PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Morpho-physiological traits, biochemical response and phytoextraction potential of short-term copper stress on kenaf (Hibiscus cannabinus L.) seedlings
items: Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns
items: A retrospective assessment of different endodontic treatment protocols
items: Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses
items: The immunostimulatory activity of polysaccharides from Glycyrrhiza uralensis
items: Post-treatment of hyaluronan to decrease the apoptotic effects of carprofen in canine articular chondrocyte culture
items: Remarks on Mastigodiaptomus (Calanoida: Diaptomidae) from Mexico using integrative taxonomy, with a key of identification and three new species
items: Candidal carriage in saliva and subgingival plaque among smokers and non-smokers with chronic periodontitis—a cross-sectional study
items: A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice
items: Long non-coding RNA ERICH3-AS1 is an unfavorable prognostic factor for gastric cancer

Morpho-physiological traits, biochemical response and phytoextraction potential of short-term copper stress on kenaf (Hibiscus cannabinus L.) seedlings
type: item
type: AcademicArticle
description: Kenaf (Hibiscus cannabinus L.) is a fibrous crop, grown in tropical climate having huge biomass and can be a good candidate for the phytoremediation of different heavy metals. Consequently, the present study was conducted to explore morpho-physiological traits, photosynthetic pigments, gaseous exchange attributes, antioxidative response and phytoextraction of copper (Cu) in H. cannabinus grown under different levels of Cu i.e. 0 (control), 60, 120 and 180 µmol L−1 in Hoagland nutrient solution (pH 6.2). The results from the present study revealed that Cu toxicity reduced plant height, plant diameter, plant fresh weight, plant dry weight, photosynthetic pigments and gaseous exchange attributes compared to control. Moreover, excess Cu in the nutrient solution ameliorates contents of malondialdehyde (MDA), hydrogen peroxide (H2O2) and electrolyte leakage (EL) which showed that Cu induced oxidative damage in the roots and leaves of H. cannabinus. The oxidative stress which was induced by a high concentration of Cu in the nutrient solution is overcome by enzymatic activities of antioxidants which increased with the increase in Cu concentration, i.e. 60 and 120 µmol L−1, while the addition of Cu (180 µmol L−1) caused a reduction in the activities of superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in the roots and leaves of H. cannabinus. The results also demonstrated that an increase in Cu concentration in the nutrient solution causes an increase in Cu accumulation through roots, leaves and stems of H. cannabinus, although the highest Cu concentration was accumulated in roots while only a little transported to the above ground parts (leaves and stems) of the plants. All the values of bioaccumulation factor (BAF) and translocation factor (TF) were less than 1, which also indicated that a small quantity of Cu concentration is transported to the aboveground part of the plants. These findings suggested that phytotoxicity of Cu aff…
format: application/pdf
format: text/html
creator: Muhammad Hamzah Saleem
creator: Shah Fahad
creator: Muzammal Rehman
creator: Shah Saud
creator: Yousaf Jamal
creator: Sajjad Khan
creator: Lijun Liu
subject: Agricultural Science
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8321
publisher: PeerJ Inc.
rights: © 2020 Saleem et al.
abstract: Kenaf (Hibiscus cannabinus L.) is a fibrous crop, grown in tropical climate having huge biomass and can be a good candidate for the phytoremediation of different heavy metals. Consequently, the present study was conducted to explore morpho-physiological traits, photosynthetic pigments, gaseous exchange attributes, antioxidative response and phytoextraction of copper (Cu) in H. cannabinus grown under different levels of Cu i.e. 0 (control), 60, 120 and 180 µmol L−1 in Hoagland nutrient solution (pH 6.2). The results from the present study revealed that Cu toxicity reduced plant height, plant diameter, plant fresh weight, plant dry weight, photosynthetic pigments and gaseous exchange attributes compared to control. Moreover, excess Cu in the nutrient solution ameliorates contents of malondialdehyde (MDA), hydrogen peroxide (H2O2) and electrolyte leakage (EL) which showed that Cu induced oxidative damage in the roots and leaves of H. cannabinus. The oxidative stress which was induced by a high concentration of Cu in the nutrient solution is overcome by enzymatic activities of antioxidants which increased with the increase in Cu concentration, i.e. 60 and 120 µmol L−1, while the addition of Cu (180 µmol L−1) caused a reduction in the activities of superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in the roots and leaves of H. cannabinus. The results also demonstrated that an increase in Cu concentration in the nutrient solution causes an increase in Cu accumulation through roots, leaves and stems of H. cannabinus, although the highest Cu concentration was accumulated in roots while only a little transported to the above ground parts (leaves and stems) of the plants. All the values of bioaccumulation factor (BAF) and translocation factor (TF) were less than 1, which also indicated that a small quantity of Cu concentration is transported to the aboveground part of the plants. These findings suggested that phytotoxicity of Cu aff…
bibliographic citation: Saleem et al. (2020) Morpho-physiological traits, biochemical response and phytoextraction potential of short-term copper stress on kenaf (Hibiscus cannabinus L.) seedlings. PeerJ 8:e8321 https://doi.org/10.7717/peerj.8321
date submitted: 2019-10-21
date accepted: 2019-11-30
issued: 2020-01-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saleem
  given name: Muhammad Hamzah
author list: Agent
  family name: Fahad
  given name: Shah
author list: Agent
  family name: Rehman
  given name: Muzammal
author list: Agent
  family name: Saud
  given name: Shah
author list: Agent
  family name: Jamal
  given name: Yousaf
author list: Agent
  family name: Khan
  given name: Sajjad
author list: Agent
  family name: Liu
  given name: Lijun
doi: 10.7717/peerj.8321
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-30
copyright: ©2020 Saleem et al.
attribution name: Saleem et al.

Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns
type: item
type: AcademicArticle
description: Background When considering therapies for lung adenocarcinoma (LUAD) patients, the carcinogenic mechanisms of smokers are believed to differ from those who have never smoked. The rising trend in the proportion of nonsmokers in LUAD urgently requires the understanding of such differences at a molecular level for the development of precision medicine. Methods Three independent LUAD tumor sample sets—TCGA, SPORE and EDRN—were used. Genome patterns of expression (GE), copy number variation (CNV) and methylation (ME) were reviewed to discover the differences between them for both smokers and nonsmokers. Tobacco-related signature genes distinguishing these two groups of LUAD were identified using the GE, ME and CNV values of the whole genome. To do this, a novel iterative multi-step selection method based on the partial least squares (PLS) algorithm was proposed to overcome the high variable dimension and high noise inherent in the data. This method can thoroughly evaluate the importance of genes according to their statistical differences, biological functions and contributions to the tobacco exposure classification model. The kernel partial least squares (KPLS) method was used to further optimize the accuracies of the classification models. Results Forty-three, forty-eight and seventy-five genes were identified as GE, ME and CNV signatures, respectively, to distinguish smokers from nonsmokers. Using only the gene expression values of these 43 GE signature genes, ME values of the 48 ME signature genes or copy numbers of the 75 CNV signature genes, the accuracies of TCGA training and SPORE/EDRN independent validation datasets all exceed 76%. More importantly, the focal amplicon in Telomerase Reverse Transcriptase in nonsmokers, the broad deletion in ChrY in male nonsmokers and the greater amplification of MDM2 in female nonsmokers may explain why nonsmokers of both genders tend to suffer LUAD. These pattern analysis results may have clear biological interpretation in the m…
format: application/pdf
format: text/html
creator: Yan-mei Dong
creator: Li-da Qin
creator: Yi-fan Tong
creator: Qi-en He
creator: Ling Wang
creator: Kai Song
subject: Bioinformatics
subject: Genomics
subject: Oncology
subject: Statistics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.8349
publisher: PeerJ Inc.
rights: © 2020 Dong et al.
abstract: Background When considering therapies for lung adenocarcinoma (LUAD) patients, the carcinogenic mechanisms of smokers are believed to differ from those who have never smoked. The rising trend in the proportion of nonsmokers in LUAD urgently requires the understanding of such differences at a molecular level for the development of precision medicine. Methods Three independent LUAD tumor sample sets—TCGA, SPORE and EDRN—were used. Genome patterns of expression (GE), copy number variation (CNV) and methylation (ME) were reviewed to discover the differences between them for both smokers and nonsmokers. Tobacco-related signature genes distinguishing these two groups of LUAD were identified using the GE, ME and CNV values of the whole genome. To do this, a novel iterative multi-step selection method based on the partial least squares (PLS) algorithm was proposed to overcome the high variable dimension and high noise inherent in the data. This method can thoroughly evaluate the importance of genes according to their statistical differences, biological functions and contributions to the tobacco exposure classification model. The kernel partial least squares (KPLS) method was used to further optimize the accuracies of the classification models. Results Forty-three, forty-eight and seventy-five genes were identified as GE, ME and CNV signatures, respectively, to distinguish smokers from nonsmokers. Using only the gene expression values of these 43 GE signature genes, ME values of the 48 ME signature genes or copy numbers of the 75 CNV signature genes, the accuracies of TCGA training and SPORE/EDRN independent validation datasets all exceed 76%. More importantly, the focal amplicon in Telomerase Reverse Transcriptase in nonsmokers, the broad deletion in ChrY in male nonsmokers and the greater amplification of MDM2 in female nonsmokers may explain why nonsmokers of both genders tend to suffer LUAD. These pattern analysis results may have clear biological interpretation in the m…
bibliographic citation: Dong et al. (2020) Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns. PeerJ 8:e8349 https://doi.org/10.7717/peerj.8349
date submitted: 2019-06-05
date accepted: 2019-12-04
issued: 2020-01-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Yan-mei
author list: Agent
  family name: Qin
  given name: Li-da
author list: Agent
  family name: Tong
  given name: Yi-fan
author list: Agent
  family name: He
  given name: Qi-en
author list: Agent
  family name: Wang
  given name: Ling
author list: Agent
  family name: Song
  given name: Kai
doi: 10.7717/peerj.8349
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-30
copyright: © 2020 Dong et al.
attribution name: Dong et al.

