PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Fuyuanichthys wangi gen. et sp. nov. from the Middle Triassic (Ladinian) of China highlights the early diversification of ginglymodian fishes
items: An exploration of the effect of proprioceptive knee bracing on biomechanics during a badminton lunge to the net, and the implications to injury mechanisms
items: Morphology and genome size of Epipactis helleborine (L.) Crantz (Orchidaceae) growing in anthropogenic and natural habitats
items: The oldest ceratosaurian (Dinosauria: Theropoda), from the Lower Jurassic of Italy, sheds light on the evolution of the three-fingered hand of birds
items: Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed
items: Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
items: First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes
items: Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids
items: ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV
items: Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes

Fuyuanichthys wangi gen. et sp. nov. from the Middle Triassic (Ladinian) of China highlights the early diversification of ginglymodian fishes
type: item
type: AcademicArticle
description: A series of well-preserved fossil assemblages from the Middle Triassic marine rock succession in Southwest China provide unique evidences for studying the early evolution of holostean fishes, including Halecomorphi (e.g., bownfin) and Ginglymodi (e.g., gars). Ginglymodi have the earliest record in the early Middle Triassic (Anisian, ∼244 Ma) of China, represented by Kyphosichthys and Sangiorgioichthys sui from Yunnan and S. yangjuanensis from Guizhou. Here, we report the discovery of a new ginglymodian, Fuyuanichthys wangi gen. et sp. nov., based on 22 well-preserved specimens from the lower part of the Zhuganpo member of the Falang Formation in eastern Yunnan and western Guizhou, which documents the first discovery of convincing ginglymodians from the late Middle Triassic (Ladinian, ∼240 Ma) Xingyi biota in China. Fuyuanichthys possesses a unique combination of features that easily distinguishes it from other ginglymodians, such as presence of a median gular and short and edentulous maxillae, and absence of a supramaxilla and supraorbitals. As one of the smallest known ginglymodians with a maximum standard length of ∼75 mm, the new finding further supports that the Middle Triassic Ginglymodi have a relatively small range of body sizes compared with the Halecomorphi from the same ecosystems in China. Results of a phylogenetic analysis recover Fuyuanichthys as a sister taxon to Kyphosichthys at the ginglymodian stem, and provide new insights into the early evolution of this clade.
format: application/pdf
format: text/html
creator: Guang-Hui Xu
creator: Xin-Ying Ma
creator: Yi Ren
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6054
publisher: PeerJ Inc.
rights: © 2018 Xu et al.
abstract: A series of well-preserved fossil assemblages from the Middle Triassic marine rock succession in Southwest China provide unique evidences for studying the early evolution of holostean fishes, including Halecomorphi (e.g., bownfin) and Ginglymodi (e.g., gars). Ginglymodi have the earliest record in the early Middle Triassic (Anisian, ∼244 Ma) of China, represented by Kyphosichthys and Sangiorgioichthys sui from Yunnan and S. yangjuanensis from Guizhou. Here, we report the discovery of a new ginglymodian, Fuyuanichthys wangi gen. et sp. nov., based on 22 well-preserved specimens from the lower part of the Zhuganpo member of the Falang Formation in eastern Yunnan and western Guizhou, which documents the first discovery of convincing ginglymodians from the late Middle Triassic (Ladinian, ∼240 Ma) Xingyi biota in China. Fuyuanichthys possesses a unique combination of features that easily distinguishes it from other ginglymodians, such as presence of a median gular and short and edentulous maxillae, and absence of a supramaxilla and supraorbitals. As one of the smallest known ginglymodians with a maximum standard length of ∼75 mm, the new finding further supports that the Middle Triassic Ginglymodi have a relatively small range of body sizes compared with the Halecomorphi from the same ecosystems in China. Results of a phylogenetic analysis recover Fuyuanichthys as a sister taxon to Kyphosichthys at the ginglymodian stem, and provide new insights into the early evolution of this clade.
bibliographic citation: Xu et al. (2018) Fuyuanichthys wangi gen. et sp. nov. from the Middle Triassic (Ladinian) of China highlights the early diversification of ginglymodian fishes. PeerJ 6:e6054 https://doi.org/10.7717/peerj.6054
date submitted: 2018-09-11
date accepted: 2018-11-01
issued: 2018-12-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Guang-Hui
author list: Agent
  family name: Ma
  given name: Xin-Ying
author list: Agent
  family name: Ren
  given name: Yi
doi: 10.7717/peerj.6054
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-20
copyright: ©2018 Xu et al.
attribution name: Xu et al.

