PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects
items: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog
items: Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study
items: Genome-wide sequence identification and expression analysis of N6-methyladenosine demethylase in sugar beet (Beta vulgaris L.) under salt stress
items: Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma
items: Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach
items: Beyond the prey: male spiders highly invest in silk when producing worthless gifts
items: Protection of catalpol against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway
items: Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma
items: Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola

Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects
type: item
type: AcademicArticle
description: Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the clone CCN 51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao industry will be discussed highlighting the major challenges for flavor enhancement and its relevance as a platform for the identification of novel genetic markers for cultivar improvement in breeding programs.
format: application/pdf
format: text/html
creator: Ramon E. Jaimez
creator: Luigy Barragan
creator: Miguel Fernández-Niño
creator: Ludger A. Wessjohann
creator: George Cedeño-Garcia
creator: Ignacio Sotomayor Cantos
creator: Francisco Arteaga
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.12676
publisher: PeerJ Inc.
rights: © 2022 Jaimez et al.
abstract: Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the clone CCN 51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao industry will be discussed highlighting the major challenges for flavor enhancement and its relevance as a platform for the identification of novel genetic markers for cultivar improvement in breeding programs.
bibliographic citation: Jaimez et al. (2022) Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects. PeerJ 10:e12676 https://doi.org/10.7717/peerj.12676
date submitted: 2021-09-03
date accepted: 2021-12-02
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaimez
  given name: Ramon E.
author list: Agent
  family name: Barragan
  given name: Luigy
author list: Agent
  family name: Fernández-Niño
  given name: Miguel
author list: Agent
  family name: Wessjohann
  given name: Ludger A.
author list: Agent
  family name: Cedeño-Garcia
  given name: George
author list: Agent
  family name: Sotomayor Cantos
  given name: Ignacio
author list: Agent
  family name: Arteaga
  given name: Francisco
doi: 10.7717/peerj.12676
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Jaimez et al.
attribution name: Jaimez et al.

Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog
type: item
type: AcademicArticle
description: The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect agains…
format: application/pdf
format: text/html
creator: Roland A. Knapp
creator: Maxwell B. Joseph
creator: Thomas C. Smith
creator: Ericka E. Hegeman
creator: Vance T. Vredenburg
creator: James E. Erdman Jr
creator: Daniel M. Boiano
creator: Andrea J. Jani
creator: Cheryl J. Briggs
subject: Conservation Biology
subject: Ecology
subject: Mycology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12712
publisher: PeerJ Inc.
rights: © 2022 Knapp et al.
abstract: The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect agains…
bibliographic citation: Knapp et al. (2022) Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog. PeerJ 10:e12712 https://doi.org/10.7717/peerj.12712
date submitted: 2021-07-29
date accepted: 2021-12-09
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Knapp
  given name: Roland A.
author list: Agent
  family name: Joseph
  given name: Maxwell B.
author list: Agent
  family name: Smith
  given name: Thomas C.
author list: Agent
  family name: Hegeman
  given name: Ericka E.
author list: Agent
  family name: Vredenburg
  given name: Vance T.
author list: Agent
  family name: Erdman Jr
  given name: James E.
author list: Agent
  family name: Boiano
  given name: Daniel M.
author list: Agent
  family name: Jani
  given name: Andrea J.
author list: Agent
  family name: Briggs
  given name: Cheryl J.
doi: 10.7717/peerj.12712
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: © 2022 Knapp et al.
attribution name: Knapp et al.

Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study
type: item
type: AcademicArticle
description: Background Improved detection of hepatocellular carcinoma (HCC) is needed, as current detection methods, such as alpha fetoprotein (AFP) and ultrasound, suffer from poor sensitivity. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate many cellular functions and impact cancer development and progression. Notably, miRNAs are detectable in saliva and have shown potential as non-invasive biomarkers for a number of cancers including breast, oral, and lung cancers. Here, we present, to our knowledge, the first report of salivary miRNAs in HCC and compare these findings to patients with cirrhosis, a high-risk cohort for HCC. Methods We performed small RNA sequencing in 20 patients with HCC and 19 with cirrhosis. Eleven patients with HCC had chronic liver disease, and analyses were performed with these samples combined and stratified by the presence of chronic liver disease. P values were adjusted for multiple comparisons using a false discovery rate (FDR) approach and miRNA with FDR P < 0.05 were considered statistically significant. Differential expression of salivary miRNAs was compared to a previously published report of miRNAs in liver tissue of patients with HCC vs cirrhosis. Support vector machines and leave-one-out cross-validation were performed to determine if salivary miRNAs have predictive potential for detecting HCC. Results A total of 4,565 precursor and mature miRNAs were detected in saliva and 365 were significantly different between those with HCC compared to cirrhosis (FDR P < 0.05). Interestingly, 283 of these miRNAs were significantly downregulated in patients with HCC. Machine-learning identified a combination of 10 miRNAs and covariates that accurately classified patients with HCC (AUC = 0.87). In addition, we identified three miRNAs that were differentially expressed in HCC saliva samples and in a previously published study of miRNAs in HCC tissue compared to cirrhotic liver tissue. Conclusions This study demonstrates, for the first time, tha…
format: application/pdf
format: text/html
creator: Arshiya Mariam
creator: Galen Miller-Atkins
creator: Amika Moro
creator: Alejandro I. Rodarte
creator: Shirin Siddiqi
creator: Lou-Anne Acevedo-Moreno
creator: J. Mark Brown
creator: Daniela S. Allende
creator: Federico Aucejo
creator: Daniel M. Rotroff
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12715
publisher: PeerJ Inc.
rights: © 2022 Mariam et al.
abstract: Background Improved detection of hepatocellular carcinoma (HCC) is needed, as current detection methods, such as alpha fetoprotein (AFP) and ultrasound, suffer from poor sensitivity. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate many cellular functions and impact cancer development and progression. Notably, miRNAs are detectable in saliva and have shown potential as non-invasive biomarkers for a number of cancers including breast, oral, and lung cancers. Here, we present, to our knowledge, the first report of salivary miRNAs in HCC and compare these findings to patients with cirrhosis, a high-risk cohort for HCC. Methods We performed small RNA sequencing in 20 patients with HCC and 19 with cirrhosis. Eleven patients with HCC had chronic liver disease, and analyses were performed with these samples combined and stratified by the presence of chronic liver disease. P values were adjusted for multiple comparisons using a false discovery rate (FDR) approach and miRNA with FDR P < 0.05 were considered statistically significant. Differential expression of salivary miRNAs was compared to a previously published report of miRNAs in liver tissue of patients with HCC vs cirrhosis. Support vector machines and leave-one-out cross-validation were performed to determine if salivary miRNAs have predictive potential for detecting HCC. Results A total of 4,565 precursor and mature miRNAs were detected in saliva and 365 were significantly different between those with HCC compared to cirrhosis (FDR P < 0.05). Interestingly, 283 of these miRNAs were significantly downregulated in patients with HCC. Machine-learning identified a combination of 10 miRNAs and covariates that accurately classified patients with HCC (AUC = 0.87). In addition, we identified three miRNAs that were differentially expressed in HCC saliva samples and in a previously published study of miRNAs in HCC tissue compared to cirrhotic liver tissue. Conclusions This study demonstrates, for the first time, tha…
bibliographic citation: Mariam et al. (2022) Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study. PeerJ 10:e12715 https://doi.org/10.7717/peerj.12715
date submitted: 2021-08-18
date accepted: 2021-12-09
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Mariam
  given name: Arshiya
author list: Agent
  family name: Miller-Atkins
  given name: Galen
author list: Agent
  family name: Moro
  given name: Amika
author list: Agent
  family name: Rodarte
  given name: Alejandro I.
author list: Agent
  family name: Siddiqi
  given name: Shirin
author list: Agent
  family name: Acevedo-Moreno
  given name: Lou-Anne
author list: Agent
  family name: Brown
  given name: J. Mark
author list: Agent
  family name: Allende
  given name: Daniela S.
author list: Agent
  family name: Aucejo
  given name: Federico
author list: Agent
  family name: Rotroff
  given name: Daniel M.
doi: 10.7717/peerj.12715
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: © 2022 Mariam et al.
attribution name: Mariam et al.

