PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis
items: Assigning confidence scores to homoeologs using fuzzy logic
items: Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition
items: Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity
items: Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)
items: Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria
items: Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve
items: Network models of driver behavior
items: cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences
items: Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste

Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis
type: item
type: AcademicArticle
description: Background Leishmaniasis is a parasitic disease caused by more than 20 species of the Leishmania genus. The disease is globally distributed and is endemic in 97 countries and three territories in the tropical and subtropical regions. The efficacy of the current treatments is becoming increasingly low either due to incomplete treatment or resistant parasites. Failure of treatment is frequent, and therefore, the search for early biomarkers of therapeutic response in cutaneous leishmaniasis (CL) is urgently needed. Objective The aim of this study was to compare the proteomic profiles in patients with CL before and after 7 days of treatment and identify early biomarkers of curative response. Methods Four patients with a parasitological diagnosis of leishmaniasis with confirmation of species by PCR-RFLP were recruited. All patients had a single lesion, and a protein from the middle of the ulcer was quantified by liquid chromatography and mass spectrometry. Results A total of 12 proteins showed differential expression in the comparative LC-electrospray ionization MS/MS (LC-ESI-MS/MS) triplicate analysis. Seven of them were up-regulated and five of them were down-regulated. Calcium binding proteins A2, A8, and A9 and hemoglobin subunits alpha-2 and delta showed high correlation with epidermis development and immune response. Conclusion We identified changes in the profiles of proteins that had a positive therapeutic response to the treatment. The proteins identified with differential expression are related to the reduction of inflammation and increased tissue repair. These proteins can be useful as biomarkers for early monitoring of therapeutic response in CL.
format: application/pdf
format: text/html
creator: Andrés Montoya
creator: Manuel Carlos López
creator: Ivan D. Vélez
creator: Sara M. Robledo
subject: Parasitology
subject: Infectious Diseases
description: doi:10.7717/peerj.6228
publisher: PeerJ Inc.
rights: © 2019 Montoya et al.
abstract: Background Leishmaniasis is a parasitic disease caused by more than 20 species of the Leishmania genus. The disease is globally distributed and is endemic in 97 countries and three territories in the tropical and subtropical regions. The efficacy of the current treatments is becoming increasingly low either due to incomplete treatment or resistant parasites. Failure of treatment is frequent, and therefore, the search for early biomarkers of therapeutic response in cutaneous leishmaniasis (CL) is urgently needed. Objective The aim of this study was to compare the proteomic profiles in patients with CL before and after 7 days of treatment and identify early biomarkers of curative response. Methods Four patients with a parasitological diagnosis of leishmaniasis with confirmation of species by PCR-RFLP were recruited. All patients had a single lesion, and a protein from the middle of the ulcer was quantified by liquid chromatography and mass spectrometry. Results A total of 12 proteins showed differential expression in the comparative LC-electrospray ionization MS/MS (LC-ESI-MS/MS) triplicate analysis. Seven of them were up-regulated and five of them were down-regulated. Calcium binding proteins A2, A8, and A9 and hemoglobin subunits alpha-2 and delta showed high correlation with epidermis development and immune response. Conclusion We identified changes in the profiles of proteins that had a positive therapeutic response to the treatment. The proteins identified with differential expression are related to the reduction of inflammation and increased tissue repair. These proteins can be useful as biomarkers for early monitoring of therapeutic response in CL.
bibliographic citation: Montoya et al. (2019) Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis. PeerJ 6:e6228 https://doi.org/10.7717/peerj.6228
date submitted: 2018-09-27
date accepted: 2018-12-06
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montoya
  given name: Andrés
author list: Agent
  family name: López
  given name: Manuel Carlos
author list: Agent
  family name: Vélez
  given name: Ivan D.
author list: Agent
  family name: Robledo
  given name: Sara M.
doi: 10.7717/peerj.6228
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Montoya et al.
attribution name: Montoya et al.

