PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities
items: Assessment of different factors on the influence of glass wool concentration for detection of main swine viruses in water samples
items: SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction
items: Exploring the relationship between environmental DNA concentration and biomass in Asian giant softshell turtle (Pelochelys cantorii)
items: CmHem, a hemolin-like gene identified from Cnaphalocrocis medinalis, involved in metamorphosis and baculovirus infection
items: Maize ZmHSP90 plays a role in acclimation to salt stress
items: The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae)
items: An acoustic-based method for locating maternity colonies of rare woodland bats
items: Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project
items: High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration

Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities
type: item
type: AcademicArticle
description: The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2–6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10–14) characterized by acid-tolerant taxa and fruity (p < 3.03e−03), sour (p < 1.60e−01), and fermented (p < 1.47e−05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.
format: application/pdf
format: text/html
creator: Erin A. McKenney
creator: Lauren M. Nichols
creator: Samuel Alvarado
creator: Shannon Hardy
creator: Kristen Kemp
creator: Rachael Polmanteer
creator: April Shoemaker
creator: Robert R. Dunn
subject: Biochemistry
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.16163
publisher: PeerJ Inc.
rights: © 2023 McKenney et al.
abstract: The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2–6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10–14) characterized by acid-tolerant taxa and fruity (p < 3.03e−03), sour (p < 1.60e−01), and fermented (p < 1.47e−05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.
bibliographic citation: McKenney et al. (2023) Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities. PeerJ 11:e16163 https://doi.org/10.7717/peerj.16163
date submitted: 2023-05-18
date accepted: 2023-09-01
issued: 2023-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McKenney
  given name: Erin A.
author list: Agent
  family name: Nichols
  given name: Lauren M.
author list: Agent
  family name: Alvarado
  given name: Samuel
author list: Agent
  family name: Hardy
  given name: Shannon
author list: Agent
  family name: Kemp
  given name: Kristen
author list: Agent
  family name: Polmanteer
  given name: Rachael
author list: Agent
  family name: Shoemaker
  given name: April
author list: Agent
  family name: Dunn
  given name: Robert R.
doi: 10.7717/peerj.16163
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-04
copyright: © 2023 McKenney et al.
attribution name: McKenney et al.

Assessment of different factors on the influence of glass wool concentration for detection of main swine viruses in water samples
type: item
type: AcademicArticle
description: Viruses existed in wastewaters might pose a biosecurity risk to human and animal health. However, it is generally difficult to detect viruses in wastewater directly as they usually occur in low numbers in water. Therefore, processing large volumes of water to concentrate viruses in a much smaller final volume for detection is necessary. Glass wool has been recognized as an effective material to concentrate multiple in water, and in this study, we assessed the use of glass wools on concentrating pseudorabies virus (PRV), African swine fever virus (ASFV), and porcine epidemic diarrhea virus (PEDV) in water samples. The influence of pH values, water matrix, water volume, filtration rate, temperature on the effect of the method concentrating these viruses for detection was evaluated in laboratory. Our results revealed that glass wool was suitable for the concentration of above-mentioned viruses from different water samples, and demonstrated a good application effect for water with pH between 6.0–9.0. Furthermore, glass wool also showed a good recovery effect on concentrating viral nucleic acids and viral particles, as well as living viruses. In addition, combining use of glass wool with skim milk, polyethylene glycol (PEG)-NaCl, or ultracentrifuge had good effects on concentrating ASFV, PRV, and PEDV. Detection of wastewater samples (n = 70) collected from 70 pig farms in 13 regions across Hubei Province in Central China after glass-wool-concentration determined one sample positive for ASFV, eighteen samples positive for PRV, but no sample positive for PEDV. However, these positive samples were detected to be negative before glass wool enrichment was implemented. Our results suggest that glass wool-based water concentration method developed in this study represents an effective tool for detecting viruses in wastewater.