Genome-wide sequence identification and expression analysis of N6-methyladenosine demethylase in sugar beet (Beta vulgaris L.) under salt stress
type: item
type: AcademicArticle
description: In eukaryotes, N6-methyladenosine (m6A) is the most abundant and highly conserved RNA modification. In vivo, m6A demethylase dynamically regulates the m6A level by removing the m6A marker where it plays an important role in plant growth, development and response to abiotic stress. The confirmed m6A demethylases in Arabidopsis thaliana include ALKBH9B and ALKBH10B, both belonging to the ALKB family. In this study, BvALKB family members were identified in sugar beet genome-wide database, and their conserved domains, gene structures, chromosomal locations, phylogeny, conserved motifs and expression of BvALKB genes were analyzed. Almost all BvALKB proteins contained the conserved domain of 2OG-Fe II-Oxy. Phylogenetic analysis suggested that the ten proteins were clustered into five groups, each of which had similar motifs and gene structures. Three Arabidopsis m6A demethylase-homologous proteins (BvALKBH6B, BvALKBH8B and BvALKBH10B) were of particular interest in our study. Expression profile analysis showed that almost all genes were up-regulated or down-regulated to varying degrees under salt stress. More specifically, BvALKBH10B homologous to AtALKBH10B was significantly up-regulated, suggesting that the transcriptional activity of this gene is responsive to salt stress. This study provides a theoretical basis for further screening of m6A demethylase in sugar beet, and also lays a foundation for studying the role of ALKB family proteins in growth, development and response to salinity stress.
format: application/pdf
format: text/html
creator: Jie Cui
creator: Junli Liu
creator: Junliang Li
creator: Dayou Cheng
creator: Cuihong Dai
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12719
publisher: PeerJ Inc.
rights: © 2022 Cui et al.
abstract: In eukaryotes, N6-methyladenosine (m6A) is the most abundant and highly conserved RNA modification. In vivo, m6A demethylase dynamically regulates the m6A level by removing the m6A marker where it plays an important role in plant growth, development and response to abiotic stress. The confirmed m6A demethylases in Arabidopsis thaliana include ALKBH9B and ALKBH10B, both belonging to the ALKB family. In this study, BvALKB family members were identified in sugar beet genome-wide database, and their conserved domains, gene structures, chromosomal locations, phylogeny, conserved motifs and expression of BvALKB genes were analyzed. Almost all BvALKB proteins contained the conserved domain of 2OG-Fe II-Oxy. Phylogenetic analysis suggested that the ten proteins were clustered into five groups, each of which had similar motifs and gene structures. Three Arabidopsis m6A demethylase-homologous proteins (BvALKBH6B, BvALKBH8B and BvALKBH10B) were of particular interest in our study. Expression profile analysis showed that almost all genes were up-regulated or down-regulated to varying degrees under salt stress. More specifically, BvALKBH10B homologous to AtALKBH10B was significantly up-regulated, suggesting that the transcriptional activity of this gene is responsive to salt stress. This study provides a theoretical basis for further screening of m6A demethylase in sugar beet, and also lays a foundation for studying the role of ALKB family proteins in growth, development and response to salinity stress.
bibliographic citation: Cui et al. (2022) Genome-wide sequence identification and expression analysis of N6-methyladenosine demethylase in sugar beet (Beta vulgaris L.) under salt stress. PeerJ 10:e12719 https://doi.org/10.7717/peerj.12719
date submitted: 2021-06-01
date accepted: 2021-12-09
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Jie
author list: Agent
  family name: Liu
  given name: Junli
author list: Agent
  family name: Li
  given name: Junliang
author list: Agent
  family name: Cheng
  given name: Dayou
author list: Agent
  family name: Dai
  given name: Cuihong
doi: 10.7717/peerj.12719
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Cui et al.
attribution name: Cui et al.

Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma
type: item
type: AcademicArticle
description: Pancreatic ductal adenocarcinoma (PDAC) is one of the common malignant tumors with high lethal rate and poor prognosis. Dysregulation of many genes have been reported to be involved in the occurrence and development of PDAC. However, as a highly conserved gene in eukaryotes, the role of Fasciculation and Elongation protein Zeta 2 (FEZ2) in pancreatic cancer progression is not clear. In this study, we identified the oncogenic effect of FEZ2 on PDAC. By mining of The Cancer Genome Atlas (TCGA) database, we found that FEZ2 was upregulated in PDAC tissues and FEZ2 expression was negatively regulated by its methylation. Moreover, high expression and low methylation of FEZ2 correlated with poor prognosis in PDAC patients. Besides, we found that FEZ2 could promote PDAC cells proliferation, migration and 5-FU resistance in vitro. Furthermore, Gene pathway enrichment analysis demonstrated a positive correlation between Wnt signaling activation and FEZ2 expression in PDAC patients. Western blot showed that FEZ2 knockdown significantly suppressed β-catenin expression. Collectively, our finding revealed that FEZ2 functioned as a potential oncogene on PDAC progression and migration, and the expression of FEZ2 had guidance value for the treatment and chemotherapy program of PDAC patients.