Assigning confidence scores to homoeologs using fuzzy logic
type: item
type: AcademicArticle
description: In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
format: application/pdf
format: text/html
creator: Natasha M. Glover
creator: Adrian Altenhoff
creator: Christophe Dessimoz
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.6231
publisher: PeerJ Inc.
rights: © 2019 Glover et al.
abstract: In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
bibliographic citation: Glover et al. (2019) Assigning confidence scores to homoeologs using fuzzy logic. PeerJ 6:e6231 https://doi.org/10.7717/peerj.6231
date submitted: 2018-07-11
date accepted: 2018-12-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glover
  given name: Natasha M.
author list: Agent
  family name: Altenhoff
  given name: Adrian
author list: Agent
  family name: Dessimoz
  given name: Christophe
doi: 10.7717/peerj.6231
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Glover et al.
attribution name: Glover et al.

Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition
type: item
type: AcademicArticle
description: We analyze the multivariate pattern of lower and upper cheek dentition for the family Hyaenidae along its evolutionary history. A total of 11,698 individual measurements of lengths and widths for the main postcanine teeth were collected for 54 extinct and three extant species of this family and analyzed by means of principal component analyses. Our results indicate that the functional aspects are better reflected by lower cheek dentition as a result of mosaic evolution. The multivariate structure captured by the three first principal components correspond to different adaptive strategies. The two first components characterize the main groups of ecomorphs, while hunting species separate from scavengers along the third axis. In the context of Hyaenidae, the post-canine cheek dentition of Parahyaena brunnea and Hyaena hyaena shows an extreme degree of specialization in scavenging.
format: application/pdf
format: text/html
creator: Carlos Coca-Ortega
creator: Juan Antonio Pérez-Claros
subject: Biodiversity
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6238
publisher: PeerJ Inc.
rights: © 2019 Coca-Ortega and Pérez-Claros
abstract: We analyze the multivariate pattern of lower and upper cheek dentition for the family Hyaenidae along its evolutionary history. A total of 11,698 individual measurements of lengths and widths for the main postcanine teeth were collected for 54 extinct and three extant species of this family and analyzed by means of principal component analyses. Our results indicate that the functional aspects are better reflected by lower cheek dentition as a result of mosaic evolution. The multivariate structure captured by the three first principal components correspond to different adaptive strategies. The two first components characterize the main groups of ecomorphs, while hunting species separate from scavengers along the third axis. In the context of Hyaenidae, the post-canine cheek dentition of Parahyaena brunnea and Hyaena hyaena shows an extreme degree of specialization in scavenging.
bibliographic citation: Coca-Ortega et al. (2019) Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition. PeerJ 6:e6238 https://doi.org/10.7717/peerj.6238
date submitted: 2018-09-13
date accepted: 2018-12-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coca-Ortega
  given name: Carlos
author list: Agent
  family name: Pérez-Claros
  given name: Juan Antonio
doi: 10.7717/peerj.6238
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Coca-Ortega and Pérez-Claros
attribution name: Coca-Ortega and Pérez-Claros

Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity
type: item
type: AcademicArticle
description: Improving the accuracy of predicting plant productivity is a key element in planning nutrient management strategies to ensure a balance between nutrient supply and demand under climate change. A calculation based on intercepted photosynthetically active radiation is an effective and relatively reliable way to determine the climate impact on a crop above-ground biomass (AGB). This research shows that using variations in a chlorophyll content index (CCI) in a mathematical function could effectively obtain good statistical diagnostic results between simulated and observed crop biomass. In this study, the leaf CCI, which is used as a biochemical photosynthetic component and calibration parameter, increased simulation accuracy across the growing stages during 2016–2017. This calculation improves the accuracy of prediction and modelling of crops under specific agroecosystems, and it may also improve projections of AGB for a variety of other crops.
format: application/pdf
format: text/html
creator: Chuang Liu
creator: Yi Liu
creator: Yanhong Lu
creator: Yulin Liao
creator: Jun Nie
creator: Xiaoliang Yuan
creator: Fang Chen
subject: Agricultural Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6240
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Improving the accuracy of predicting plant productivity is a key element in planning nutrient management strategies to ensure a balance between nutrient supply and demand under climate change. A calculation based on intercepted photosynthetically active radiation is an effective and relatively reliable way to determine the climate impact on a crop above-ground biomass (AGB). This research shows that using variations in a chlorophyll content index (CCI) in a mathematical function could effectively obtain good statistical diagnostic results between simulated and observed crop biomass. In this study, the leaf CCI, which is used as a biochemical photosynthetic component and calibration parameter, increased simulation accuracy across the growing stages during 2016–2017. This calculation improves the accuracy of prediction and modelling of crops under specific agroecosystems, and it may also improve projections of AGB for a variety of other crops.