format: application/pdf
format: text/html
creator: Jie Fan
creator: Hongjian Chen
creator: Wenbo Song
creator: Hao Yang
creator: Rui Xie
creator: Mengfei Zhao
creator: Wenqing Wu
creator: Zhong Peng
creator: Bin Wu
subject: Agricultural Science
subject: Molecular Biology
subject: Virology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.16171
publisher: PeerJ Inc.
rights: © 2023 Fan et al.
abstract: Viruses existed in wastewaters might pose a biosecurity risk to human and animal health. However, it is generally difficult to detect viruses in wastewater directly as they usually occur in low numbers in water. Therefore, processing large volumes of water to concentrate viruses in a much smaller final volume for detection is necessary. Glass wool has been recognized as an effective material to concentrate multiple in water, and in this study, we assessed the use of glass wools on concentrating pseudorabies virus (PRV), African swine fever virus (ASFV), and porcine epidemic diarrhea virus (PEDV) in water samples. The influence of pH values, water matrix, water volume, filtration rate, temperature on the effect of the method concentrating these viruses for detection was evaluated in laboratory. Our results revealed that glass wool was suitable for the concentration of above-mentioned viruses from different water samples, and demonstrated a good application effect for water with pH between 6.0–9.0. Furthermore, glass wool also showed a good recovery effect on concentrating viral nucleic acids and viral particles, as well as living viruses. In addition, combining use of glass wool with skim milk, polyethylene glycol (PEG)-NaCl, or ultracentrifuge had good effects on concentrating ASFV, PRV, and PEDV. Detection of wastewater samples (n = 70) collected from 70 pig farms in 13 regions across Hubei Province in Central China after glass-wool-concentration determined one sample positive for ASFV, eighteen samples positive for PRV, but no sample positive for PEDV. However, these positive samples were detected to be negative before glass wool enrichment was implemented. Our results suggest that glass wool-based water concentration method developed in this study represents an effective tool for detecting viruses in wastewater.
bibliographic citation: Fan et al. (2023) Assessment of different factors on the influence of glass wool concentration for detection of main swine viruses in water samples. PeerJ 11:e16171 https://doi.org/10.7717/peerj.16171
date submitted: 2023-05-02
date accepted: 2023-09-03
issued: 2023-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Jie
author list: Agent
  family name: Chen
  given name: Hongjian
author list: Agent
  family name: Song
  given name: Wenbo
author list: Agent
  family name: Yang
  given name: Hao
author list: Agent
  family name: Xie
  given name: Rui
author list: Agent
  family name: Zhao
  given name: Mengfei
author list: Agent
  family name: Wu
  given name: Wenqing
author list: Agent
  family name: Peng
  given name: Zhong
author list: Agent
  family name: Wu
  given name: Bin
doi: 10.7717/peerj.16171
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-04
copyright: © 2023 Fan et al.
attribution name: Fan et al.

SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction
type: item
type: AcademicArticle
description: Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism. Therefore, in the article, biological sequences are represented with time series to obtain biological time sequence (BTS). Hybrid ensemble learning framework (SaPt-CNN-LSTM-AR-EA) for BTS is proposed. Single-sequence and multi-sequence models are respectively constructed with self-adaption pre-training one-dimensional convolutional recurrent neural network and autoregressive fractional integrated moving average fused evolutionary algorithm. In DNA sequence experiments with six viruses, SaPt-CNN-LSTM-AR-EA realized the good overall prediction performance and the prediction accuracy and correlation respectively reached 1.7073 and 0.9186. SaPt-CNN-LSTM-AR-EA was compared with other five benchmark models so as to verify its effectiveness and stability. SaPt-CNN-LSTM-AR-EA increased the average accuracy by about 30%. The framework proposed in this article is significant in biology, biomedicine, and computer science, and can be widely applied in sequence splicing, computational biology, bioinformation, and other fields.
format: application/pdf
format: text/html
creator: Wu Yan
creator: Li Tan
creator: Li Meng-Shan
creator: Sheng Sheng
creator: Wang Jun
creator: Wu Fu-an
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.16192
publisher: PeerJ Inc.
rights: © 2023 Yan et al.