A retrospective assessment of different endodontic treatment protocols
type: item
type: AcademicArticle
description: Background The aim of this study was to assess the clinical impact of non-surgical root canal treatments (NSRCT) performed with different treatment protocols on the probability of tooth survival without untoward events and to identify predictors influencing the outcome. Methods During the period from July 1999 to October 2016, 5,858 patients were identified in which 9,967 NSRCTs were performed. The treatments were followed up and divided into three groups. In Group 1 root canal treatment was performed with hand instruments, in Group 2 with multiple file rotary instruments and passive ultrasonic irrigation (PUI), and Group 3 was treated with Reciproc instruments and PUI. Untoward events were defined as orthograde retreatment, apicoectomy or extraction of the tooth after initial treatment. Weibull regression was used to analyse the data. Results A total of 9,938 cases could be included into the analyses. The results showed 5-years predicted survival rates without untoward events of 73.9% (95% CI [71.7%–76.1%]), 75.1% (95% CI [71.7%–78.0%]) and 78.4% (95% CI [75.1%–81.4%]) for study group 1 (N = 5,580), 2 (N = 1,700) and 3 (N = 2,658), respectively. The differences between Group 1 and 3 were statistically significant (p < 0.006). Higher age of the patient (per year increase) and number of earlier NSRCTs (per unit increase) reduce the survival without untoward events statistically significant (both p < 0.02), while treatment of premolars had a statistically significant lower hazard ratio [0.89 (95% CI [0.79–0.99]; p = 0.030)] compared to treatment of molars and anterior teeth. A higher number of supportive periodontal treatments (per unit increase) improved tooth survival without untoward events highly significant (p < 0.0001). Discussion More recent endodontic treatment protocols involving reciprocating instruments and PUI appear to be associated with higher tooth survival rates without untoward events compared to hand instruments.
format: application/pdf
format: text/html
creator: Andreas Bartols
creator: Carsten Bormann
creator: Luisa Werner
creator: Melanie Schienle
creator: Winfried Walther
creator: Christof E. Dörfer
subject: Dentistry
description: doi:10.7717/peerj.8495
publisher: PeerJ Inc.
rights: © 2020 Bartols et al.
abstract: Background The aim of this study was to assess the clinical impact of non-surgical root canal treatments (NSRCT) performed with different treatment protocols on the probability of tooth survival without untoward events and to identify predictors influencing the outcome. Methods During the period from July 1999 to October 2016, 5,858 patients were identified in which 9,967 NSRCTs were performed. The treatments were followed up and divided into three groups. In Group 1 root canal treatment was performed with hand instruments, in Group 2 with multiple file rotary instruments and passive ultrasonic irrigation (PUI), and Group 3 was treated with Reciproc instruments and PUI. Untoward events were defined as orthograde retreatment, apicoectomy or extraction of the tooth after initial treatment. Weibull regression was used to analyse the data. Results A total of 9,938 cases could be included into the analyses. The results showed 5-years predicted survival rates without untoward events of 73.9% (95% CI [71.7%–76.1%]), 75.1% (95% CI [71.7%–78.0%]) and 78.4% (95% CI [75.1%–81.4%]) for study group 1 (N = 5,580), 2 (N = 1,700) and 3 (N = 2,658), respectively. The differences between Group 1 and 3 were statistically significant (p < 0.006). Higher age of the patient (per year increase) and number of earlier NSRCTs (per unit increase) reduce the survival without untoward events statistically significant (both p < 0.02), while treatment of premolars had a statistically significant lower hazard ratio [0.89 (95% CI [0.79–0.99]; p = 0.030)] compared to treatment of molars and anterior teeth. A higher number of supportive periodontal treatments (per unit increase) improved tooth survival without untoward events highly significant (p < 0.0001). Discussion More recent endodontic treatment protocols involving reciprocating instruments and PUI appear to be associated with higher tooth survival rates without untoward events compared to hand instruments.
bibliographic citation: Bartols et al. (2020) A retrospective assessment of different endodontic treatment protocols. PeerJ 8:e8495 https://doi.org/10.7717/peerj.8495
date submitted: 2019-06-17
date accepted: 2019-12-31
issued: 2020-01-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartols
  given name: Andreas
author list: Agent
  family name: Bormann
  given name: Carsten
author list: Agent
  family name: Werner
  given name: Luisa
author list: Agent
  family name: Schienle
  given name: Melanie
author list: Agent
  family name: Walther
  given name: Winfried
author list: Agent
  family name: Dörfer
  given name: Christof E.
doi: 10.7717/peerj.8495
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-30
copyright: ©2020 Bartols et al.
attribution name: Bartols et al.

Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses
type: item
type: AcademicArticle
description: Drought and heat stresses can influence the expressions of genes, and thereby affect the growth and development of plants. Alternative splicing (AS) of genes plays crucial roles through increasing transcriptome diversity in plant stress responses. Tea plants, widely cultivated in the tropics and subtropics, are often simultaneously exposed to drought and heat stresses. In the present study, we performed a global transcriptome of tea leaves treated with drought, heat or their combination. In total, 19,019, 20,025 and 20,253 genes underwent AS in response to drought (DT), heat (HT) and their combined stress (HD), respectively, of which 12,178, 11,912 and 14,413 genes differentially spliced in response to DT, HT and HD, respectively. Also, 2,447 specific differentially spliced genes (DSGs) were found only in response to HD. All DSGs accounted for 48% of the annotated genes in tea tree genome. Comparison of DSGs and differentially expressive genes (DEGs) showed that the proportions of HT and HD-induced DSGs were 13.4% and 9.2%, while the proportion of DT increased to 28.1%. Moreover, the DEG-DSG overlapped genes tended to be enriched in a wide large of pathways in response to DT. The results indicated that the AS of genes in tea leaves was extensively triggered by drought, heat and their combined stresses. In addition, the AS enhanced the transcriptome adaption in response to drought and heat stresses, and the AS also provoked specific molecular functions in response to drought and heat synergy stress. The study might have practical significance for molecular genetic breeding of tea plants with stress resistance.