An exploration of the effect of proprioceptive knee bracing on biomechanics during a badminton lunge to the net, and the implications to injury mechanisms
type: item
type: AcademicArticle
description: The aim of this study was to determine changes in knee biomechanics during badminton lunges due to fatigue, lunge strategy and knee bracing. Kinetic and kinematic data were collected from 16 experienced right-handed badminton players. Three factor repeated measures ANOVAs (lunge direction—fatigue—brace) were performed with Least Significant Difference pairwise comparisons. In addition, clinical assessments including; Y-balance test, one leg hop distance and ankle dorsiflexion range of motion were performed pre- and postfatigue. The knee showed significantly greater flexion during the forehand lunge compared to backhand. In contrast, the internal rotation velocity and the knee extension moment were greater during backhand. Knee angular velocity in the sagittal plane, peak knee moment and range of moment in the coronal plane and stance time showed significantly lower values postfatigue. In addition, the peak knee adduction moment showed significantly lower values in the braced condition in both the fatigued and nonfatigues states, and no significant differences were seen for peak vertical force, loading rate, approach velocity, or in any of the clinical assessment scores. There appears to be greater risk factors when performing a backhand lunge to the net compared to a forehand lunge, and proprioceptive bracing appears to reduce the loading at the knee.
format: application/pdf
format: text/html
creator: Raúl Valldecabres
creator: Ana María de Benito
creator: Greg Littler
creator: Jim Richards
subject: Kinesiology
subject: Orthopedics
subject: Public Health
description: doi:10.7717/peerj.6033
publisher: PeerJ Inc.
rights: © 2018 Valldecabres et al.
abstract: The aim of this study was to determine changes in knee biomechanics during badminton lunges due to fatigue, lunge strategy and knee bracing. Kinetic and kinematic data were collected from 16 experienced right-handed badminton players. Three factor repeated measures ANOVAs (lunge direction—fatigue—brace) were performed with Least Significant Difference pairwise comparisons. In addition, clinical assessments including; Y-balance test, one leg hop distance and ankle dorsiflexion range of motion were performed pre- and postfatigue. The knee showed significantly greater flexion during the forehand lunge compared to backhand. In contrast, the internal rotation velocity and the knee extension moment were greater during backhand. Knee angular velocity in the sagittal plane, peak knee moment and range of moment in the coronal plane and stance time showed significantly lower values postfatigue. In addition, the peak knee adduction moment showed significantly lower values in the braced condition in both the fatigued and nonfatigues states, and no significant differences were seen for peak vertical force, loading rate, approach velocity, or in any of the clinical assessment scores. There appears to be greater risk factors when performing a backhand lunge to the net compared to a forehand lunge, and proprioceptive bracing appears to reduce the loading at the knee.
bibliographic citation: Valldecabres et al. (2018) An exploration of the effect of proprioceptive knee bracing on biomechanics during a badminton lunge to the net, and the implications to injury mechanisms. PeerJ 6:e6033 https://doi.org/10.7717/peerj.6033
date submitted: 2018-08-07
date accepted: 2018-10-30
issued: 2018-12-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valldecabres
  given name: Raúl
author list: Agent
  family name: de Benito
  given name: Ana María
author list: Agent
  family name: Littler
  given name: Greg
author list: Agent
  family name: Richards
  given name: Jim
doi: 10.7717/peerj.6033
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-20
copyright: © 2018 Valldecabres et al.
attribution name: Valldecabres et al.