abstract: Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism. Therefore, in the article, biological sequences are represented with time series to obtain biological time sequence (BTS). Hybrid ensemble learning framework (SaPt-CNN-LSTM-AR-EA) for BTS is proposed. Single-sequence and multi-sequence models are respectively constructed with self-adaption pre-training one-dimensional convolutional recurrent neural network and autoregressive fractional integrated moving average fused evolutionary algorithm. In DNA sequence experiments with six viruses, SaPt-CNN-LSTM-AR-EA realized the good overall prediction performance and the prediction accuracy and correlation respectively reached 1.7073 and 0.9186. SaPt-CNN-LSTM-AR-EA was compared with other five benchmark models so as to verify its effectiveness and stability. SaPt-CNN-LSTM-AR-EA increased the average accuracy by about 30%. The framework proposed in this article is significant in biology, biomedicine, and computer science, and can be widely applied in sequence splicing, computational biology, bioinformation, and other fields.
bibliographic citation: Yan et al. (2023) SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction. PeerJ 11:e16192 https://doi.org/10.7717/peerj.16192
date submitted: 2023-03-31
date accepted: 2023-09-06
issued: 2023-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Wu
author list: Agent
  family name: Tan
  given name: Li
author list: Agent
  family name: Meng-Shan
  given name: Li
author list: Agent
  family name: Sheng
  given name: Sheng
author list: Agent
  family name: Jun
  given name: Wang
author list: Agent
  family name: Fu-an
  given name: Wu
doi: 10.7717/peerj.16192
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-04
copyright: © 2023 Yan et al.
attribution name: Yan et al.

Exploring the relationship between environmental DNA concentration and biomass in Asian giant softshell turtle (Pelochelys cantorii)
type: item
type: AcademicArticle
description: In recent years, environmental DNA (eDNA) technology has become an accepted approach for investigating rare and endangered species because of its economic efficiency, high sensitivity, and non-invasiveness. The Asian giant softshell turtle (Pelochelys cantorii) is a first-class protected aquatic animal in China, and traditional resource survey methods have not identified its natural populations for many years. In this study, primers and a TaqMan probe targeting ND5 were designed, reaction conditions were optimized, a standard curve was constructed using synthetic DNA, and an eDNA quantitative PCR (qPCR) detection method was established. The eDNA detection technology for P. cantorii revealed that the number of species in the experimental pools showed a significant linear relationship with the eDNA concentration (p < 0.05). The eDNA concentration was negatively correlated with the length of time after the removal of P. cantorii and retention in the water body for 9 days. The qPCR detection method for P. cantorii eDNA established in this study can be applied to the qualitative detection of P. cantorii in water bodies, as well as to preliminary evaluation of its relative biomass. This can serve as a baseline for the investigation of natural P. cantorii population and the evaluation of its wild release effects.
format: application/pdf
format: text/html
creator: Xiaoyou Hong
creator: Kaikuo Wang
creator: Liqin Ji
creator: Xiaoli Liu
creator: Lingyun Yu
creator: Jie Wei
creator: Yakun Wang
creator: Chengqing Wei
creator: Wei Li
creator: Xinping Zhu
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.16218
publisher: PeerJ Inc.
rights: © 2023 Hong et al.
abstract: In recent years, environmental DNA (eDNA) technology has become an accepted approach for investigating rare and endangered species because of its economic efficiency, high sensitivity, and non-invasiveness. The Asian giant softshell turtle (Pelochelys cantorii) is a first-class protected aquatic animal in China, and traditional resource survey methods have not identified its natural populations for many years. In this study, primers and a TaqMan probe targeting ND5 were designed, reaction conditions were optimized, a standard curve was constructed using synthetic DNA, and an eDNA quantitative PCR (qPCR) detection method was established. The eDNA detection technology for P. cantorii revealed that the number of species in the experimental pools showed a significant linear relationship with the eDNA concentration (p < 0.05). The eDNA concentration was negatively correlated with the length of time after the removal of P. cantorii and retention in the water body for 9 days. The qPCR detection method for P. cantorii eDNA established in this study can be applied to the qualitative detection of P. cantorii in water bodies, as well as to preliminary evaluation of its relative biomass. This can serve as a baseline for the investigation of natural P. cantorii population and the evaluation of its wild release effects.