bibliographic citation: Liu et al. (2019) Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity. PeerJ 6:e6240 https://doi.org/10.7717/peerj.6240
date submitted: 2018-08-20
date accepted: 2018-12-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chuang
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Lu
  given name: Yanhong
author list: Agent
  family name: Liao
  given name: Yulin
author list: Agent
  family name: Nie
  given name: Jun
author list: Agent
  family name: Yuan
  given name: Xiaoliang
author list: Agent
  family name: Chen
  given name: Fang
doi: 10.7717/peerj.6240
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)
type: item
type: AcademicArticle
description: The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.
format: application/pdf
format: text/html
creator: Kebin Yang
creator: Ying Li
creator: Sining Wang
creator: Xiurong Xu
creator: Huayu Sun
creator: Hansheng Zhao
creator: Xueping Li
creator: Zhimin Gao
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6242
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.
bibliographic citation: Yang et al. (2019) Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis). PeerJ 6:e6242 https://doi.org/10.7717/peerj.6242
date submitted: 2018-09-12
date accepted: 2018-12-08
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Kebin
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Wang
  given name: Sining
author list: Agent
  family name: Xu
  given name: Xiurong
author list: Agent
  family name: Sun
  given name: Huayu
author list: Agent
  family name: Zhao
  given name: Hansheng
author list: Agent
  family name: Li
  given name: Xueping
author list: Agent
  family name: Gao
  given name: Zhimin
doi: 10.7717/peerj.6242
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria
type: item
type: AcademicArticle
description: Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and that glucose is taken up by natural Prochlorococcus populations. We demonstrated that the kinetic parameters of glucose uptake show significant diversity in different Prochlorococcus and Synechococcus strains. Here, we tested whether the transcriptional response of glcH to several glucose concentrations and light conditions was also different depending on the studied strain. Methods Cultures were grown in the light, supplemented with five different glucose concentrations or subjected to darkness, and cells harvested after 24 h of treatment. qRT-PCR was used to determine glcH expression in four Prochlorococcus and two Synechococcus strains. Results In all studied strains glcH was expressed in the absence of glucose, and it increased upon glucose addition to cultures. The changes differed depending on the strain, both in the magnitude and in the way cells responded to the tested glucose concentrations. Unlike the other strains, Synechococcus BL107 showed the maximum glucose uptake at 5 nM glucose. Darkness induced a strong decrease in glcH expression, especially remarkable in Prochlorococcus MIT9313. Discussion Our results suggest that marine picocyanobacteria are actively monitoring the availability of glucose, to upregulate glcH expression in order to exploit the presence of sugars in the environment. The diverse responses observed in different strains suggest that the transcriptional regulation of glucose uptake has been adjusted by evolutive selection. Darkness promotes a strong decrease in glcH expression in all studied strains, which fits with previous results on glucose uptake in Prochlorococcus. Overall, this work reinforces the importance of mixotrophy for marine picocyanobacteria.
format: application/pdf
format: text/html
creator: José Ángel Moreno-Cabezuelo
creator: Antonio López-Lozano
creator: Jesús Díez
creator: José Manuel García-Fernández
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.6248
publisher: PeerJ Inc.
rights: © 2019 Moreno-Cabezuelo et al.
