PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
items: Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
items: Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
items: Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations
items: Sea urchins: an update on their pharmacological properties
items: The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species
items: Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
items: Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
items: Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
items: What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors

Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
type: item
type: AcademicArticle
description: Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
format: application/pdf
format: text/html
creator: Zhaokui Du
creator: Weida Lin
creator: Jinxing Zhu
creator: Junmin Li
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.13689
publisher: PeerJ Inc.
rights: © 2022 Du et al.
abstract: Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
bibliographic citation: Du et al. (2022) Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 10:e13689 https://doi.org/10.7717/peerj.13689
date submitted: 2021-08-31
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Zhaokui
author list: Agent
  family name: Lin
  given name: Weida
author list: Agent
  family name: Zhu
  given name: Jinxing
author list: Agent
  family name: Li
  given name: Junmin
doi: 10.7717/peerj.13689
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Du et al.
attribution name: Du et al.

Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
type: item
type: AcademicArticle
description: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could b…
format: application/pdf
format: text/html
creator: Mauricio Heredia-Pech
creator: Mariana Chávez-Pesqueira
creator: Matilde M. Ortiz-García
creator: Rubén Humberto Andueza-Noh
creator: María Isabel Chacón-Sánchez
creator: Jaime Martínez-Castillo
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13690
publisher: PeerJ Inc.
rights: © 2022 Heredia-Pech et al.
abstract: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could b…
bibliographic citation: Heredia-Pech et al. (2022) Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area. PeerJ 10:e13690 https://doi.org/10.7717/peerj.13690
date submitted: 2022-01-28
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heredia-Pech
  given name: Mauricio
author list: Agent
  family name: Chávez-Pesqueira
  given name: Mariana
author list: Agent
  family name: Ortiz-García
  given name: Matilde M.
author list: Agent
  family name: Andueza-Noh
  given name: Rubén Humberto
author list: Agent
  family name: Chacón-Sánchez
  given name: María Isabel
author list: Agent
  family name: Martínez-Castillo
  given name: Jaime
doi: 10.7717/peerj.13690
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Heredia-Pech et al.
attribution name: Heredia-Pech et al.

Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
type: item
type: AcademicArticle
description: Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
format: application/pdf
format: text/html
creator: Zhenfan Yu
creator: Dongdong Zhang
creator: Bin Zeng
creator: Xingyue Liu
creator: Jiahui Yang
creator: Wenwen Gao
creator: Xintong Ma
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13491
publisher: PeerJ Inc.
rights: © 2022 Yu et al.
abstract: Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
bibliographic citation: Yu et al. (2022) Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis). PeerJ 10:e13491 https://doi.org/10.7717/peerj.13491
date submitted: 2022-01-31
date accepted: 2022-05-03
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Zhenfan
author list: Agent
  family name: Zhang
  given name: Dongdong
author list: Agent
  family name: Zeng
  given name: Bin
author list: Agent
  family name: Liu
  given name: Xingyue
author list: Agent
  family name: Yang
  given name: Jiahui
author list: Agent
  family name: Gao
  given name: Wenwen
author list: Agent
  family name: Ma
  given name: Xintong
doi: 10.7717/peerj.13491
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Yu et al.
attribution name: Yu et al.

Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations
type: item
type: AcademicArticle
description: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
format: application/pdf
format: text/html
creator: Fidji Berio
creator: Yann Bayle
creator: Daniel Baum
creator: Nicolas Goudemand
creator: Mélanie Debiais-Thibaud
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.13575
publisher: PeerJ Inc.
rights: © 2022 Berio et al.
abstract: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
bibliographic citation: Berio et al. (2022) Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations. PeerJ 10:e13575 https://doi.org/10.7717/peerj.13575
date submitted: 2022-01-18
date accepted: 2022-05-22
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berio
  given name: Fidji
author list: Agent
  family name: Bayle
  given name: Yann
author list: Agent
  family name: Baum
  given name: Daniel
author list: Agent
  family name: Goudemand
  given name: Nicolas
author list: Agent
  family name: Debiais-Thibaud
  given name: Mélanie
doi: 10.7717/peerj.13575
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Berio et al.
attribution name: Berio et al.