format: application/pdf
format: text/html
creator: Yiqian Ding
creator: Yu Wang
creator: Chen Qiu
creator: Wenjun Qian
creator: Hui Xie
creator: Zhaotang Ding
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.8258
publisher: PeerJ Inc.
rights: © 2020 Ding et al.
abstract: Drought and heat stresses can influence the expressions of genes, and thereby affect the growth and development of plants. Alternative splicing (AS) of genes plays crucial roles through increasing transcriptome diversity in plant stress responses. Tea plants, widely cultivated in the tropics and subtropics, are often simultaneously exposed to drought and heat stresses. In the present study, we performed a global transcriptome of tea leaves treated with drought, heat or their combination. In total, 19,019, 20,025 and 20,253 genes underwent AS in response to drought (DT), heat (HT) and their combined stress (HD), respectively, of which 12,178, 11,912 and 14,413 genes differentially spliced in response to DT, HT and HD, respectively. Also, 2,447 specific differentially spliced genes (DSGs) were found only in response to HD. All DSGs accounted for 48% of the annotated genes in tea tree genome. Comparison of DSGs and differentially expressive genes (DEGs) showed that the proportions of HT and HD-induced DSGs were 13.4% and 9.2%, while the proportion of DT increased to 28.1%. Moreover, the DEG-DSG overlapped genes tended to be enriched in a wide large of pathways in response to DT. The results indicated that the AS of genes in tea leaves was extensively triggered by drought, heat and their combined stresses. In addition, the AS enhanced the transcriptome adaption in response to drought and heat stresses, and the AS also provoked specific molecular functions in response to drought and heat synergy stress. The study might have practical significance for molecular genetic breeding of tea plants with stress resistance.
bibliographic citation: Ding et al. (2020) Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses. PeerJ 8:e8258 https://doi.org/10.7717/peerj.8258
date submitted: 2019-05-31
date accepted: 2019-11-20
issued: 2020-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Yiqian
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Qiu
  given name: Chen
author list: Agent
  family name: Qian
  given name: Wenjun
author list: Agent
  family name: Xie
  given name: Hui
author list: Agent
  family name: Ding
  given name: Zhaotang
doi: 10.7717/peerj.8258
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-29
copyright: ©2020 Ding et al.
attribution name: Ding et al.

The immunostimulatory activity of polysaccharides from Glycyrrhiza uralensis
type: item
type: AcademicArticle
description: Background The enhancement of immunity is very important for immunocompromised patients such as cancer patients with radiotherapy or chemotherapy. Glycyrrhiza uralensis has been used as food and medicine for a long history. G. uralensis polysaccharides (GUPS) were prepared and its immunostimulatory effects were investigated. Methods Human monocyte-derived dendritic cells (DCs) and murine bone marrow-derived DCs were treated with different concentrations of GUPS. The DCs maturation and cytokine production were analyzed by flow cytometry and ELISA, respectively. Inhibitors and Western blot were used to study the mechanism of GUPS. The immunostimulatory effects of GUPS were further evaluated by naïve mouse model and immunosuppressive mouse model induced by cyclophosphamide. Results GUPS significantly promoted the maturation and cytokine secretion of human monocyte-derived DCs and murine bone marrow-derived DCs through TLR4 and down-stream p38, JNK and NF-κB signaling pathways. Interestingly, the migration of GUPS treated-DCs to lymph node was increased. In the mouse model, GUPS increased IL-12 production in sera but not for TNF-α. Moreover, GUPS ameliorated the side effect of cyclophosphamide and improved the immunity of immunosuppressive mice induced by cyclophosphamide. These results suggested that GUPS might be used for cancer therapy to ameliorate the side effect of chemotherapy and enhance the immunity.
format: application/pdf
format: text/html
creator: Adila Aipire
creator: Mahepali Mahabati
creator: Shanshan Cai
creator: Xianxian Wei
creator: Pengfei Yuan
creator: Alimu Aimaier
creator: Xinhui Wang
creator: Jinyao Li
subject: Cell Biology
subject: Immunology
description: doi:10.7717/peerj.8294
publisher: PeerJ Inc.
rights: © 2020 Aipire et al.
abstract: Background The enhancement of immunity is very important for immunocompromised patients such as cancer patients with radiotherapy or chemotherapy. Glycyrrhiza uralensis has been used as food and medicine for a long history. G. uralensis polysaccharides (GUPS) were prepared and its immunostimulatory effects were investigated. Methods Human monocyte-derived dendritic cells (DCs) and murine bone marrow-derived DCs were treated with different concentrations of GUPS. The DCs maturation and cytokine production were analyzed by flow cytometry and ELISA, respectively. Inhibitors and Western blot were used to study the mechanism of GUPS. The immunostimulatory effects of GUPS were further evaluated by naïve mouse model and immunosuppressive mouse model induced by cyclophosphamide. Results GUPS significantly promoted the maturation and cytokine secretion of human monocyte-derived DCs and murine bone marrow-derived DCs through TLR4 and down-stream p38, JNK and NF-κB signaling pathways. Interestingly, the migration of GUPS treated-DCs to lymph node was increased. In the mouse model, GUPS increased IL-12 production in sera but not for TNF-α. Moreover, GUPS ameliorated the side effect of cyclophosphamide and improved the immunity of immunosuppressive mice induced by cyclophosphamide. These results suggested that GUPS might be used for cancer therapy to ameliorate the side effect of chemotherapy and enhance the immunity.
