PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus
items: Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct
items: Cancer types with high numbers of driver events are largely preventable
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

Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus
type: item
type: AcademicArticle
description: The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.
format: application/pdf
format: text/html
creator: Qiangqiang Ding
creator: Hongyuan Zhao
creator: Peilei Zhu
creator: Xiangting Jiang
creator: Fan Nie
creator: Guoqing Li
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.12654
publisher: PeerJ Inc.
rights: © 2022 Ding et al.
abstract: The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.
bibliographic citation: Ding et al. (2022) Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus. PeerJ 10:e12654 https://doi.org/10.7717/peerj.12654
date submitted: 2021-07-07
date accepted: 2021-11-29
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Qiangqiang
author list: Agent
  family name: Zhao
  given name: Hongyuan
author list: Agent
  family name: Zhu
  given name: Peilei
author list: Agent
  family name: Jiang
  given name: Xiangting
author list: Agent
  family name: Nie
  given name: Fan
author list: Agent
  family name: Li
  given name: Guoqing
doi: 10.7717/peerj.12654
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Ding et al.
attribution name: Ding et al.

Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct
type: item
type: AcademicArticle
description: The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species’ triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
format: application/pdf
format: text/html
creator: Sen Zhang
creator: Shaoping Wu
creator: Chunhua Hu
creator: Qiaosong Yang
creator: Tao Dong
creator: Ou Sheng
creator: Guiming Deng
creator: Weidi He
creator: Tongxin Dou
creator: Chunyu Li
creator: Chenkang Sun
creator: Ganjun Yi
creator: Fangcheng Bi
subject: Agricultural Science
subject: Biochemistry
subject: Bioengineering
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12664
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species’ triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
bibliographic citation: Zhang et al. (2022) Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct. PeerJ 10:e12664 https://doi.org/10.7717/peerj.12664
date submitted: 2021-08-17
date accepted: 2021-11-30
issued: 2022-01-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Sen
author list: Agent
  family name: Wu
  given name: Shaoping
author list: Agent
  family name: Hu
  given name: Chunhua
author list: Agent
  family name: Yang
  given name: Qiaosong
author list: Agent
  family name: Dong
  given name: Tao
author list: Agent
  family name: Sheng
  given name: Ou
author list: Agent
  family name: Deng
  given name: Guiming
author list: Agent
  family name: He
  given name: Weidi
author list: Agent
  family name: Dou
  given name: Tongxin
author list: Agent
  family name: Li
  given name: Chunyu
author list: Agent
  family name: Sun
  given name: Chenkang
author list: Agent
  family name: Yi
  given name: Ganjun
author list: Agent
  family name: Bi
  given name: Fangcheng
doi: 10.7717/peerj.12664
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Cancer types with high numbers of driver events are largely preventable
type: item
type: AcademicArticle
description: There is a long-standing debate on whether cancer is predominantly driven by extrinsic risk factors such as smoking, or by intrinsic processes such as errors in DNA replication. We have previously shown that the number of rate-limiting driver events per tumor can be estimated from the age distribution of cancer incidence using the gamma/Erlang probability distribution. Here, we show that this number strongly correlates with the proportion of cancer cases attributable to modifiable risk factors for all cancer types except the ones inducible by infection or ultraviolet radiation. The correlation was confirmed for three countries, three corresponding incidence databases and risk estimation studies, as well as for both sexes: USA, males (r = 0.80, P = 0.002), females (r = 0.81, P = 0.0003); England, males (r = 0.90, P < 0.0001), females (r = 0.67, P = 0.002); Australia, males (r = 0.90, P = 0.0004), females (r = 0.68, P = 0.01). Hence, this study suggests that the more driver events a cancer type requires, the more of its cases are due to preventable anthropogenic risk factors.
format: application/pdf
format: text/html
creator: Aleksey V. Belikov
creator: Sergey V. Leonov
subject: Mathematical Biology
subject: Epidemiology
subject: Oncology
subject: Statistics
subject: Environmental Health
description: doi:10.7717/peerj.12672
publisher: PeerJ Inc.
rights: © 2022 Belikov and Leonov
abstract: There is a long-standing debate on whether cancer is predominantly driven by extrinsic risk factors such as smoking, or by intrinsic processes such as errors in DNA replication. We have previously shown that the number of rate-limiting driver events per tumor can be estimated from the age distribution of cancer incidence using the gamma/Erlang probability distribution. Here, we show that this number strongly correlates with the proportion of cancer cases attributable to modifiable risk factors for all cancer types except the ones inducible by infection or ultraviolet radiation. The correlation was confirmed for three countries, three corresponding incidence databases and risk estimation studies, as well as for both sexes: USA, males (r = 0.80, P = 0.002), females (r = 0.81, P = 0.0003); England, males (r = 0.90, P < 0.0001), females (r = 0.67, P = 0.002); Australia, males (r = 0.90, P = 0.0004), females (r = 0.68, P = 0.01). Hence, this study suggests that the more driver events a cancer type requires, the more of its cases are due to preventable anthropogenic risk factors.
bibliographic citation: Belikov et al. (2022) Cancer types with high numbers of driver events are largely preventable. PeerJ 10:e12672 https://doi.org/10.7717/peerj.12672
date submitted: 2021-08-17
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: Belikov
  given name: Aleksey V.
author list: Agent
  family name: Leonov
  given name: Sergey V.
doi: 10.7717/peerj.12672
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-05
copyright: ©2022 Belikov and Leonov
attribution name: Belikov and Leonov

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.

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