format: application/pdf
format: text/html
creator: Chaozhi Yang
creator: Xuebing Wang
creator: Chenjie Qiu
creator: Ziruo Zheng
creator: Kai Lin
creator: Min Tu
creator: Kai Zhang
creator: Kuirong Jiang
creator: Wentao Gao
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.12736
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Pancreatic ductal adenocarcinoma (PDAC) is one of the common malignant tumors with high lethal rate and poor prognosis. Dysregulation of many genes have been reported to be involved in the occurrence and development of PDAC. However, as a highly conserved gene in eukaryotes, the role of Fasciculation and Elongation protein Zeta 2 (FEZ2) in pancreatic cancer progression is not clear. In this study, we identified the oncogenic effect of FEZ2 on PDAC. By mining of The Cancer Genome Atlas (TCGA) database, we found that FEZ2 was upregulated in PDAC tissues and FEZ2 expression was negatively regulated by its methylation. Moreover, high expression and low methylation of FEZ2 correlated with poor prognosis in PDAC patients. Besides, we found that FEZ2 could promote PDAC cells proliferation, migration and 5-FU resistance in vitro. Furthermore, Gene pathway enrichment analysis demonstrated a positive correlation between Wnt signaling activation and FEZ2 expression in PDAC patients. Western blot showed that FEZ2 knockdown significantly suppressed β-catenin expression. Collectively, our finding revealed that FEZ2 functioned as a potential oncogene on PDAC progression and migration, and the expression of FEZ2 had guidance value for the treatment and chemotherapy program of PDAC patients.
bibliographic citation: Yang et al. (2022) Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma. PeerJ 10:e12736 https://doi.org/10.7717/peerj.12736
date submitted: 2021-07-27
date accepted: 2021-12-12
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Chaozhi
author list: Agent
  family name: Wang
  given name: Xuebing
author list: Agent
  family name: Qiu
  given name: Chenjie
author list: Agent
  family name: Zheng
  given name: Ziruo
author list: Agent
  family name: Lin
  given name: Kai
author list: Agent
  family name: Tu
  given name: Min
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Jiang
  given name: Kuirong
author list: Agent
  family name: Gao
  given name: Wentao
doi: 10.7717/peerj.12736
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach
type: item
type: AcademicArticle
description: Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.
format: application/pdf
format: text/html
creator: Kantinan Leetanasaksakul
creator: Sittiruk Roytrakul
creator: Narumon Phaonakrop
creator: Suthathip Kittisenachai
creator: Siriwan Thaisakun
creator: Nitiya Srithuanok
creator: Klanarong Sriroth
creator: Laurent Soulard
subject: Biotechnology
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12740
publisher: PeerJ Inc.
rights: © 2022 Leetanasaksakul et al.
abstract: Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.
bibliographic citation: Leetanasaksakul et al. (2022) Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach. PeerJ 10:e12740 https://doi.org/10.7717/peerj.12740
date submitted: 2021-08-24
date accepted: 2021-12-13
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leetanasaksakul
  given name: Kantinan
author list: Agent
  family name: Roytrakul
  given name: Sittiruk
author list: Agent
  family name: Phaonakrop
  given name: Narumon
author list: Agent
  family name: Kittisenachai
  given name: Suthathip
author list: Agent
  family name: Thaisakun
  given name: Siriwan
author list: Agent
  family name: Srithuanok
  given name: Nitiya
author list: Agent
  family name: Sriroth
  given name: Klanarong
author list: Agent
  family name: Soulard
  given name: Laurent
doi: 10.7717/peerj.12740
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Leetanasaksakul et al.
attribution name: Leetanasaksakul et al.