bibliographic citation: Hong et al. (2023) Exploring the relationship between environmental DNA concentration and biomass in Asian giant softshell turtle (Pelochelys cantorii). PeerJ 11:e16218 https://doi.org/10.7717/peerj.16218
date submitted: 2022-11-14
date accepted: 2023-09-11
issued: 2023-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Xiaoyou
author list: Agent
  family name: Wang
  given name: Kaikuo
author list: Agent
  family name: Ji
  given name: Liqin
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Yu
  given name: Lingyun
author list: Agent
  family name: Wei
  given name: Jie
author list: Agent
  family name: Wang
  given name: Yakun
author list: Agent
  family name: Wei
  given name: Chengqing
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Xinping
doi: 10.7717/peerj.16218
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-04
copyright: © 2023 Hong et al.
attribution name: Hong et al.

CmHem, a hemolin-like gene identified from Cnaphalocrocis medinalis, involved in metamorphosis and baculovirus infection
type: item
type: AcademicArticle
description: Background As a member of the immunoglobulin superfamily, hemolins play a vital role in insect development and defense against pathogens. However, the innate immune response of hemolin to baculovirus infection varies among different insects. Methods and results In this study, the hemolin-like gene from a Crambidae insect, Cnaphalocrocis medinalis, CmHem was cloned, and its role in insect development and baculovirus infection was analyzed. A 1,528 bp contig as potential hemolin-like gene of C. medinalis was reassembled from the transcriptome. Further, the complete hemolin sequence of C. medinalis (CmHem) was cloned and sequenced. The cDNA of CmHem was 1,515 bp in length and encoded 408 amino acids. The deduced amino acid of CmHem has relatively low identities (41.9–62.3%) to various insect hemolins. However, it contains four Ig domains similarity to other insect hemolins. The expression level of CmHem was the highest in eggs, followed by pupae and adults, and maintained a low expression level at larval stage. The synthesized siRNAs were injected into mature larvae, and the CmHem transcription decreased by 51.7%. Moreover, the abdominal somites of larvae became straightened, could not pupate normally, and then died. Infection with a baculovirus, C. medinalis granulovirus (CnmeGV), the expression levels of CmHem in the midgut and fat body of C. medinalis significantly increased at 12 and 24 h, respectively, and then soon returned to normal levels. Conclusions Our results suggested that hemolin may be related to the metamorphosis of C. medinalis. Exposure to baculovirus induced the phased expression of hemolin gene in the midgut and fat body of C. medinalis, indicated that hemolin involved in the immune recognition of Crambidae insects to baculovirus.
format: application/pdf
format: text/html
creator: Guangjie Han
creator: Chuanming Li
creator: Nan Zhang
creator: Qin Liu
creator: Lixin Huang
creator: Yang Xia
creator: Jian Xu
subject: Agricultural Science
subject: Entomology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.16225
publisher: PeerJ Inc.
rights: © 2023 Han et al.
abstract: Background As a member of the immunoglobulin superfamily, hemolins play a vital role in insect development and defense against pathogens. However, the innate immune response of hemolin to baculovirus infection varies among different insects. Methods and results In this study, the hemolin-like gene from a Crambidae insect, Cnaphalocrocis medinalis, CmHem was cloned, and its role in insect development and baculovirus infection was analyzed. A 1,528 bp contig as potential hemolin-like gene of C. medinalis was reassembled from the transcriptome. Further, the complete hemolin sequence of C. medinalis (CmHem) was cloned and sequenced. The cDNA of CmHem was 1,515 bp in length and encoded 408 amino acids. The deduced amino acid of CmHem has relatively low identities (41.9–62.3%) to various insect hemolins. However, it contains four Ig domains similarity to other insect hemolins. The expression level of CmHem was the highest in eggs, followed by pupae and adults, and maintained a low expression level at larval stage. The synthesized siRNAs were injected into mature larvae, and the CmHem transcription decreased by 51.7%. Moreover, the abdominal somites of larvae became straightened, could not pupate normally, and then died. Infection with a baculovirus, C. medinalis granulovirus (CnmeGV), the expression levels of CmHem in the midgut and fat body of C. medinalis significantly increased at 12 and 24 h, respectively, and then soon returned to normal levels. Conclusions Our results suggested that hemolin may be related to the metamorphosis of C. medinalis. Exposure to baculovirus induced the phased expression of hemolin gene in the midgut and fat body of C. medinalis, indicated that hemolin involved in the immune recognition of Crambidae insects to baculovirus.