Morphology and genome size of Epipactis helleborine (L.) Crantz (Orchidaceae) growing in anthropogenic and natural habitats
type: item
type: AcademicArticle
description: Background The process of apophytism or spreading native species to human-made habitats is one of the main elements in the creation of plant cover in anthropogenic areas. Lately, an increase of anthropogenic localities with valuable flora has been observed. Apophytes are also members of the family Orchidaceae, especially from the genus Epipactis. The aim of the study was to (i) determine and compare the phenotypic variation of E. helleborine (L.) Crantz plants in anthropogenic and natural habitats, (ii) compare the genome size of plants growing in natural and anthropogenic habitats. The results reported in this study may indicate that a habitat influences morphological characteristics of plant species. Methods Field studies were conducted on four native stands and four stands in anthropogenic areas of E. helleborine in Poland in years 2011–2013. Biometrical analyses were performed on shoots and flowers. The flowers were characterised by 25 biometric features and measured using a Nikon SMZ 800 binocular, microscopic Moticam-1SP cameras and the MIPlus07 programme (Conbest Co.). The nuclear DNA content was determined in fresh and young leaves of E. helleborine, collected from four natural and four anthropogenic populations. Results We observed that in anthropogenic populations: (i) shoots were higher than shoots from natural populations, (ii) flowers differed significantly in terms of ten biometric features between habitats, (iii) the genome size of some population differed significantly between plants growing in natural and anthropogenic habitats. Discussion According to some researchers, the presence of phenotypic variability and the occurrence of ecotypes are adaptation strategies of plants to environmental changes. In our opinion, in the case of the studied anthropogenic habitats (roadside) in which the E. helleborine populations grew, we can talk about ecofen due to the often repeated set of characteristic features, i.e., high shoots, long inflorescence and long, …
format: application/pdf
format: text/html
creator: Agnieszka Rewicz
creator: Monika Rewers
creator: Iwona Jędrzejczyk
creator: Tomasz Rewicz
creator: Jeremi Kołodziejek
creator: Anna Jakubska-Busse
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.5992
publisher: PeerJ Inc.
rights: © 2018 Rewicz et al.
abstract: Background The process of apophytism or spreading native species to human-made habitats is one of the main elements in the creation of plant cover in anthropogenic areas. Lately, an increase of anthropogenic localities with valuable flora has been observed. Apophytes are also members of the family Orchidaceae, especially from the genus Epipactis. The aim of the study was to (i) determine and compare the phenotypic variation of E. helleborine (L.) Crantz plants in anthropogenic and natural habitats, (ii) compare the genome size of plants growing in natural and anthropogenic habitats. The results reported in this study may indicate that a habitat influences morphological characteristics of plant species. Methods Field studies were conducted on four native stands and four stands in anthropogenic areas of E. helleborine in Poland in years 2011–2013. Biometrical analyses were performed on shoots and flowers. The flowers were characterised by 25 biometric features and measured using a Nikon SMZ 800 binocular, microscopic Moticam-1SP cameras and the MIPlus07 programme (Conbest Co.). The nuclear DNA content was determined in fresh and young leaves of E. helleborine, collected from four natural and four anthropogenic populations. Results We observed that in anthropogenic populations: (i) shoots were higher than shoots from natural populations, (ii) flowers differed significantly in terms of ten biometric features between habitats, (iii) the genome size of some population differed significantly between plants growing in natural and anthropogenic habitats. Discussion According to some researchers, the presence of phenotypic variability and the occurrence of ecotypes are adaptation strategies of plants to environmental changes. In our opinion, in the case of the studied anthropogenic habitats (roadside) in which the E. helleborine populations grew, we can talk about ecofen due to the often repeated set of characteristic features, i.e., high shoots, long inflorescence and long, …
bibliographic citation: Rewicz et al. (2018) Morphology and genome size of Epipactis helleborine (L.) Crantz (Orchidaceae) growing in anthropogenic and natural habitats. PeerJ 6:e5992 https://doi.org/10.7717/peerj.5992
date submitted: 2018-01-17
date accepted: 2018-10-23
issued: 2018-12-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rewicz
  given name: Agnieszka
author list: Agent
  family name: Rewers
  given name: Monika
author list: Agent
  family name: Jędrzejczyk
  given name: Iwona
author list: Agent
  family name: Rewicz
  given name: Tomasz
author list: Agent
  family name: Kołodziejek
  given name: Jeremi
author list: Agent
  family name: Jakubska-Busse
  given name: Anna
doi: 10.7717/peerj.5992
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-20
copyright: ©2018 Rewicz et al.
attribution name: Rewicz et al.