abstract: Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and that glucose is taken up by natural Prochlorococcus populations. We demonstrated that the kinetic parameters of glucose uptake show significant diversity in different Prochlorococcus and Synechococcus strains. Here, we tested whether the transcriptional response of glcH to several glucose concentrations and light conditions was also different depending on the studied strain. Methods Cultures were grown in the light, supplemented with five different glucose concentrations or subjected to darkness, and cells harvested after 24 h of treatment. qRT-PCR was used to determine glcH expression in four Prochlorococcus and two Synechococcus strains. Results In all studied strains glcH was expressed in the absence of glucose, and it increased upon glucose addition to cultures. The changes differed depending on the strain, both in the magnitude and in the way cells responded to the tested glucose concentrations. Unlike the other strains, Synechococcus BL107 showed the maximum glucose uptake at 5 nM glucose. Darkness induced a strong decrease in glcH expression, especially remarkable in Prochlorococcus MIT9313. Discussion Our results suggest that marine picocyanobacteria are actively monitoring the availability of glucose, to upregulate glcH expression in order to exploit the presence of sugars in the environment. The diverse responses observed in different strains suggest that the transcriptional regulation of glucose uptake has been adjusted by evolutive selection. Darkness promotes a strong decrease in glcH expression in all studied strains, which fits with previous results on glucose uptake in Prochlorococcus. Overall, this work reinforces the importance of mixotrophy for marine picocyanobacteria.
bibliographic citation: Moreno-Cabezuelo et al. (2019) Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria. PeerJ 6:e6248 https://doi.org/10.7717/peerj.6248
date submitted: 2018-10-24
date accepted: 2018-12-09
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-Cabezuelo
  given name: José Ángel
author list: Agent
  family name: López-Lozano
  given name: Antonio
author list: Agent
  family name: Díez
  given name: Jesús
author list: Agent
  family name: García-Fernández
  given name: José Manuel
doi: 10.7717/peerj.6248
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Moreno-Cabezuelo et al.
attribution name: Moreno-Cabezuelo et al.

Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve
type: item
type: AcademicArticle
description: The effects of different revegetation types on soil physical–chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
format: application/pdf
format: text/html
creator: Jiaojiao Deng
creator: You Yin
creator: Jiyao Luo
creator: Wenxu Zhu
creator: Yongbin Zhou
subject: Ecology
subject: Mycology
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.6251
publisher: PeerJ Inc.
rights: © 2018 Deng et al.
abstract: The effects of different revegetation types on soil physical–chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
bibliographic citation: Deng et al. (2019) Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve. PeerJ 6:e6251 https://doi.org/10.7717/peerj.6251
date submitted: 2018-08-30
date accepted: 2018-12-08
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Jiaojiao
author list: Agent
  family name: Yin
  given name: You
author list: Agent
  family name: Luo
  given name: Jiyao
author list: Agent
  family name: Zhu
  given name: Wenxu
author list: Agent
  family name: Zhou
  given name: Yongbin
doi: 10.7717/peerj.6251
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2018 Deng et al.
attribution name: Deng et al.

Network models of driver behavior
type: item
type: AcademicArticle
description: The way people behave in traffic is not always optimal from the road safety perspective: drivers exceed speed limits, misjudge speeds or distances, tailgate other road users or fail to perceive them. Such behaviors are commonly investigated using self-report-based latent variable models, and conceptualized as reflections of violation- and error-proneness. However, attributing dangerous behavior to stable properties of individuals may not be the optimal way of improving traffic safety, whereas investigating direct relationships between traffic behaviors offers a fruitful way forward. Network models of driver behavior and background factors influencing behavior were constructed using a large UK sample of novice drivers. The models show how individual violations, such as speeding, are related to and may contribute to individual errors such as tailgating and braking to avoid an accident. In addition, a network model of the background factors and driver behaviors was constructed. Finally, a model predicting crashes based on prior behavior was built and tested in separate datasets. This contribution helps to bridge a gap between experimental/theoretical studies and self-report-based studies in traffic research: the former have recognized the importance of focusing on relationships between individual driver behaviors, while network analysis offers a way to do so for self-report studies.
format: application/pdf
format: text/html
creator: Markus T. Mattsson
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.6119
publisher: PeerJ Inc.
rights: © 2019 Mattsson
abstract: The way people behave in traffic is not always optimal from the road safety perspective: drivers exceed speed limits, misjudge speeds or distances, tailgate other road users or fail to perceive them. Such behaviors are commonly investigated using self-report-based latent variable models, and conceptualized as reflections of violation- and error-proneness. However, attributing dangerous behavior to stable properties of individuals may not be the optimal way of improving traffic safety, whereas investigating direct relationships between traffic behaviors offers a fruitful way forward. Network models of driver behavior and background factors influencing behavior were constructed using a large UK sample of novice drivers. The models show how individual violations, such as speeding, are related to and may contribute to individual errors such as tailgating and braking to avoid an accident. In addition, a network model of the background factors and driver behaviors was constructed. Finally, a model predicting crashes based on prior behavior was built and tested in separate datasets. This contribution helps to bridge a gap between experimental/theoretical studies and self-report-based studies in traffic research: the former have recognized the importance of focusing on relationships between individual driver behaviors, while network analysis offers a way to do so for self-report studies.