Sea urchins: an update on their pharmacological properties
type: item
type: AcademicArticle
description: Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients.
format: application/pdf
format: text/html
creator: Dulce María Moreno-García
creator: Monica Salas-Rojas
creator: Eduardo Fernández-Martínez
creator: Ma del Rocío López-Cuellar
creator: Carolina G. Sosa-Gutierrez
creator: Armando Peláez-Acero
creator: Nallely Rivero-Perez
creator: Adrian Zaragoza-Bastida
creator: Deyanira Ojeda-Ramírez
subject: Marine Biology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.13606
publisher: PeerJ Inc.
rights: © 2022 Moreno-García et al.
abstract: Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients.
bibliographic citation: Moreno-García et al. (2022) Sea urchins: an update on their pharmacological properties. PeerJ 10:e13606 https://doi.org/10.7717/peerj.13606
date submitted: 2021-12-06
date accepted: 2022-05-26
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-García
  given name: Dulce María
author list: Agent
  family name: Salas-Rojas
  given name: Monica
author list: Agent
  family name: Fernández-Martínez
  given name: Eduardo
author list: Agent
  family name: López-Cuellar
  given name: Ma del Rocío
author list: Agent
  family name: Sosa-Gutierrez
  given name: Carolina G.
author list: Agent
  family name: Peláez-Acero
  given name: Armando
author list: Agent
  family name: Rivero-Perez
  given name: Nallely
author list: Agent
  family name: Zaragoza-Bastida
  given name: Adrian
author list: Agent
  family name: Ojeda-Ramírez
  given name: Deyanira
doi: 10.7717/peerj.13606
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Moreno-García et al.
attribution name: Moreno-García et al.

The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species
type: item
type: AcademicArticle
description: Background Ice-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce. Methods Samples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages. Results The disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence.
format: application/pdf
format: text/html
creator: Natalia Kochman-Kędziora
creator: Teresa Noga
creator: Maria Olech
creator: Bart Van de Vijver
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Taxonomy
description: doi:10.7717/peerj.13624
publisher: PeerJ Inc.
rights: © 2022 Kochman-Kędziora et al.
abstract: Background Ice-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce. Methods Samples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages. Results The disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence.
bibliographic citation: Kochman-Kędziora et al. (2022) The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species. PeerJ 10:e13624 https://doi.org/10.7717/peerj.13624
date submitted: 2022-01-21
date accepted: 2022-06-02
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kochman-Kędziora
  given name: Natalia
author list: Agent
  family name: Noga
  given name: Teresa
author list: Agent
  family name: Olech
  given name: Maria
author list: Agent
  family name: Van de Vijver
  given name: Bart
doi: 10.7717/peerj.13624
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Kochman-Kędziora et al.
attribution name: Kochman-Kędziora et al.

Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
type: item
type: AcademicArticle
description: Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely.
format: application/pdf
format: text/html
creator: Tomasz Brachaniec
creator: Dorota Środek
creator: Dawid Surmik
creator: Robert Niedźwiedzki
creator: Georgios L. Georgalis
creator: Bartosz J. Płachno
creator: Piotr Duda
creator: Alexander Lukeneder
creator: Przemysław Gorzelak
creator: Mariusz A. Salamon
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.13652
publisher: PeerJ Inc.
rights: © 2022 Brachaniec et al.
abstract: Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely.
bibliographic citation: Brachaniec et al. (2022) Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland. PeerJ 10:e13652 https://doi.org/10.7717/peerj.13652
date submitted: 2022-02-04
date accepted: 2022-06-08
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Środek
  given name: Dorota
author list: Agent
  family name: Surmik
  given name: Dawid
author list: Agent
  family name: Niedźwiedzki
  given name: Robert
author list: Agent
  family name: Georgalis
  given name: Georgios L.
author list: Agent
  family name: Płachno
  given name: Bartosz J.
author list: Agent
  family name: Duda
  given name: Piotr
author list: Agent
  family name: Lukeneder
  given name: Alexander
author list: Agent
  family name: Gorzelak
  given name: Przemysław
author list: Agent
  family name: Salamon
  given name: Mariusz A.
doi: 10.7717/peerj.13652
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Brachaniec et al.
attribution name: Brachaniec et al.

Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
type: item
type: AcademicArticle
description: Background Curcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level. Methods In this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR. Results A. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, …
format: application/pdf
format: text/html
creator: Rachasak Boonhok
creator: Suthinee Sangkanu
creator: Suganya Phumjan
creator: Ramita Jongboonjua
creator: Nawarat Sangnopparat
creator: Pattamaporn Kwankaew
creator: Aman Tedasen
creator: Chooi Ling Lim
creator: Maria de Lourdes Pereira
creator: Mohammed Rahmatullah
creator: Polrat Wilairatana
creator: Christophe Wiart
creator: Karma G. Dolma
creator: Alok K. Paul
creator: Madhu Gupta
creator: Veeranoot Nissapatorn
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.13657
publisher: PeerJ Inc.
rights: © 2022 Boonhok et al.
abstract: Background Curcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level. Methods In this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR. Results A. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, …
bibliographic citation: Boonhok et al. (2022) Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation. PeerJ 10:e13657 https://doi.org/10.7717/peerj.13657
date submitted: 2022-03-25
date accepted: 2022-06-09
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boonhok
  given name: Rachasak
author list: Agent
  family name: Sangkanu
  given name: Suthinee
author list: Agent
  family name: Phumjan
  given name: Suganya
author list: Agent
  family name: Jongboonjua
  given name: Ramita
author list: Agent
  family name: Sangnopparat
  given name: Nawarat
author list: Agent
  family name: Kwankaew
  given name: Pattamaporn
author list: Agent
  family name: Tedasen
  given name: Aman
author list: Agent
  family name: Lim
  given name: Chooi Ling
author list: Agent
  family name: Pereira
  given name: Maria de Lourdes
author list: Agent
  family name: Rahmatullah
  given name: Mohammed
author list: Agent
  family name: Wilairatana
  given name: Polrat
author list: Agent
  family name: Wiart
  given name: Christophe
author list: Agent
  family name: Dolma
  given name: Karma G.
author list: Agent
  family name: Paul
  given name: Alok K.
author list: Agent
  family name: Gupta
  given name: Madhu
author list: Agent
  family name: Nissapatorn
  given name: Veeranoot
doi: 10.7717/peerj.13657
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Boonhok et al.
attribution name: Boonhok et al.

Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
type: item
type: AcademicArticle
description: Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
format: application/pdf
format: text/html
creator: Lin Yan
creator: Haijun Yang
creator: Qiang Ye
creator: Zhihua Huang
creator: Hongying Zhou
creator: Dafang Cui
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13659
publisher: PeerJ Inc.
rights: © 2022 Yan et al.
abstract: Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
bibliographic citation: Yan et al. (2022) Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.. PeerJ 10:e13659 https://doi.org/10.7717/peerj.13659
date submitted: 2021-09-22
date accepted: 2022-06-09
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Lin
author list: Agent
  family name: Yang
  given name: Haijun
author list: Agent
  family name: Ye
  given name: Qiang
author list: Agent
  family name: Huang
  given name: Zhihua
author list: Agent
  family name: Zhou
  given name: Hongying
author list: Agent
  family name: Cui
  given name: Dafang
doi: 10.7717/peerj.13659
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: ©2022 Yan et al.
attribution name: Yan et al.

What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors
type: item
type: AcademicArticle
description: Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclima…
format: application/pdf
format: text/html
creator: Abigail Gazzard
creator: Philip J. Baker
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13662
publisher: PeerJ Inc.
rights: © 2022 Gazzard and Baker
abstract: Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclima…
bibliographic citation: Gazzard et al. (2022) What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors. PeerJ 10:e13662 https://doi.org/10.7717/peerj.13662
date submitted: 2022-03-09
date accepted: 2022-06-10
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gazzard
  given name: Abigail
author list: Agent
  family name: Baker
  given name: Philip J.
doi: 10.7717/peerj.13662
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: ©2022 Gazzard and Baker
attribution name: Gazzard and Baker

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