bibliographic citation: Han et al. (2023) CmHem, a hemolin-like gene identified from Cnaphalocrocis medinalis, involved in metamorphosis and baculovirus infection. PeerJ 11:e16225 https://doi.org/10.7717/peerj.16225
date submitted: 2023-06-02
date accepted: 2023-09-12
issued: 2023-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Guangjie
author list: Agent
  family name: Li
  given name: Chuanming
author list: Agent
  family name: Zhang
  given name: Nan
author list: Agent
  family name: Liu
  given name: Qin
author list: Agent
  family name: Huang
  given name: Lixin
author list: Agent
  family name: Xia
  given name: Yang
author list: Agent
  family name: Xu
  given name: Jian
doi: 10.7717/peerj.16225
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-04
copyright: © 2023 Han et al.
attribution name: Han et al.

Maize ZmHSP90 plays a role in acclimation to salt stress
type: item
type: AcademicArticle
description: Background Maize is sensitive to salt stress, especially during the germination and seedling stages. Methods We conducted germination experiments on 60 maize materials under salt stress, and screened out the most salt-tolerant and salt-sensitive varieties based on germination indicators. Afterwards, transcriptome analysis was performed to screen for key regulators in the plumule and flag leaf at the germination and seedling stages, respectively. Following that, transgenic tobacco was developed to expose the roles and mechanisms of the candidate genes, enabling a deeper investigation of their functions. Results Out of the 60 inbred lines of maize, “975-12” exhibits the highest level of salt tolerance, while “GEMS64” displays the lowest. The application of salt stress resulted in a significant increase in the levels of antioxidant enzymes in both “975-12” and “GEMS64”. ABA signal transduction and jasmonic acid pathways were the pathways that mainly affected by salt stress. In addition, a significant finding has been made indicating that when exposed to high levels of salt stress, the expression of ZmHSP90 in ‘975-12’ increased while in ‘GEMS64’ decreased. Furthermore, in tobacco plants overexpressing ZmHSP90, there was an increase in antioxidant enzyme activity associated with salt tolerance. ZmHSP90 enhanced the expression levels of NtSOS1, NtHKT1, and NtNHX1 as compared to those in the salt treatment, causing the maintenance of Na+ and K+ homeostasis, suggesting that high expression of ZmHSP90 was conducive to regulate Na+ transporters to maintain K+/Na+ balanced in tobacco.
format: application/pdf
format: text/html
creator: Xinyan Yu
creator: Yanxin Zhao
creator: Yun Wang
creator: Zhiqing Zou
creator: Fenghai Li
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15819
publisher: PeerJ Inc.
rights: © 2023 Yu et al.