bibliographic citation: Mattsson (2019) Network models of driver behavior. PeerJ 6:e6119 https://doi.org/10.7717/peerj.6119
date submitted: 2018-07-03
date accepted: 2018-11-16
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mattsson
  given name: Markus T.
doi: 10.7717/peerj.6119
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Mattsson
attribution name: Mattsson

cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences
type: item
type: AcademicArticle
description: Identifying cis-acting elements and understanding regulatory mechanisms of a gene is crucial to fully understand the molecular biology of an organism. In general, it is difficult to identify previously uncharacterised cis-acting elements with an unknown consensus sequence. The task is especially problematic with viruses containing regions of limited or no similarity to other previously characterised sequences. Fortunately, the fast increase in the number of sequenced genomes allows us to detect some of these elusive cis-elements. In this work, we introduce a web-based tool called cRegions. It was developed to identify regions within a protein-coding sequence where the conservation in the amino acid sequence is caused by the conservation in the nucleotide sequence. The cRegion can be the first step in discovering novel cis-acting sequences from diverged protein-coding genes. The results can be used as a basis for future experimental analysis. We applied cRegions on the non-structural and structural polyproteins of alphaviruses as an example and successfully detected all known cis-acting elements. In this publication and in previous work, we have shown that cRegions is able to detect a wide variety of functional elements in DNA and RNA viruses. These functional elements include splice sites, stem-loops, overlapping reading frames, internal promoters, ribosome frameshifting signals and other embedded elements with yet unknown function. The cRegions web tool is available at http://bioinfo.ut.ee/cRegions/.
format: application/pdf
format: text/html
creator: Mikk Puustusmaa
creator: Aare Abroi
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Virology
subject: Data Science
description: doi:10.7717/peerj.6176
publisher: PeerJ Inc.
rights: © 2019 Puustusmaa and Abroi
abstract: Identifying cis-acting elements and understanding regulatory mechanisms of a gene is crucial to fully understand the molecular biology of an organism. In general, it is difficult to identify previously uncharacterised cis-acting elements with an unknown consensus sequence. The task is especially problematic with viruses containing regions of limited or no similarity to other previously characterised sequences. Fortunately, the fast increase in the number of sequenced genomes allows us to detect some of these elusive cis-elements. In this work, we introduce a web-based tool called cRegions. It was developed to identify regions within a protein-coding sequence where the conservation in the amino acid sequence is caused by the conservation in the nucleotide sequence. The cRegion can be the first step in discovering novel cis-acting sequences from diverged protein-coding genes. The results can be used as a basis for future experimental analysis. We applied cRegions on the non-structural and structural polyproteins of alphaviruses as an example and successfully detected all known cis-acting elements. In this publication and in previous work, we have shown that cRegions is able to detect a wide variety of functional elements in DNA and RNA viruses. These functional elements include splice sites, stem-loops, overlapping reading frames, internal promoters, ribosome frameshifting signals and other embedded elements with yet unknown function. The cRegions web tool is available at http://bioinfo.ut.ee/cRegions/.
