PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach
items: Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod
items: Construction patterns of birds’ nests provide insight into nest-building behaviours
items: Effects of enhanced hydrological connectivity on Mediterranean salt marsh fish assemblages with emphasis on the endangered Spanish toothcarp (Aphanius iberus)
items: Limited effects of source population identity and number on seagrass transplant performance
items: Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase
items: Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids
items: Evidence for high inter-generational individual quality in yellow-eyed penguins
items: FUCHS—towards full circular RNA characterization using RNAseq
items: Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt

Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach
type: item
type: AcademicArticle
description: Background Resilience of midsole material and the upper structure of the shoe are conceptual characteristics that can interfere in running biomechanics patterns. Artificial intelligence techniques can capture features from the entire waveform, adding new perspective for biomechanical analysis. This study tested the influence of shoe midsole resilience and upper structure on running kinematics and kinetics of non-professional runners by using feature selection, information gain, and artificial neural network analysis. Methods Twenty-seven experienced male runners (63 ± 44 km/week run) ran in four-shoe design that combined two resilience-cushioning materials (low and high) and two uppers (minimalist and structured). Kinematic data was acquired by six infrared cameras at 300 Hz, and ground reaction forces were acquired by two force plates at 1,200 Hz. We conducted a Machine Learning analysis to identify features from the complete kinematic and kinetic time series and from 42 discrete variables that had better discriminate the four shoes studied. For that analysis, we built an input data matrix of dimensions 1,080 (10 trials × 4 shoes × 27 subjects) × 1,254 (3 joints × 3 planes of movement × 101 data points + 3 vectors forces × 101 data points + 42 discrete calculated kinetic and kinematic features). Results The applied feature selection by information gain and artificial neural networks successfully differentiated the two resilience materials using 200(16%) biomechanical variables with an accuracy of 84.8% by detecting alterations of running biomechanics, and the two upper structures with an accuracy of 93.9%. Discussion The discrimination of midsole resilience resulted in lower accuracy levels than did the discrimination of the shoe uppers. In both cases, the ground reaction forces were among the 25 most relevant features. The resilience of the cushioning material caused significant effects on initial heel impact, while the effects of different uppers were distributed…
format: application/pdf
format: text/html
creator: Andrea N. Onodera
creator: Wilson P. Gavião Neto
creator: Maria Isabel Roveri
creator: Wagner R. Oliveira
creator: Isabel CN Sacco
subject: Bioengineering
subject: Kinesiology
description: doi:10.7717/peerj.3026
publisher: PeerJ Inc.
rights: © 2017 Onodera et al.
abstract: Background Resilience of midsole material and the upper structure of the shoe are conceptual characteristics that can interfere in running biomechanics patterns. Artificial intelligence techniques can capture features from the entire waveform, adding new perspective for biomechanical analysis. This study tested the influence of shoe midsole resilience and upper structure on running kinematics and kinetics of non-professional runners by using feature selection, information gain, and artificial neural network analysis. Methods Twenty-seven experienced male runners (63 ± 44 km/week run) ran in four-shoe design that combined two resilience-cushioning materials (low and high) and two uppers (minimalist and structured). Kinematic data was acquired by six infrared cameras at 300 Hz, and ground reaction forces were acquired by two force plates at 1,200 Hz. We conducted a Machine Learning analysis to identify features from the complete kinematic and kinetic time series and from 42 discrete variables that had better discriminate the four shoes studied. For that analysis, we built an input data matrix of dimensions 1,080 (10 trials × 4 shoes × 27 subjects) × 1,254 (3 joints × 3 planes of movement × 101 data points + 3 vectors forces × 101 data points + 42 discrete calculated kinetic and kinematic features). Results The applied feature selection by information gain and artificial neural networks successfully differentiated the two resilience materials using 200(16%) biomechanical variables with an accuracy of 84.8% by detecting alterations of running biomechanics, and the two upper structures with an accuracy of 93.9%. Discussion The discrimination of midsole resilience resulted in lower accuracy levels than did the discrimination of the shoe uppers. In both cases, the ground reaction forces were among the 25 most relevant features. The resilience of the cushioning material caused significant effects on initial heel impact, while the effects of different uppers were distributed…
bibliographic citation: Onodera et al. (2017) Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach. PeerJ 5:e3026 https://doi.org/10.7717/peerj.3026
date submitted: 2016-10-26
date accepted: 2017-01-25
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Onodera
  given name: Andrea N.
author list: Agent
  family name: Gavião Neto
  given name: Wilson P.
author list: Agent
  family name: Roveri
  given name: Maria Isabel
author list: Agent
  family name: Oliveira
  given name: Wagner R.
author list: Agent
  family name: Sacco
  given name: Isabel CN
doi: 10.7717/peerj.3026
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Onodera et al.
attribution name: Onodera et al.

Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod
type: item
type: AcademicArticle
description: Background The Balkans are a major worldwide biodiversity and endemism hotspot. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods DNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results We revealed that G. roeselii includes at least 13 cryptic species…
format: application/pdf
format: text/html
creator: Michał Grabowski
creator: Tomasz Mamos
creator: Karolina Bącela-Spychalska
creator: Tomasz Rewicz
creator: Remi A. Wattier
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.3016
publisher: PeerJ Inc.
rights: © 2017 Grabowski et al.
abstract: Background The Balkans are a major worldwide biodiversity and endemism hotspot. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods DNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results We revealed that G. roeselii includes at least 13 cryptic species…
bibliographic citation: Grabowski et al. (2017) Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod. PeerJ 5:e3016 https://doi.org/10.7717/peerj.3016
date submitted: 2016-06-27
date accepted: 2017-01-23
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grabowski
  given name: Michał
author list: Agent
  family name: Mamos
  given name: Tomasz
author list: Agent
  family name: Bącela-Spychalska
  given name: Karolina
author list: Agent
  family name: Rewicz
  given name: Tomasz
author list: Agent
  family name: Wattier
  given name: Remi A.
doi: 10.7717/peerj.3016
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Grabowski et al.
attribution name: Grabowski et al.

Construction patterns of birds’ nests provide insight into nest-building behaviours
type: item
type: AcademicArticle
description: Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.
format: application/pdf
format: text/html
creator: Lucia Biddle
creator: Adrian M. Goodman
creator: D. Charles Deeming
subject: Animal Behavior
subject: Bioengineering
subject: Zoology
description: doi:10.7717/peerj.3010
publisher: PeerJ Inc.
rights: © 2017 Biddle et al.
abstract: Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.
bibliographic citation: Biddle et al. (2017) Construction patterns of birds’ nests provide insight into nest-building behaviours. PeerJ 5:e3010 https://doi.org/10.7717/peerj.3010
date submitted: 2016-07-05
date accepted: 2017-01-21
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biddle
  given name: Lucia
author list: Agent
  family name: Goodman
  given name: Adrian M.
author list: Agent
  family name: Deeming
  given name: D. Charles
doi: 10.7717/peerj.3010
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Biddle et al.
attribution name: Biddle et al.

Effects of enhanced hydrological connectivity on Mediterranean salt marsh fish assemblages with emphasis on the endangered Spanish toothcarp (Aphanius iberus)
type: item
type: AcademicArticle
description: The hydrological connectivity between the salt marsh and the sea was partially restored in a Mediterranean wetland containing isolated ponds resulting from former salt extraction and aquaculture activities. A preliminary assessment provided evidence that ponds farther from the sea hosted very large numbers of the endangered Spanish toothcarp, Aphanius iberus, suggesting that individuals had been trapped and consequently reach unnaturally high densities. In order to achieve both habitat rehabilitation and toothcarp conservation, efforts were made to create a gradient of hydrologically connected areas, including isolated fish reservoirs, semi-isolated, and connected salt marsh-sea areas that could allow migratory movements of fish and provide some protection for A. iberus. The fish community was monitored prior to, and for three years after rehabilitation. Results showed an increase in the number of fish species within semi-isolated areas (Zone A), whereas areas adjacent to the sea (Zone B) increased the number of marine species and decreased that of estuarine species (ES). Yet overall differences in fish assemblages were much higher between zones than among study years. Generalized linear models (GLMs) evidenced that distance to the sea was the most important variable explaining the local diversity of the fish community after restoration, with occasional influence of other factors such as temperature, and depth. The abundance of A. iberus was consistently higher in semi-isolated areas at greater distances from the sea, but a decline occurred in both zones and in isolated reservoir ponds after restoration efforts, which may be attributable to interannual differences in recruitment success and, to a lesser extent, to dispersal into adjacent habitats. A negative effect of restoration works on fish population cannot be excluded, but the final outcome of the intervention likely needs a longer period.
format: application/pdf
format: text/html
creator: Patricia Prado
creator: Carles Alcaraz
creator: Lluis Jornet
creator: Nuno Caiola
creator: Carles Ibáñez
subject: Biodiversity
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3009
publisher: PeerJ Inc.