Beyond the prey: male spiders highly invest in silk when producing worthless gifts
type: item
type: AcademicArticle
description: In the spider Paratrechalea ornata, males have two gift-giving mating tactics, offering either a nutritive (prey) or a worthless (prey leftovers) silk wrapped gift to females. Both gift types confer similar mating success and duration and afford males a higher success rate than when they offer no gift. If this lack of difference in the reproductive benefits is true, we would expect all males to offer a gift but some males to offer a worthless gift even if prey are available. To test this, we allowed 18 males to court multiple females over five consecutive trials. In each trial, a male was able to produce a nutritive gift (a live housefly) or a worthless gift (mealworm exuviae). We found that, in line with our predictions, 20% of the males produced worthless gifts even when they had the opportunity to produce a nutritive one. However, rather than worthless gifts being a cheap tactic, they were related to a higher investment in silk wrapping. This latter result was replicated for worthless gifts produced in both the presence and absence of a live prey item. We propose that variation in gift-giving tactics likely evolved initially as a conditional strategy related to prey availability and male condition in P. ornata. Selection may then have favoured silk wrapping as a trait involved in female attraction, leading worthless gift-giving to invade.
format: application/pdf
format: text/html
creator: Camila Pavón-Peláez
creator: Valentina Franco-Trecu
creator: Irene Pandulli-Alonso
creator: Therésa M. Jones
creator: Maria J. Albo
subject: Animal Behavior
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.12757
publisher: PeerJ Inc.
rights: © 2022 Pavón-Peláez et al.
abstract: In the spider Paratrechalea ornata, males have two gift-giving mating tactics, offering either a nutritive (prey) or a worthless (prey leftovers) silk wrapped gift to females. Both gift types confer similar mating success and duration and afford males a higher success rate than when they offer no gift. If this lack of difference in the reproductive benefits is true, we would expect all males to offer a gift but some males to offer a worthless gift even if prey are available. To test this, we allowed 18 males to court multiple females over five consecutive trials. In each trial, a male was able to produce a nutritive gift (a live housefly) or a worthless gift (mealworm exuviae). We found that, in line with our predictions, 20% of the males produced worthless gifts even when they had the opportunity to produce a nutritive one. However, rather than worthless gifts being a cheap tactic, they were related to a higher investment in silk wrapping. This latter result was replicated for worthless gifts produced in both the presence and absence of a live prey item. We propose that variation in gift-giving tactics likely evolved initially as a conditional strategy related to prey availability and male condition in P. ornata. Selection may then have favoured silk wrapping as a trait involved in female attraction, leading worthless gift-giving to invade.
bibliographic citation: Pavón-Peláez et al. (2022) Beyond the prey: male spiders highly invest in silk when producing worthless gifts. PeerJ 10:e12757 https://doi.org/10.7717/peerj.12757
date submitted: 2021-07-29
date accepted: 2021-12-16
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pavón-Peláez
  given name: Camila
author list: Agent
  family name: Franco-Trecu
  given name: Valentina
author list: Agent
  family name: Pandulli-Alonso
  given name: Irene
author list: Agent
  family name: Jones
  given name: Therésa M.
author list: Agent
  family name: Albo
  given name: Maria J.
doi: 10.7717/peerj.12757
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Pavón-Peláez et al.
attribution name: Pavón-Peláez et al.

Protection of catalpol against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway
type: item
type: AcademicArticle
description: Catalpol significantly reduces triptolide-induced hepatotoxicity, which is closely related to autophagy. The aim of this study was to explore the unclear protective mechanism of catalpol against triptolide. The detoxification effect of catalpol on triptolide was investigated in HepaRG cell line. The detoxification effects were assessed by measuring cell viability, autophagy, and apoptosis, as well as the endoplasmic reticulum stress protein and mRNA expression levels. We found that 5–20 µg/L triptolide treatments increased the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH), as well as the expression of autophagy proteins including LC3 and Beclin1. The expression of P62 was downregulated and the production of autophagosomes was increased, as determined by transmission electron microscope and monodansylcadaverine staining. In contrast, 40 µg/L catalpol reversed these triptolide-induced changes in the liver function index, autophagy level, and apoptotic protein expression, including Cleaved-caspase3 and Cleaved-caspase9 by inhibiting excessive autophagy. Simultaneously, catalpol reversed endoplasmic reticulum stress, including the expression of PERK, which regulates autophagy. Moreover, we used the PERK inhibitor GSK2656157 to prove that the PERK-ATF4-CHOP pathway of the unfolded protein response is an important pathway that could induce autophagy. Catalpol inhibited excessive autophagy by suppressing the PERK pathway. Altogether, catalpol protects against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway. The results of this study are beneficial to clarify the detoxification mechanism of catalpol against triptolide-induced hepatotoxicity and to promote the application of triptolide.