The oldest ceratosaurian (Dinosauria: Theropoda), from the Lower Jurassic of Italy, sheds light on the evolution of the three-fingered hand of birds
type: item
type: AcademicArticle
description: The homology of the tridactyl hand of birds is a still debated subject, with both paleontological and developmental evidence used in support of alternative identity patterns in the avian fingers. With its simplified phalangeal morphology, the Late Jurassic ceratosaurian Limusaurus has been argued to support a II–III–IV digital identity in birds and a complex pattern of homeotic transformations in three-fingered (tetanuran) theropods. We report a new large-bodied theropod, Saltriovenator zanellai gen. et sp. nov., based on a partial skeleton from the marine Saltrio Formation (Sinemurian, lowermost Jurassic) of Lombardy (Northern Italy). Taphonomical analyses show bone bioerosion by marine invertebrates (first record for dinosaurian remains) and suggest a complex history for the carcass before being deposited on a well-oxygenated and well-illuminated sea bottom. Saltriovenator shows a mosaic of features seen in four-fingered theropods and in basal tetanurans. Phylogenetic analysis supports sister taxon relationships between the new Italian theropod and the younger Early Jurassic Berberosaurus from Morocco, in a lineage which is the basalmost of Ceratosauria. Compared to the atrophied hand of later members of Ceratosauria, Saltriovenator demonstrates that a fully functional hand, well-adapted for struggling and grasping, was primitively present in ceratosaurians. Ancestral state reconstruction along the avian stem supports 2-3-4-1-X and 2-3-4-0-X as the manual phalangeal formulae at the roots of Ceratosauria and Tetanurae, confirming the I–II–III pattern in the homology of the avian fingers. Accordingly, the peculiar hand of Limusaurus represents a derived condition restricted to late-diverging ceratosaurians and cannot help in elucidating the origin of the three-fingered condition of tetanurans. The evolution of the tridactyl hand of birds is explained by step-wise lateral simplification among non-tetanuran theropod dinosaurs, followed by a single primary axis shift f…
format: application/pdf
format: text/html
creator: Cristiano Dal Sasso
creator: Simone Maganuco
creator: Andrea Cau
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.5976
publisher: PeerJ Inc.
rights: © 2018 Dal Sasso et al.
abstract: The homology of the tridactyl hand of birds is a still debated subject, with both paleontological and developmental evidence used in support of alternative identity patterns in the avian fingers. With its simplified phalangeal morphology, the Late Jurassic ceratosaurian Limusaurus has been argued to support a II–III–IV digital identity in birds and a complex pattern of homeotic transformations in three-fingered (tetanuran) theropods. We report a new large-bodied theropod, Saltriovenator zanellai gen. et sp. nov., based on a partial skeleton from the marine Saltrio Formation (Sinemurian, lowermost Jurassic) of Lombardy (Northern Italy). Taphonomical analyses show bone bioerosion by marine invertebrates (first record for dinosaurian remains) and suggest a complex history for the carcass before being deposited on a well-oxygenated and well-illuminated sea bottom. Saltriovenator shows a mosaic of features seen in four-fingered theropods and in basal tetanurans. Phylogenetic analysis supports sister taxon relationships between the new Italian theropod and the younger Early Jurassic Berberosaurus from Morocco, in a lineage which is the basalmost of Ceratosauria. Compared to the atrophied hand of later members of Ceratosauria, Saltriovenator demonstrates that a fully functional hand, well-adapted for struggling and grasping, was primitively present in ceratosaurians. Ancestral state reconstruction along the avian stem supports 2-3-4-1-X and 2-3-4-0-X as the manual phalangeal formulae at the roots of Ceratosauria and Tetanurae, confirming the I–II–III pattern in the homology of the avian fingers. Accordingly, the peculiar hand of Limusaurus represents a derived condition restricted to late-diverging ceratosaurians and cannot help in elucidating the origin of the three-fingered condition of tetanurans. The evolution of the tridactyl hand of birds is explained by step-wise lateral simplification among non-tetanuran theropod dinosaurs, followed by a single primary axis shift f…
bibliographic citation: Dal Sasso et al. (2018) The oldest ceratosaurian (Dinosauria: Theropoda), from the Lower Jurassic of Italy, sheds light on the evolution of the three-fingered hand of birds. PeerJ 6:e5976 https://doi.org/10.7717/peerj.5976
date submitted: 2018-09-13
date accepted: 2018-10-22
issued: 2018-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dal Sasso
  given name: Cristiano
author list: Agent
  family name: Maganuco
  given name: Simone
author list: Agent
  family name: Cau
  given name: Andrea
doi: 10.7717/peerj.5976
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-19
copyright: © 2018 Dal Sasso et al.