bibliographic citation: Aipire et al. (2020) The immunostimulatory activity of polysaccharides from Glycyrrhiza uralensis. PeerJ 8:e8294 https://doi.org/10.7717/peerj.8294
date submitted: 2019-08-08
date accepted: 2019-11-25
issued: 2020-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aipire
  given name: Adila
author list: Agent
  family name: Mahabati
  given name: Mahepali
author list: Agent
  family name: Cai
  given name: Shanshan
author list: Agent
  family name: Wei
  given name: Xianxian
author list: Agent
  family name: Yuan
  given name: Pengfei
author list: Agent
  family name: Aimaier
  given name: Alimu
author list: Agent
  family name: Wang
  given name: Xinhui
author list: Agent
  family name: Li
  given name: Jinyao
doi: 10.7717/peerj.8294
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-29
copyright: ©2020 Aipire et al.
attribution name: Aipire et al.

Post-treatment of hyaluronan to decrease the apoptotic effects of carprofen in canine articular chondrocyte culture
type: item
type: AcademicArticle
description: A major concern associated with the use of drugs is their adverse side effects. Specific examples of the drugs of concern include antibiotic agents and non-steroidal anti-inflammatory drugs. Despite the presence of a high degree of efficacy for specific conditions, these drugs may deteriorate the surrounding tissues that are exposed to them. Often, carprofen is used for joint inflammation; however, it may stimulate cartilage degradation which can then lead to osteoarthritis progression. In this study, hyaluronan was combined with carprofen treatment in three different applications (pre-treatment, co-treatment and post-treatment) on normal canine chondrocytes to determine whether Hyaluronan (HA) is capable of mitigating the degree of chondrotoxicity of carprofen. Our findings revealed that carprofen at IC20 (0.16 mg/mL) decreased viability and increased nitric oxide (NO) production. Importantly, carprofen induced the apoptosis of canine chondrocytes via the up-regulation of Bax, Casp3, Casp8, Casp9 and NOS2 as compared to the control group. Although the co-treatment of HA and carprofen appeared not to further alleviate the chondrotoxicity of carprofen due to the presence of a high number of apoptotic chondrocytes, post-treatment with HA (carprofen treatment for 24 h and then changed to HA for 24 h) resulted in a decrease in chondrocyte apoptosis by the down-regulation of Bax, Casp3, Casp8, Casp9, NOS2, along with NO production when compared with the treatment of carprofen for 48 h (P < 0.05). These results suggest that HA can be used as a therapeutic agent to mitigate the degree of chondrotoxicity of carprofen.
format: application/pdf
format: text/html
creator: Korakot Nganvongpanit
creator: Thippaporn Euppayo
creator: Puntita Siengdee
creator: Kittisak Buddhachat
creator: Siriwadee Chomdej
creator: Siriwan Ongchai
subject: Veterinary Medicine
subject: Orthopedics
subject: Pharmacology
description: doi:10.7717/peerj.8355
publisher: PeerJ Inc.
rights: © 2020 Nganvongpanit et al.
abstract: A major concern associated with the use of drugs is their adverse side effects. Specific examples of the drugs of concern include antibiotic agents and non-steroidal anti-inflammatory drugs. Despite the presence of a high degree of efficacy for specific conditions, these drugs may deteriorate the surrounding tissues that are exposed to them. Often, carprofen is used for joint inflammation; however, it may stimulate cartilage degradation which can then lead to osteoarthritis progression. In this study, hyaluronan was combined with carprofen treatment in three different applications (pre-treatment, co-treatment and post-treatment) on normal canine chondrocytes to determine whether Hyaluronan (HA) is capable of mitigating the degree of chondrotoxicity of carprofen. Our findings revealed that carprofen at IC20 (0.16 mg/mL) decreased viability and increased nitric oxide (NO) production. Importantly, carprofen induced the apoptosis of canine chondrocytes via the up-regulation of Bax, Casp3, Casp8, Casp9 and NOS2 as compared to the control group. Although the co-treatment of HA and carprofen appeared not to further alleviate the chondrotoxicity of carprofen due to the presence of a high number of apoptotic chondrocytes, post-treatment with HA (carprofen treatment for 24 h and then changed to HA for 24 h) resulted in a decrease in chondrocyte apoptosis by the down-regulation of Bax, Casp3, Casp8, Casp9, NOS2, along with NO production when compared with the treatment of carprofen for 48 h (P < 0.05). These results suggest that HA can be used as a therapeutic agent to mitigate the degree of chondrotoxicity of carprofen.
bibliographic citation: Nganvongpanit et al. (2020) Post-treatment of hyaluronan to decrease the apoptotic effects of carprofen in canine articular chondrocyte culture. PeerJ 8:e8355 https://doi.org/10.7717/peerj.8355
date submitted: 2019-07-08
date accepted: 2019-12-04
issued: 2020-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nganvongpanit
  given name: Korakot
author list: Agent
  family name: Euppayo
  given name: Thippaporn
author list: Agent
  family name: Siengdee
  given name: Puntita
author list: Agent
  family name: Buddhachat
  given name: Kittisak
author list: Agent
  family name: Chomdej
  given name: Siriwadee
author list: Agent
  family name: Ongchai
  given name: Siriwan
doi: 10.7717/peerj.8355
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-29
copyright: © 2020 Nganvongpanit et al.
attribution name: Nganvongpanit et al.