format: application/pdf
format: text/html
creator: Linluo Zhang
creator: Changqing Li
creator: Ling Fu
creator: Zhichao Yu
creator: Gengrui Xu
creator: Jie Zhou
creator: Meiyu Shen
creator: Zhe Feng
creator: Huaxu Zhu
creator: Tong Xie
creator: Lingling Zhou
creator: Xueping Zhou
subject: Cell Biology
subject: Toxicology
subject: Pharmacology
description: doi:10.7717/peerj.12759
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Catalpol significantly reduces triptolide-induced hepatotoxicity, which is closely related to autophagy. The aim of this study was to explore the unclear protective mechanism of catalpol against triptolide. The detoxification effect of catalpol on triptolide was investigated in HepaRG cell line. The detoxification effects were assessed by measuring cell viability, autophagy, and apoptosis, as well as the endoplasmic reticulum stress protein and mRNA expression levels. We found that 5–20 µg/L triptolide treatments increased the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH), as well as the expression of autophagy proteins including LC3 and Beclin1. The expression of P62 was downregulated and the production of autophagosomes was increased, as determined by transmission electron microscope and monodansylcadaverine staining. In contrast, 40 µg/L catalpol reversed these triptolide-induced changes in the liver function index, autophagy level, and apoptotic protein expression, including Cleaved-caspase3 and Cleaved-caspase9 by inhibiting excessive autophagy. Simultaneously, catalpol reversed endoplasmic reticulum stress, including the expression of PERK, which regulates autophagy. Moreover, we used the PERK inhibitor GSK2656157 to prove that the PERK-ATF4-CHOP pathway of the unfolded protein response is an important pathway that could induce autophagy. Catalpol inhibited excessive autophagy by suppressing the PERK pathway. Altogether, catalpol protects against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway. The results of this study are beneficial to clarify the detoxification mechanism of catalpol against triptolide-induced hepatotoxicity and to promote the application of triptolide.
bibliographic citation: Zhang et al. (2022) Protection of catalpol against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway. PeerJ 10:e12759 https://doi.org/10.7717/peerj.12759
date submitted: 2021-09-06
date accepted: 2021-12-16
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Linluo
author list: Agent
  family name: Li
  given name: Changqing
author list: Agent
  family name: Fu
  given name: Ling
author list: Agent
  family name: Yu
  given name: Zhichao
author list: Agent
  family name: Xu
  given name: Gengrui
author list: Agent
  family name: Zhou
  given name: Jie
author list: Agent
  family name: Shen
  given name: Meiyu
author list: Agent
  family name: Feng
  given name: Zhe
author list: Agent
  family name: Zhu
  given name: Huaxu
author list: Agent
  family name: Xie
  given name: Tong
author list: Agent
  family name: Zhou
  given name: Lingling
author list: Agent
  family name: Zhou
  given name: Xueping
doi: 10.7717/peerj.12759
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma
type: item
type: AcademicArticle
description: Background Clear cell renal cell carcinoma (ccRCC) is a tumor that frequently shows the hematogenous pathway and tends to be resistant to radiotherapy and chemotherapy. However, the exact mechanism of ccRCC metastasis remains unknown. Methods Differentially expressed genes (DEGs) of three gene expression profiles (GSE85258, GSE105288 and GSE22541) downloaded from the Gene Expression Omnibus (GEO) database were analyzed by GEO2R analysis, and co-expressed DEGs among the datasets were identified using a Venn drawing tool. The co-expressed DEGs were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and hub genes were determined based on the protein-protein interaction network established by STRING. After survival analysis performed on UALCAN website, possible key genes were selected and verified in ccRCC cell lines and ccRCC tissues (n = 44). Statistical analysis was conducted using GraphPad Prism (Version 8.1.1). Results A total of 104 co-expressed DEGs were identified in the three datasets. Pathway analysis revealed that these genes were enriched in the extracellular matrix (ECM)–receptor interaction, protein digestion and absorption and focal adhesion. Survival analysis on 17 hub genes revealed that four key genes with a significant impact on survival: procollagen C-endopeptidase enhancer (PCOLCE), prolyl 4-hydroxylase subunit beta (P4HB), collagen type VI alpha 2 (COL6A2) and collagen type VI alpha 3 (COL6A3). Patients with higher expression of these key genes had worse survival than those with lower expression. In vitro experiments revealed that the mRNA expression levels of PCOLCE, P4HB and COL6A2 were three times higher and that of COL6A3 mRNA was 16 times higher in the metastatic ccRCC cell line Caki-1 than the corresponding primary cell line Caki-2. Immunohistochemistry revealed higher expression of the proteins encoded by these four genes in metastatic ccRCC compared with tumors from the corresponding pr…
format: application/pdf
format: text/html
creator: Tingting Zhong
creator: Zeying Jiang
creator: Xiangdong Wang
creator: Honglei Wang
creator: Meiyi Song
creator: Wenfang Chen
creator: Shicong Yang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.12493
publisher: PeerJ Inc.