abstract: Background Maize is sensitive to salt stress, especially during the germination and seedling stages. Methods We conducted germination experiments on 60 maize materials under salt stress, and screened out the most salt-tolerant and salt-sensitive varieties based on germination indicators. Afterwards, transcriptome analysis was performed to screen for key regulators in the plumule and flag leaf at the germination and seedling stages, respectively. Following that, transgenic tobacco was developed to expose the roles and mechanisms of the candidate genes, enabling a deeper investigation of their functions. Results Out of the 60 inbred lines of maize, “975-12” exhibits the highest level of salt tolerance, while “GEMS64” displays the lowest. The application of salt stress resulted in a significant increase in the levels of antioxidant enzymes in both “975-12” and “GEMS64”. ABA signal transduction and jasmonic acid pathways were the pathways that mainly affected by salt stress. In addition, a significant finding has been made indicating that when exposed to high levels of salt stress, the expression of ZmHSP90 in ‘975-12’ increased while in ‘GEMS64’ decreased. Furthermore, in tobacco plants overexpressing ZmHSP90, there was an increase in antioxidant enzyme activity associated with salt tolerance. ZmHSP90 enhanced the expression levels of NtSOS1, NtHKT1, and NtNHX1 as compared to those in the salt treatment, causing the maintenance of Na+ and K+ homeostasis, suggesting that high expression of ZmHSP90 was conducive to regulate Na+ transporters to maintain K+/Na+ balanced in tobacco.
bibliographic citation: Yu et al. (2023) Maize ZmHSP90 plays a role in acclimation to salt stress. PeerJ 11:e15819 https://doi.org/10.7717/peerj.15819
date submitted: 2022-09-09
date accepted: 2023-07-10
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Xinyan
author list: Agent
  family name: Zhao
  given name: Yanxin
author list: Agent
  family name: Wang
  given name: Yun
author list: Agent
  family name: Zou
  given name: Zhiqing
author list: Agent
  family name: Li
  given name: Fenghai
doi: 10.7717/peerj.15819
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: ©2023 Yu et al.
attribution name: Yu et al.

The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae)
type: item
type: AcademicArticle
description: Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1–trnI–trnL2–trnW–trnM–trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.
format: application/pdf
format: text/html
creator: Cheng-Yuan Su
creator: Dao-Hong Zhu
creator: Yoshihisa Abe
creator: Tatsuya Ide
creator: Zhiwei Liu
subject: Entomology
description: doi:10.7717/peerj.15865
publisher: PeerJ Inc.
rights: © 2023 Su et al.
abstract: Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1–trnI–trnL2–trnW–trnM–trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.
bibliographic citation: Su et al. (2023) The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae). PeerJ 11:e15865 https://doi.org/10.7717/peerj.15865
date submitted: 2021-03-29
date accepted: 2023-07-17
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Cheng-Yuan
author list: Agent
  family name: Zhu
  given name: Dao-Hong
author list: Agent
  family name: Abe
  given name: Yoshihisa
author list: Agent
  family name: Ide
  given name: Tatsuya
author list: Agent
  family name: Liu
  given name: Zhiwei
doi: 10.7717/peerj.15865
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: ©2023 Su et al.
attribution name: Su et al.

An acoustic-based method for locating maternity colonies of rare woodland bats
type: item
type: AcademicArticle
description: Locating colonies of rare bats can be a time consuming process, as it is often difficult to know where to focus survey effort. However, identifying peaks of bat activity via acoustic monitoring may provide insights into whether a colony is locally present, and help screen out sites with low potential. Using a triage approach, we developed a survey methodology for locating colonies of the woodland-specialist barbastelle bat (Barbastella barbastellus). We investigated whether woodland occupancy by a colony could be predicted by acoustic data, and assessed the influence of survey effort (number of acoustic detectors deployed) on detectability. The methodology was then trialled in citizen science surveys of 77 woodlands, with follow-up radio-tracking surveys by specialists being used to confirm presence or absence. Using Receiver Operating Characteristic (ROC) curve analysis, we found that a threshold of four barbastelle passes recorded by at least one detector within one hour of sunset optimised the balance between the true- and false-positive rates. Subsequently, we found that a minimum survey effort of one detector per 6.25 hectares of woodland was needed to ensure a colony would be detected using this threshold, based on a survey sensitivity of 90%. Radio-tracking surveys in a subset of the woodlands, identified as having a high probability of being occupied by a colony based on acoustic monitoring, confirmed the presence of five previously unknown barbastelle maternity colonies. These results demonstrate that a triage system, in which high probability woodland sites are identified based on acoustic survey data, can be used to prioritise sites for future specialist surveys and conservation action.