rights: © 2017 Prado et al.
abstract: The hydrological connectivity between the salt marsh and the sea was partially restored in a Mediterranean wetland containing isolated ponds resulting from former salt extraction and aquaculture activities. A preliminary assessment provided evidence that ponds farther from the sea hosted very large numbers of the endangered Spanish toothcarp, Aphanius iberus, suggesting that individuals had been trapped and consequently reach unnaturally high densities. In order to achieve both habitat rehabilitation and toothcarp conservation, efforts were made to create a gradient of hydrologically connected areas, including isolated fish reservoirs, semi-isolated, and connected salt marsh-sea areas that could allow migratory movements of fish and provide some protection for A. iberus. The fish community was monitored prior to, and for three years after rehabilitation. Results showed an increase in the number of fish species within semi-isolated areas (Zone A), whereas areas adjacent to the sea (Zone B) increased the number of marine species and decreased that of estuarine species (ES). Yet overall differences in fish assemblages were much higher between zones than among study years. Generalized linear models (GLMs) evidenced that distance to the sea was the most important variable explaining the local diversity of the fish community after restoration, with occasional influence of other factors such as temperature, and depth. The abundance of A. iberus was consistently higher in semi-isolated areas at greater distances from the sea, but a decline occurred in both zones and in isolated reservoir ponds after restoration efforts, which may be attributable to interannual differences in recruitment success and, to a lesser extent, to dispersal into adjacent habitats. A negative effect of restoration works on fish population cannot be excluded, but the final outcome of the intervention likely needs a longer period.
bibliographic citation: Prado et al. (2017) Effects of enhanced hydrological connectivity on Mediterranean salt marsh fish assemblages with emphasis on the endangered Spanish toothcarp (Aphanius iberus). PeerJ 5:e3009 https://doi.org/10.7717/peerj.3009
date submitted: 2016-10-09
date accepted: 2017-01-21
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prado
  given name: Patricia
author list: Agent
  family name: Alcaraz
  given name: Carles
author list: Agent
  family name: Jornet
  given name: Lluis
author list: Agent
  family name: Caiola
  given name: Nuno
author list: Agent
  family name: Ibáñez
  given name: Carles
doi: 10.7717/peerj.3009
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Prado et al.
attribution name: Prado et al.

Limited effects of source population identity and number on seagrass transplant performance
type: item
type: AcademicArticle
description: Global declines in coastal foundation species highlight the importance of effective restoration. In this study, we examined the effects of source population identity and diversity (one vs. three sources per plot) on seagrass (Zostera marina) transplant success. The field experiment was replicated at two locations in Massachusetts with adjacent natural Zostera marina beds to test for local adaptation and source diversity effects on shoot density. We also collected morphological and genetic data to characterize variation within and among source populations, and evaluate whether they were related to performance. Transplants grew and expanded until six months post-transplantation, but then steadily declined at both sites. Prior to declines, we observed variation in performance among source populations at one site that was related to morphological traits: the populations with the longest leaves had the highest shoot densities, whereas the population with the shortest leaves performed the worst at six months post-transplantation. In addition, multiple source plots at this same transplant site consistently had similar or higher shoot densities than single source plots, and shoots from weak-performing populations showed improved performance in multiple source plots. We found no evidence for home site advantage or benefits of population-level genetic variation in early transplant performance at either site. Our results show limited effects of source population on early transplant performance and suggest that factors (e.g., morphology) other than home site advantage and population genetic variation serve a role. Based on our overall findings that transplant success varied among source populations and that population diversity at the plot level had positive but limited effects on individual and plot performance, we support planting shoots from multiple source sites in combination to enhance transplant success, particularly in the absence of detailed information on individual s…
format: application/pdf
format: text/html
creator: Alyssa B. Novak
creator: Holly K. Plaisted
creator: Cynthia G. Hays
creator: Randall A. Hughes
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.2972
publisher: PeerJ Inc.
rights: © 2017 Novak et al.