Remarks on Mastigodiaptomus (Calanoida: Diaptomidae) from Mexico using integrative taxonomy, with a key of identification and three new species
type: item
type: AcademicArticle
description: Background In Mexico, species of four families of free-living calanoid copepods have been recorded as inhabitants of several freshwater systems. These families are Centropagidae, Temoridae, Pseudodiaptomidae and Diaptomidae. The genera Leptodiaptomus and Mastigodiaptomus are the most speciose diaptomid genera in Mexico, and they inhabit natural and artificial lakes, ephemeral ponds, springs, and caverns. Leptodiaptomus is considered as an endemic Nearctic genus, whereas Mastigodiaptomus is a widely distributed Neotropical genus in the southern USA, Mexico, the Caribbean Islands and Central America. Based on new and recent evidence, Mastigodiaptomus diversity has been underestimated: six species of the genus were known before 2000. In this work three new Mastigodiaptomus species have been described from different regions of Mexico by using integrative taxonomy. We also gave amended diagnosis of M. nesus Bowman (1986) and M. patzcuarensis s. str. (Kiefer, 1938). Methods In this work, the taxonomic status of the species was clarified using modern, integrative method based on the COI gene as a DNA marker, plus micro-structural analysis (based on SEM and ligth microscopy). Results Three new species of Mastigodiaptomus were described based on genetic and morphological analyses: M. alexei sp. n., M. ha sp. n. and M. cihuatlan sp. n. Also amended description of M. nesus, morphological variation of M. patzcuarensis s. str., and a comparison of them with all known sequences within the genus are provided. These new findings show that in Mastigodiaptomus differences in several cuticular microstructures of several appendages (such as the antennules, the fifth legs, or the urosomites of these copepods) agree with the interspecific genetic divergence >3% observed in sequences of the COI gene, and the integration of this information is a powerful tool in species delineation.
format: application/pdf
format: text/html
creator: Martha A. Gutiérrez-Aguirre
creator: Adrián Cervantes-Martínez
creator: Manuel Elías-Gutiérrez
creator: Alfonso Lugo-Vázquez
subject: Biodiversity
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.8416
publisher: PeerJ Inc.
rights: © 2020 Gutiérrez-Aguirre et al.
abstract: Background In Mexico, species of four families of free-living calanoid copepods have been recorded as inhabitants of several freshwater systems. These families are Centropagidae, Temoridae, Pseudodiaptomidae and Diaptomidae. The genera Leptodiaptomus and Mastigodiaptomus are the most speciose diaptomid genera in Mexico, and they inhabit natural and artificial lakes, ephemeral ponds, springs, and caverns. Leptodiaptomus is considered as an endemic Nearctic genus, whereas Mastigodiaptomus is a widely distributed Neotropical genus in the southern USA, Mexico, the Caribbean Islands and Central America. Based on new and recent evidence, Mastigodiaptomus diversity has been underestimated: six species of the genus were known before 2000. In this work three new Mastigodiaptomus species have been described from different regions of Mexico by using integrative taxonomy. We also gave amended diagnosis of M. nesus Bowman (1986) and M. patzcuarensis s. str. (Kiefer, 1938). Methods In this work, the taxonomic status of the species was clarified using modern, integrative method based on the COI gene as a DNA marker, plus micro-structural analysis (based on SEM and ligth microscopy). Results Three new species of Mastigodiaptomus were described based on genetic and morphological analyses: M. alexei sp. n., M. ha sp. n. and M. cihuatlan sp. n. Also amended description of M. nesus, morphological variation of M. patzcuarensis s. str., and a comparison of them with all known sequences within the genus are provided. These new findings show that in Mastigodiaptomus differences in several cuticular microstructures of several appendages (such as the antennules, the fifth legs, or the urosomites of these copepods) agree with the interspecific genetic divergence >3% observed in sequences of the COI gene, and the integration of this information is a powerful tool in species delineation.
bibliographic citation: Gutiérrez-Aguirre et al. (2020) Remarks on Mastigodiaptomus (Calanoida: Diaptomidae) from Mexico using integrative taxonomy, with a key of identification and three new species. PeerJ 8:e8416 https://doi.org/10.7717/peerj.8416
date submitted: 2019-09-27
date accepted: 2019-12-16
issued: 2020-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gutiérrez-Aguirre
  given name: Martha A.
author list: Agent
  family name: Cervantes-Martínez
  given name: Adrián
author list: Agent
  family name: Elías-Gutiérrez
  given name: Manuel
author list: Agent
  family name: Lugo-Vázquez
  given name: Alfonso
doi: 10.7717/peerj.8416
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-29
copyright: © 2020 Gutiérrez-Aguirre et al.
attribution name: Gutiérrez-Aguirre et al.