bibliographic citation: Puustusmaa et al. (2019) cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences. PeerJ 6:e6176 https://doi.org/10.7717/peerj.6176
date submitted: 2018-07-18
date accepted: 2018-11-27
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puustusmaa
  given name: Mikk
author list: Agent
  family name: Abroi
  given name: Aare
doi: 10.7717/peerj.6176
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Puustusmaa and Abroi
attribution name: Puustusmaa and Abroi

Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste
type: item
type: AcademicArticle
description: Background Sweet sorghum bagasse (SSB), comprising both a dermal layer and pith, is a solid waste generated by agricultural activities. Open burning was previously used to treat agricultural solid waste but is harmful to the environment and human health. Recent reports showed that certain techniques can convert this agricultural waste into valuable products. While SSB has been considered an attractive raw material for sugar extraction and the production of value-added products, the pith root in the SSB can be difficult to process. Therefore, it is necessary to pretreat bagasse before conventional hydrolysis. Methods A thorough analysis and comparison of various pretreatment methods were conducted based on physicochemical and microscopic approaches. The responses of agricultural SSB stem pith with different particle sizes to pretreatment temperature, acid and alkali concentration and enzyme dosage were investigated to determine the optimal pretreatment. The integrated methods are beneficial to the utilization of carbohydrate-based and unknown compounds in agricultural solid waste. Results Acid (1.5−4.5%, v/v) and alkali (5−8%, w/v) reagents were used to collect cellulose from different meshes of pith at 25–100 °C. The results showed that the use of 100 mesh pith soaked in 8% (w/v) NaOH solution at 100 °C resulted in 32.47% ± 0.01% solid recovery. Follow-up fermentation with 3% (v/v) acid and 6.5% (w/v) alkali at 50 °C for enzymolysis was performed with the optimal enzyme ratio. An analysis of the surface topography and porosity before and after pretreatment showed that both the pore size of the pith and the amount of exposed cellulose increased as the mesh size increased. Interestingly, various compounds, including 42 compounds previously known to be present and 13 compounds not previously known to be present, were detected in the pretreatment liquid, while 10 types of monosaccharides, including D-glucose, D-xylose and D-arabinose, were found in the enzymatic solutio…
format: application/pdf
format: text/html
creator: Ting-Ting Jiang
creator: Yan Liang
creator: Xiang Zhou
creator: Zi-Wei Shi
creator: Zhi-Jun Xin
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Food, Water and Energy Nexus
subject: Green Chemistry
description: doi:10.7717/peerj.6186
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: Background Sweet sorghum bagasse (SSB), comprising both a dermal layer and pith, is a solid waste generated by agricultural activities. Open burning was previously used to treat agricultural solid waste but is harmful to the environment and human health. Recent reports showed that certain techniques can convert this agricultural waste into valuable products. While SSB has been considered an attractive raw material for sugar extraction and the production of value-added products, the pith root in the SSB can be difficult to process. Therefore, it is necessary to pretreat bagasse before conventional hydrolysis. Methods A thorough analysis and comparison of various pretreatment methods were conducted based on physicochemical and microscopic approaches. The responses of agricultural SSB stem pith with different particle sizes to pretreatment temperature, acid and alkali concentration and enzyme dosage were investigated to determine the optimal pretreatment. The integrated methods are beneficial to the utilization of carbohydrate-based and unknown compounds in agricultural solid waste. Results Acid (1.5−4.5%, v/v) and alkali (5−8%, w/v) reagents were used to collect cellulose from different meshes of pith at 25–100 °C. The results showed that the use of 100 mesh pith soaked in 8% (w/v) NaOH solution at 100 °C resulted in 32.47% ± 0.01% solid recovery. Follow-up fermentation with 3% (v/v) acid and 6.5% (w/v) alkali at 50 °C for enzymolysis was performed with the optimal enzyme ratio. An analysis of the surface topography and porosity before and after pretreatment showed that both the pore size of the pith and the amount of exposed cellulose increased as the mesh size increased. Interestingly, various compounds, including 42 compounds previously known to be present and 13 compounds not previously known to be present, were detected in the pretreatment liquid, while 10 types of monosaccharides, including D-glucose, D-xylose and D-arabinose, were found in the enzymatic solutio…
bibliographic citation: Jiang et al. (2019) Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste. PeerJ 6:e6186 https://doi.org/10.7717/peerj.6186
date submitted: 2018-09-05
date accepted: 2018-11-29
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Ting-Ting
author list: Agent
  family name: Liang
  given name: Yan
author list: Agent
  family name: Zhou
  given name: Xiang
author list: Agent
  family name: Shi
  given name: Zi-Wei
author list: Agent
  family name: Xin
  given name: Zhi-Jun
doi: 10.7717/peerj.6186
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Jiang et al.
attribution name: Jiang et al.

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