format: application/pdf
format: text/html
creator: Kieran D. O’Malley
creator: Henry Schofield
creator: Patrick G.R. Wright
creator: Daniel Hargreaves
creator: Tom Kitching
creator: Marina Bollo Palacios
creator: Fiona Mathews
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.15951
publisher: PeerJ Inc.
rights: © 2023 O’Malley et al.
abstract: Locating colonies of rare bats can be a time consuming process, as it is often difficult to know where to focus survey effort. However, identifying peaks of bat activity via acoustic monitoring may provide insights into whether a colony is locally present, and help screen out sites with low potential. Using a triage approach, we developed a survey methodology for locating colonies of the woodland-specialist barbastelle bat (Barbastella barbastellus). We investigated whether woodland occupancy by a colony could be predicted by acoustic data, and assessed the influence of survey effort (number of acoustic detectors deployed) on detectability. The methodology was then trialled in citizen science surveys of 77 woodlands, with follow-up radio-tracking surveys by specialists being used to confirm presence or absence. Using Receiver Operating Characteristic (ROC) curve analysis, we found that a threshold of four barbastelle passes recorded by at least one detector within one hour of sunset optimised the balance between the true- and false-positive rates. Subsequently, we found that a minimum survey effort of one detector per 6.25 hectares of woodland was needed to ensure a colony would be detected using this threshold, based on a survey sensitivity of 90%. Radio-tracking surveys in a subset of the woodlands, identified as having a high probability of being occupied by a colony based on acoustic monitoring, confirmed the presence of five previously unknown barbastelle maternity colonies. These results demonstrate that a triage system, in which high probability woodland sites are identified based on acoustic survey data, can be used to prioritise sites for future specialist surveys and conservation action.
bibliographic citation: O’Malley et al. (2023) An acoustic-based method for locating maternity colonies of rare woodland bats. PeerJ 11:e15951 https://doi.org/10.7717/peerj.15951
date submitted: 2023-06-01
date accepted: 2023-08-01
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Malley
  given name: Kieran D.
author list: Agent
  family name: Schofield
  given name: Henry
author list: Agent
  family name: Wright
  given name: Patrick G.R.
author list: Agent
  family name: Hargreaves
  given name: Daniel
author list: Agent
  family name: Kitching
  given name: Tom
author list: Agent
  family name: Bollo Palacios
  given name: Marina
author list: Agent
  family name: Mathews
  given name: Fiona
doi: 10.7717/peerj.15951
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: ©2023 O’Malley et al.
attribution name: O’Malley et al.

Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project
type: item
type: AcademicArticle
description: Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as “microbial gardening”. In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species …
format: application/pdf
format: text/html
creator: Manuel Ochoa-Sánchez
creator: Eliana Paola Acuña Gomez
creator: Lia Ramírez-Fenández
creator: Luis E. Eguiarte
creator: Valeria Souza
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15978
publisher: PeerJ Inc.
rights: © 2023 Ochoa-Sánchez et al.
abstract: Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as “microbial gardening”. In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species …
bibliographic citation: Ochoa-Sánchez et al. (2023) Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 11:e15978 https://doi.org/10.7717/peerj.15978
date submitted: 2023-03-28
date accepted: 2023-08-07
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ochoa-Sánchez
  given name: Manuel
author list: Agent
  family name: Acuña Gomez
  given name: Eliana Paola
author list: Agent
  family name: Ramírez-Fenández
  given name: Lia
author list: Agent
  family name: Eguiarte
  given name: Luis E.
author list: Agent
  family name: Souza
  given name: Valeria
doi: 10.7717/peerj.15978
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: © 2023 Ochoa-Sánchez et al.
attribution name: Ochoa-Sánchez et al.