Candidal carriage in saliva and subgingival plaque among smokers and non-smokers with chronic periodontitis—a cross-sectional study
type: item
type: AcademicArticle
description: Background and Objectives Studies of gum or periodontal disease have focused mainly on bacterial pathogens. However, information related to fungal species in the saliva and subgingival mileu is particularly lacking in smokers with periodontitis. This cross-sectional study compared the prevalence of various Candida species in saliva and subgingival plaque samples of smokers and non-smokers with periodontal disease. Methodology Study subjects were recruited into three group—Group 1: Smokers with chronic periodontitis (N = 30), Group 2: Non-smokers with chronic periodontitis (N = 30) and Group 3: Healthy controls (N = 30). Clinical parameters recorded included plaque index (PI), gingival index (GI), periodontal probing depth (PPD) and clinical attachment loss (CAL). Saliva and subgingival plaque samples were collected from subjects from the above groups. The collected samples were processed for isolation and identification of various Candida species using CHROMagar chromogenic media. Additionally, antifungal susceptibility tests were performed for the isolated Candida species in order to assess antifungal drug resistance to fluconazole and voriconazole. Results Prevalence of Candida species in saliva samples was quantified as 76.6% in Group 1, 73.3% in Group 2 and 36.6% in Group 3 and statistically significant differences were observed between groups 1 & 3. Prevalence of Candida species in subgingival plaque samples was quantified as 73.3% in Group 1, 66.6% in Group 2 and 60% in Group 3 and no statistically significant differences were observed between groups. Candida albicans was the most frequently isolated species followed by Candida krusei and Candida tropicalis. A positive correlation was observed for smoking exposure, pack years and Candida colonization. A marginally significant positive correlation was observed between Candida colonization and increasing pocket depth and attachment loss. Antifungal drug resistance was mainly observed for Candida krusei in both s…
format: application/pdf
format: text/html
creator: Gayathri Santhana Krishnan
creator: Dilip Naik
creator: Ashita Uppoor
creator: Sangeeta Nayak
creator: Shrikala Baliga
creator: Abhiram Maddi
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.8441
publisher: PeerJ Inc.
rights: © 2020 Santhana Krishnan et al.
abstract: Background and Objectives Studies of gum or periodontal disease have focused mainly on bacterial pathogens. However, information related to fungal species in the saliva and subgingival mileu is particularly lacking in smokers with periodontitis. This cross-sectional study compared the prevalence of various Candida species in saliva and subgingival plaque samples of smokers and non-smokers with periodontal disease. Methodology Study subjects were recruited into three group—Group 1: Smokers with chronic periodontitis (N = 30), Group 2: Non-smokers with chronic periodontitis (N = 30) and Group 3: Healthy controls (N = 30). Clinical parameters recorded included plaque index (PI), gingival index (GI), periodontal probing depth (PPD) and clinical attachment loss (CAL). Saliva and subgingival plaque samples were collected from subjects from the above groups. The collected samples were processed for isolation and identification of various Candida species using CHROMagar chromogenic media. Additionally, antifungal susceptibility tests were performed for the isolated Candida species in order to assess antifungal drug resistance to fluconazole and voriconazole. Results Prevalence of Candida species in saliva samples was quantified as 76.6% in Group 1, 73.3% in Group 2 and 36.6% in Group 3 and statistically significant differences were observed between groups 1 & 3. Prevalence of Candida species in subgingival plaque samples was quantified as 73.3% in Group 1, 66.6% in Group 2 and 60% in Group 3 and no statistically significant differences were observed between groups. Candida albicans was the most frequently isolated species followed by Candida krusei and Candida tropicalis. A positive correlation was observed for smoking exposure, pack years and Candida colonization. A marginally significant positive correlation was observed between Candida colonization and increasing pocket depth and attachment loss. Antifungal drug resistance was mainly observed for Candida krusei in both s…
bibliographic citation: Santhana Krishnan et al. (2020) Candidal carriage in saliva and subgingival plaque among smokers and non-smokers with chronic periodontitis—a cross-sectional study. PeerJ 8:e8441 https://doi.org/10.7717/peerj.8441
date submitted: 2019-08-23
date accepted: 2019-12-19
issued: 2020-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santhana Krishnan
  given name: Gayathri
author list: Agent
  family name: Naik
  given name: Dilip
author list: Agent
  family name: Uppoor
  given name: Ashita
author list: Agent
  family name: Nayak
  given name: Sangeeta
author list: Agent
  family name: Baliga
  given name: Shrikala
author list: Agent
  family name: Maddi
  given name: Abhiram
doi: 10.7717/peerj.8441
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-29
copyright: ©2020 Santhana Krishnan et al.
attribution name: Santhana Krishnan et al.

