08-23
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roda-Sales
  given name: Alba
author list: Agent
  family name: Sancho-Bru
  given name: Joaquín L.
author list: Agent
  family name: Vergara
  given name: Margarita
doi: 10.7717/peerj.14051
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Roda-Sales et al.
attribution name: Roda-Sales et al.

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.
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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
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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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format: text/html
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.
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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.
format: application/pdf
format: text/html
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.

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