attribution name: Dal Sasso et al.

Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed
type: item
type: AcademicArticle
description: The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29 °C, 33 °C, and 35 °C) using the copepod Acartia erythraea, collected from Sanya Bay, China. The grazing rate of A. erythraea decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29 °C to a metazoan-dominated diet at 35 °C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29 °C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33 °C, as evaluated by the Ivlev’s selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems.
format: application/pdf
format: text/html
creator: Simin Hu
creator: Sheng Liu
creator: Lingli Wang
creator: Tao Li
creator: Hui Huang
subject: Ecosystem Science
subject: Marine Biology
subject: Environmental Contamination and Remediation
subject: Biological Oceanography
description: doi:10.7717/peerj.6129
publisher: PeerJ Inc.
rights: © 2018 Hu et al.
abstract: The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29 °C, 33 °C, and 35 °C) using the copepod Acartia erythraea, collected from Sanya Bay, China. The grazing rate of A. erythraea decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29 °C to a metazoan-dominated diet at 35 °C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29 °C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33 °C, as evaluated by the Ivlev’s selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems.
bibliographic citation: Hu et al. (2018) Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed. PeerJ 6:e6129 https://doi.org/10.7717/peerj.6129
date submitted: 2018-07-25
date accepted: 2018-11-14
issued: 2018-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Simin
author list: Agent
  family name: Liu
  given name: Sheng
author list: Agent
  family name: Wang
  given name: Lingli
author list: Agent
  family name: Li
  given name: Tao
author list: Agent
  family name: Huang
  given name: Hui
doi: 10.7717/peerj.6129
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-19
copyright: ©2018 Hu et al.
attribution name: Hu et al.

Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
type: item
type: AcademicArticle
description: Xanthomonas citri subsp. citri 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LT genes (3B family) are not essential to XccA …
format: application/pdf
format: text/html
creator: Amanda C.P. Oliveira
creator: Rafael M. Ferreira
creator: Maria Inês T. Ferro
creator: Jesus A. Ferro
creator: Mick Chandler
creator: Alessandro M. Varani
subject: Biochemistry
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6111
publisher: PeerJ Inc.
rights: © 2018 Oliveira et al.
abstract: Xanthomonas citri subsp. citri 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LT genes (3B family) are not essential to XccA …
bibliographic citation: Oliveira et al. (2018) Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness. PeerJ 6:e6111 https://doi.org/10.7717/peerj.6111
date submitted: 2018-06-09
date accepted: 2018-11-12
issued: 2018-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Amanda C.P.
author list: Agent
  family name: Ferreira
  given name: Rafael M.
author list: Agent
  family name: Ferro
  given name: Maria Inês T.
author list: Agent
  family name: Ferro
  given name: Jesus A.
author list: Agent
  family name: Chandler
  given name: Mick
author list: Agent
  family name: Varani
  given name: Alessandro M.
doi: 10.7717/peerj.6111
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-19
copyright: © 2018 Oliveira et al.
attribution name: Oliveira et al.