rights: © 2022 Zhong et al.
abstract: Background Clear cell renal cell carcinoma (ccRCC) is a tumor that frequently shows the hematogenous pathway and tends to be resistant to radiotherapy and chemotherapy. However, the exact mechanism of ccRCC metastasis remains unknown. Methods Differentially expressed genes (DEGs) of three gene expression profiles (GSE85258, GSE105288 and GSE22541) downloaded from the Gene Expression Omnibus (GEO) database were analyzed by GEO2R analysis, and co-expressed DEGs among the datasets were identified using a Venn drawing tool. The co-expressed DEGs were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and hub genes were determined based on the protein-protein interaction network established by STRING. After survival analysis performed on UALCAN website, possible key genes were selected and verified in ccRCC cell lines and ccRCC tissues (n = 44). Statistical analysis was conducted using GraphPad Prism (Version 8.1.1). Results A total of 104 co-expressed DEGs were identified in the three datasets. Pathway analysis revealed that these genes were enriched in the extracellular matrix (ECM)–receptor interaction, protein digestion and absorption and focal adhesion. Survival analysis on 17 hub genes revealed that four key genes with a significant impact on survival: procollagen C-endopeptidase enhancer (PCOLCE), prolyl 4-hydroxylase subunit beta (P4HB), collagen type VI alpha 2 (COL6A2) and collagen type VI alpha 3 (COL6A3). Patients with higher expression of these key genes had worse survival than those with lower expression. In vitro experiments revealed that the mRNA expression levels of PCOLCE, P4HB and COL6A2 were three times higher and that of COL6A3 mRNA was 16 times higher in the metastatic ccRCC cell line Caki-1 than the corresponding primary cell line Caki-2. Immunohistochemistry revealed higher expression of the proteins encoded by these four genes in metastatic ccRCC compared with tumors from the corresponding pr…
bibliographic citation: Zhong et al. (2022) Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma. PeerJ 10:e12493 https://doi.org/10.7717/peerj.12493
date submitted: 2021-07-06
date accepted: 2021-10-25
issued: 2022-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Tingting
author list: Agent
  family name: Jiang
  given name: Zeying
author list: Agent
  family name: Wang
  given name: Xiangdong
author list: Agent
  family name: Wang
  given name: Honglei
author list: Agent
  family name: Song
  given name: Meiyi
author list: Agent
  family name: Chen
  given name: Wenfang
author list: Agent
  family name: Yang
  given name: Shicong
doi: 10.7717/peerj.12493
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-04
copyright: ©2022 Zhong et al.
attribution name: Zhong et al.

Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola
type: item
type: AcademicArticle
description: Background Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available. Methods In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed. Results Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.
format: application/pdf
format: text/html
creator: Chengru Li
creator: Na Dong
creator: Liming Shen
creator: Meng Lu
creator: Junwen Zhai
creator: Yamei Zhao
creator: Lei Chen
creator: Zhiting Wan
creator: Zhongjian Liu
creator: Hui Ren
creator: Shasha Wu
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12558
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available. Methods In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed. Results Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.
bibliographic citation: Li et al. (2022) Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola. PeerJ 10:e12558 https://doi.org/10.7717/peerj.12558
date submitted: 2020-12-15
date accepted: 2021-11-05
issued: 2022-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Chengru
author list: Agent
  family name: Dong
  given name: Na
author list: Agent
  family name: Shen
  given name: Liming
author list: Agent
  family name: Lu
  given name: Meng
author list: Agent
  family name: Zhai
  given name: Junwen
author list: Agent
  family name: Zhao
  given name: Yamei
author list: Agent
  family name: Chen
  given name: Lei
author list: Agent
  family name: Wan
  given name: Zhiting
author list: Agent
  family name: Liu
  given name: Zhongjian
author list: Agent
  family name: Ren
  given name: Hui
author list: Agent
  family name: Wu
  given name: Shasha
doi: 10.7717/peerj.12558
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-04
copyright: © 2022 Li et al.
attribution name: Li et al.

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