A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice
type: item
type: AcademicArticle
description: Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing.
format: application/pdf
format: text/html
creator: Xiaoli Liu
creator: Xiujuan Zhou
creator: Kang Li
creator: Dehong Wang
creator: Yuanhao Ding
creator: Xianqing Liu
creator: Jie Luo
creator: Chuanying Fang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8491
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing.
bibliographic citation: Liu et al. (2020) A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice. PeerJ 8:e8491 https://doi.org/10.7717/peerj.8491
date submitted: 2019-10-22
date accepted: 2019-12-30
issued: 2020-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Zhou
  given name: Xiujuan
author list: Agent
  family name: Li
  given name: Kang
author list: Agent
  family name: Wang
  given name: Dehong
author list: Agent
  family name: Ding
  given name: Yuanhao
author list: Agent
  family name: Liu
  given name: Xianqing
author list: Agent
  family name: Luo
  given name: Jie
author list: Agent
  family name: Fang
  given name: Chuanying
doi: 10.7717/peerj.8491
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-29
copyright: © 2020 Liu et al.
attribution name: Liu et al.

Long non-coding RNA ERICH3-AS1 is an unfavorable prognostic factor for gastric cancer
type: item
type: AcademicArticle
description: Long non-coding RNAs (lncRNAs) play important roles in gastric cancer (GC), but the mechanism is not fully clear. ERICH3-AS1 (ERICH3 antisense RNA1) is affiliated with the non-coding RNA class which has proven to be involved in the prognostic of GC, but the function of ERICH3-AS1 is still unclear. In this study, we aim to explore the potential function of ERICH3-AS1 in the development of GC and analyze the prognostic role of ERICH3-AS1 in GC. We found that the lncRNA ERICH3-AS1 was significantly up-regulated in GC tissues in the analysis of The Cancer Genome Atlas (TCGA) data; the Kaplan-Meier analysis showed that the higher the expression of ERICH3-AS1 was, the earlier the recurrence and the poorer the prognosis would be in patients. Cox univariate and multivariate analyses revealed that ERICH3-AS1 was a risk factor of disease-free survival (DFS) (p < 0.05) and overall survival (OS) (p < 0.05) of patients. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, it demonstrated that the ERBB pathways, the mitogen-activated protein kinase (MAPK) pathways, the MTOR pathways, p53 pathways and Wnt pathways were differentially enriched in ERICH3-AS1 high expression phenotype. Furthermore, the correlation analysis showed that ERICH3-AS1 had significant correlations with apoptosis-related proteins such as BCL2L10 and CASP14; cell cycle-associated proteins CDK14 and invasion and migration-associated proteins such as MMP20, MMP26 and MMP27. In summary, we identified that increased ERICH3-AS1 might be a potential biomarker for diagnosis and independent prognostic factor of GC. Moreover, ERICH3-AS1 might participate in the oncogenesis and development of tumors via cell cycle and apoptosis pathway mediated by ERBB, MAPK, MTOR, p53 and Wnt pathways.
format: application/pdf
format: text/html
creator: Qiongyun Chen
creator: Xiaoqing Huang
creator: Xuan Dong
creator: Jingtong Wu
creator: Fei Teng
creator: Hongzhi Xu
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.8050
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Long non-coding RNAs (lncRNAs) play important roles in gastric cancer (GC), but the mechanism is not fully clear. ERICH3-AS1 (ERICH3 antisense RNA1) is affiliated with the non-coding RNA class which has proven to be involved in the prognostic of GC, but the function of ERICH3-AS1 is still unclear. In this study, we aim to explore the potential function of ERICH3-AS1 in the development of GC and analyze the prognostic role of ERICH3-AS1 in GC. We found that the lncRNA ERICH3-AS1 was significantly up-regulated in GC tissues in the analysis of The Cancer Genome Atlas (TCGA) data; the Kaplan-Meier analysis showed that the higher the expression of ERICH3-AS1 was, the earlier the recurrence and the poorer the prognosis would be in patients. Cox univariate and multivariate analyses revealed that ERICH3-AS1 was a risk factor of disease-free survival (DFS) (p < 0.05) and overall survival (OS) (p < 0.05) of patients. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, it demonstrated that the ERBB pathways, the mitogen-activated protein kinase (MAPK) pathways, the MTOR pathways, p53 pathways and Wnt pathways were differentially enriched in ERICH3-AS1 high expression phenotype. Furthermore, the correlation analysis showed that ERICH3-AS1 had significant correlations with apoptosis-related proteins such as BCL2L10 and CASP14; cell cycle-associated proteins CDK14 and invasion and migration-associated proteins such as MMP20, MMP26 and MMP27. In summary, we identified that increased ERICH3-AS1 might be a potential biomarker for diagnosis and independent prognostic factor of GC. Moreover, ERICH3-AS1 might participate in the oncogenesis and development of tumors via cell cycle and apoptosis pathway mediated by ERBB, MAPK, MTOR, p53 and Wnt pathways.
bibliographic citation: Chen et al. (2020) Long non-coding RNA ERICH3-AS1 is an unfavorable prognostic factor for gastric cancer. PeerJ 8:e8050 https://doi.org/10.7717/peerj.8050
date submitted: 2019-03-12
date accepted: 2019-10-16
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qiongyun
author list: Agent
  family name: Huang
  given name: Xiaoqing
author list: Agent
  family name: Dong
  given name: Xuan
author list: Agent
  family name: Wu
  given name: Jingtong
author list: Agent
  family name: Teng
  given name: Fei
author list: Agent
  family name: Xu
  given name: Hongzhi
doi: 10.7717/peerj.8050
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: ©2020 Chen et al.
attribution name: Chen et al.

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