First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes
type: item
type: AcademicArticle
description: There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled …
format: application/pdf
format: text/html
creator: Balázs Brankovics
creator: Tomasz Kulik
creator: Jakub Sawicki
creator: Katarzyna Bilska
creator: Hao Zhang
creator: G Sybren de Hoog
creator: Theo AJ van der Lee
creator: Cees Waalwijk
creator: Anne D. van Diepeningen
subject: Bioinformatics
subject: Genomics
subject: Population Biology
description: doi:10.7717/peerj.5963
publisher: PeerJ Inc.
rights: © 2018 Brankovics et al.
abstract: There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled …
bibliographic citation: Brankovics et al. (2018) First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes. PeerJ 6:e5963 https://doi.org/10.7717/peerj.5963
date submitted: 2018-07-02
date accepted: 2018-10-16
issued: 2018-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brankovics
  given name: Balázs
author list: Agent
  family name: Kulik
  given name: Tomasz
author list: Agent
  family name: Sawicki
  given name: Jakub
author list: Agent
  family name: Bilska
  given name: Katarzyna
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: de Hoog
  given name: G Sybren
author list: Agent
  family name: van der Lee
  given name: Theo AJ
author list: Agent
  family name: Waalwijk
  given name: Cees
author list: Agent
  family name: van Diepeningen
  given name: Anne D.
doi: 10.7717/peerj.5963
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-19
copyright: ©2018 Brankovics et al.
attribution name: Brankovics et al.

Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids
type: item
type: AcademicArticle
description: In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at −5 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P < 0.001), leucine, phenylalanine and valine (0.05 < P < 0.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present study.
format: application/pdf
format: text/html
creator: Manuel Lachica
creator: Jose Miguel Rodríguez-López
creator: Lucrecia González-Valero
creator: Ignacio Fernández-Fígares
subject: Agricultural Science
subject: Nutrition
subject: Natural Resource Management
description: doi:10.7717/peerj.6137
publisher: PeerJ Inc.
rights: © 2018 Lachica et al.
abstract: In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at −5 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P < 0.001), leucine, phenylalanine and valine (0.05 < P < 0.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present study.
bibliographic citation: Lachica et al. (2018) Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids. PeerJ 6:e6137 https://doi.org/10.7717/peerj.6137
date submitted: 2018-02-27
date accepted: 2018-11-20
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lachica
  given name: Manuel
author list: Agent
  family name: Rodríguez-López
  given name: Jose Miguel
author list: Agent
  family name: González-Valero
  given name: Lucrecia
author list: Agent
  family name: Fernández-Fígares
  given name: Ignacio
doi: 10.7717/peerj.6137
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Lachica et al.
attribution name: Lachica et al.

ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV
type: item
type: AcademicArticle
description: In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
format: application/pdf
format: text/html
creator: Ryan J. Andrews
creator: Julien Roche
creator: Walter N. Moss
subject: Bioinformatics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6136
publisher: PeerJ Inc.
rights: © 2018 Andrews et al.
abstract: In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
bibliographic citation: Andrews et al. (2018) ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV. PeerJ 6:e6136 https://doi.org/10.7717/peerj.6136
date submitted: 2018-08-08
date accepted: 2018-11-15
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Andrews
  given name: Ryan J.
author list: Agent
  family name: Roche
  given name: Julien
author list: Agent
  family name: Moss
  given name: Walter N.
doi: 10.7717/peerj.6136
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: © 2018 Andrews et al.
attribution name: Andrews et al.

Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes
type: item
type: AcademicArticle
description: Natural and anthropogenic changes (e.g., land use change, pollution) will alter many environmental factors in the coming years, including the amount of solar radiation reaching the earth’s surface. Alterations in solar radiation exposure is likely to impact the ecologies of many living organisms, including invertebrates that inhabit aquatic habitats. In this study, we assessed the effect of UV-B radiation on the metabolic rates and fitness (survival, development time, body size) of Aedes albopictus and Culex pipiens mosquitoes and the activity of their microbial food resources in experimental aquatic microcosms. We exposed single-species cohorts of newly hatched Ae. albopictus and Cx. pipiens larvae and a control treatment with no larvae to three UV-B conditions that mimicked those in full-sun and shade in the field and to a control condition with no UV-B radiation. Our results indicated that UV-B radiation affected the metabolic rates of both Ae. albopictus and Cx. pipiens larvae, with significantly higher rates found in full-sun compared to shade and no-UV conditions, 8 and 15 days after exposure began. Ae. albopictus and Cx. pipiens survival was also affected by UV-B radiation condition, with significantly lower survival in full-sun compared to shade and no UV-B conditions. Microbial metabolic rates were consistently significantly lower in full-sun compared to shade and no-UV conditions, especially at 8 days of exposure. These results show that UV-B radiation at levels found in open spaces showed strong and important impacts on the metabolic rates and survival of Ae. albopictus and Cx. pipiens larvae. Decreased survival of Ae. albopictus and Cx. pipiens with higher UV-B radiation levels may be caused by both direct exposure to radiation as well as the indirect effects of reduced microbial food, resulting in greater metabolic demands and stress. Negative impacts of UV-B radiation on the survival of Ae. albopictus and Cx. pipiens are likely to have important implic…
format: application/pdf
format: text/html
creator: Oswaldo C. Villena
creator: Bahram Momen
creator: Joseph Sullivan
creator: Paul T. Leisnham
subject: Ecology
subject: Ecosystem Science
subject: Entomology
description: doi:10.7717/peerj.6133
publisher: PeerJ Inc.
rights: © 2018 Villena et al.
abstract: Natural and anthropogenic changes (e.g., land use change, pollution) will alter many environmental factors in the coming years, including the amount of solar radiation reaching the earth’s surface. Alterations in solar radiation exposure is likely to impact the ecologies of many living organisms, including invertebrates that inhabit aquatic habitats. In this study, we assessed the effect of UV-B radiation on the metabolic rates and fitness (survival, development time, body size) of Aedes albopictus and Culex pipiens mosquitoes and the activity of their microbial food resources in experimental aquatic microcosms. We exposed single-species cohorts of newly hatched Ae. albopictus and Cx. pipiens larvae and a control treatment with no larvae to three UV-B conditions that mimicked those in full-sun and shade in the field and to a control condition with no UV-B radiation. Our results indicated that UV-B radiation affected the metabolic rates of both Ae. albopictus and Cx. pipiens larvae, with significantly higher rates found in full-sun compared to shade and no-UV conditions, 8 and 15 days after exposure began. Ae. albopictus and Cx. pipiens survival was also affected by UV-B radiation condition, with significantly lower survival in full-sun compared to shade and no UV-B conditions. Microbial metabolic rates were consistently significantly lower in full-sun compared to shade and no-UV conditions, especially at 8 days of exposure. These results show that UV-B radiation at levels found in open spaces showed strong and important impacts on the metabolic rates and survival of Ae. albopictus and Cx. pipiens larvae. Decreased survival of Ae. albopictus and Cx. pipiens with higher UV-B radiation levels may be caused by both direct exposure to radiation as well as the indirect effects of reduced microbial food, resulting in greater metabolic demands and stress. Negative impacts of UV-B radiation on the survival of Ae. albopictus and Cx. pipiens are likely to have important implic…
bibliographic citation: Villena et al. (2018) Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes. PeerJ 6:e6133 https://doi.org/10.7717/peerj.6133
date submitted: 2018-03-16
date accepted: 2018-11-19
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villena
  given name: Oswaldo C.
author list: Agent
  family name: Momen
  given name: Bahram
author list: Agent
  family name: Sullivan
  given name: Joseph
author list: Agent
  family name: Leisnham
  given name: Paul T.
doi: 10.7717/peerj.6133
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Villena et al.
attribution name: Villena et al.

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