High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration
type: item
type: AcademicArticle
description: Background Many researches proved that non-coding RNAs are important in glioma development. We screened the differentially expressed genes through The Cancer Genome Atlas (TCGA) database and identified the molecule LYRM4-AS1 associated with prognosis. As a lncRNA, the expression level and role of LYRM4-AS1 in glioma are inconclusive. Therefore, we attempted to assess the clinical significance, expression and related mechanisms of LYRM4-AS1 in glioma by employing cell experiments and an integrative in silico methodology. Methods RNA-seq data were obtained from UCSC XENA and TCGA datasets. The Gene Expression Omnibus (GEO) database was used to download glioma-related expression profile data. The LYRM4-AS1 expression level was evaluated. Survival curves were constructed by the Kaplan–Meier method. Cox regression analysis was used to analyze independent variables. Patients were divided into high and low expression group base on the median LYRM4-AS1 expression value in glioma tissues. The DESeq2 R package was used to identify differentially expressed genes (DEGs) between two different expression LYRM4-AS1 groups. Gene set enrichment analysis (GSEA) was conducted. Next, the single-sample Gene Set Enrichment Analysis (ssGSEA) was done to quantify the immune infiltration of immune cells in glioma tissues. Gene expression profiles for glioma tumor tissues were used to quantify the relative enrichment score for each immune cell. Spearman correlation analysis was used to analyze the correlation between LYRM4-AS1 and biomarkers of immune cells as well as immune checkpoints in glioma. Finally, assays for cell apoptosis, cell viability and wound healing were conducted to evaluate the function on U87 MG and U251 cells after knocking down LYRM4-AS1. Results We found that LYRM4-AS1 was upregulated and related to the grade and malignancy of glioma. Survival analyses showed that high expression LYRM4-AS1 patients had poor clinical outcomes (P < 0.01). Cox regression analyses demonstra…
format: application/pdf
format: text/html
creator: Hai yue Wang
creator: Ying Xie
creator: Hongzhen Du
creator: Bin Luo
creator: Zengning Li
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.16104
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background Many researches proved that non-coding RNAs are important in glioma development. We screened the differentially expressed genes through The Cancer Genome Atlas (TCGA) database and identified the molecule LYRM4-AS1 associated with prognosis. As a lncRNA, the expression level and role of LYRM4-AS1 in glioma are inconclusive. Therefore, we attempted to assess the clinical significance, expression and related mechanisms of LYRM4-AS1 in glioma by employing cell experiments and an integrative in silico methodology. Methods RNA-seq data were obtained from UCSC XENA and TCGA datasets. The Gene Expression Omnibus (GEO) database was used to download glioma-related expression profile data. The LYRM4-AS1 expression level was evaluated. Survival curves were constructed by the Kaplan–Meier method. Cox regression analysis was used to analyze independent variables. Patients were divided into high and low expression group base on the median LYRM4-AS1 expression value in glioma tissues. The DESeq2 R package was used to identify differentially expressed genes (DEGs) between two different expression LYRM4-AS1 groups. Gene set enrichment analysis (GSEA) was conducted. Next, the single-sample Gene Set Enrichment Analysis (ssGSEA) was done to quantify the immune infiltration of immune cells in glioma tissues. Gene expression profiles for glioma tumor tissues were used to quantify the relative enrichment score for each immune cell. Spearman correlation analysis was used to analyze the correlation between LYRM4-AS1 and biomarkers of immune cells as well as immune checkpoints in glioma. Finally, assays for cell apoptosis, cell viability and wound healing were conducted to evaluate the function on U87 MG and U251 cells after knocking down LYRM4-AS1. Results We found that LYRM4-AS1 was upregulated and related to the grade and malignancy of glioma. Survival analyses showed that high expression LYRM4-AS1 patients had poor clinical outcomes (P < 0.01). Cox regression analyses demonstra…
bibliographic citation: Wang et al. (2023) High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration. PeerJ 11:e16104 https://doi.org/10.7717/peerj.16104
date submitted: 2023-04-21
date accepted: 2023-08-25
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hai yue
author list: Agent
  family name: Xie
  given name: Ying
author list: Agent
  family name: Du
  given name: Hongzhen
author list: Agent
  family name: Luo
  given name: Bin
author list: Agent
  family name: Li
  given name: Zengning
doi: 10.7717/peerj.16104
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: © 2023 Wang et al.
attribution name: Wang et al.

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