abstract: Global declines in coastal foundation species highlight the importance of effective restoration. In this study, we examined the effects of source population identity and diversity (one vs. three sources per plot) on seagrass (Zostera marina) transplant success. The field experiment was replicated at two locations in Massachusetts with adjacent natural Zostera marina beds to test for local adaptation and source diversity effects on shoot density. We also collected morphological and genetic data to characterize variation within and among source populations, and evaluate whether they were related to performance. Transplants grew and expanded until six months post-transplantation, but then steadily declined at both sites. Prior to declines, we observed variation in performance among source populations at one site that was related to morphological traits: the populations with the longest leaves had the highest shoot densities, whereas the population with the shortest leaves performed the worst at six months post-transplantation. In addition, multiple source plots at this same transplant site consistently had similar or higher shoot densities than single source plots, and shoots from weak-performing populations showed improved performance in multiple source plots. We found no evidence for home site advantage or benefits of population-level genetic variation in early transplant performance at either site. Our results show limited effects of source population on early transplant performance and suggest that factors (e.g., morphology) other than home site advantage and population genetic variation serve a role. Based on our overall findings that transplant success varied among source populations and that population diversity at the plot level had positive but limited effects on individual and plot performance, we support planting shoots from multiple source sites in combination to enhance transplant success, particularly in the absence of detailed information on individual s…
bibliographic citation: Novak et al. (2017) Limited effects of source population identity and number on seagrass transplant performance. PeerJ 5:e2972 https://doi.org/10.7717/peerj.2972
date submitted: 2016-10-10
date accepted: 2017-01-09
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Novak
  given name: Alyssa B.
author list: Agent
  family name: Plaisted
  given name: Holly K.
author list: Agent
  family name: Hays
  given name: Cynthia G.
author list: Agent
  family name: Hughes
  given name: Randall A.
doi: 10.7717/peerj.2972
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Novak et al.
attribution name: Novak et al.

Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase
type: item
type: AcademicArticle
description: Background Sesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment. Methods The enzyme was purified in two steps using affinity and size exclusion chromatography. Enzyme assays were performed using the malachite green assay and enzymatic product was identified using gas chromatography-mass spectrometry (GC-MS) analysis. Sequence analysis of PmSTS was performed using multiple sequence alignment (MSA) against plant sesquiterpene synthase sequences. The homology model of PmSTS was generated using I-TASSER server. Results Our findings suggest that the recombinant PmSTS is mainly expressed as inclusion bodies and soluble aggregate in the E. coli protein expression system. However, the addition of 15% (v/v) glycerol to the protein purification buffer and the removal of N-terminal 24 amino acids of PmSTS helped to produce homogenous recombinant protein. Enzyme assay showed that recombinant PmSTS is active and specific to the C15 substrate FPP. The optimal temperature and pH for the recombinant PmSTS are 30 °C and pH 8.0, respectively. The GC-MS analysis further showed that PmSTS produces β-sesquiphellandrene as a major product and β-farnesene as a minor product. MSA analysis revealed that PmSTS adopts a modified conserved metal binding motif (NSE/DTE motif). Structural analysis suggests that PmSTS may binds to its substrate similarly to other plant sesquiterpene synthases. Discussion The study has revealed that homogenous PmSTS protein can be obtained with the addition of glycerol in the protein buffer. The N-terminal truncation dram…
format: application/pdf
format: text/html
creator: De-Sheng Ker
creator: Sze Lei Pang
creator: Noor Farhan Othman
creator: Sekar Kumaran
creator: Ee Fun Tan
creator: Thiba Krishnan
creator: Kok Gan Chan
creator: Roohaida Othman
creator: Maizom Hassan
creator: Chyan Leong Ng
subject: Biochemistry
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.2961
publisher: PeerJ Inc.
rights: © 2017 Ker et al.
abstract: Background Sesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment. Methods The enzyme was purified in two steps using affinity and size exclusion chromatography. Enzyme assays were performed using the malachite green assay and enzymatic product was identified using gas chromatography-mass spectrometry (GC-MS) analysis. Sequence analysis of PmSTS was performed using multiple sequence alignment (MSA) against plant sesquiterpene synthase sequences. The homology model of PmSTS was generated using I-TASSER server. Results Our findings suggest that the recombinant PmSTS is mainly expressed as inclusion bodies and soluble aggregate in the E. coli protein expression system. However, the addition of 15% (v/v) glycerol to the protein purification buffer and the removal of N-terminal 24 amino acids of PmSTS helped to produce homogenous recombinant protein. Enzyme assay showed that recombinant PmSTS is active and specific to the C15 substrate FPP. The optimal temperature and pH for the recombinant PmSTS are 30 °C and pH 8.0, respectively. The GC-MS analysis further showed that PmSTS produces β-sesquiphellandrene as a major product and β-farnesene as a minor product. MSA analysis revealed that PmSTS adopts a modified conserved metal binding motif (NSE/DTE motif). Structural analysis suggests that PmSTS may binds to its substrate similarly to other plant sesquiterpene synthases. Discussion The study has revealed that homogenous PmSTS protein can be obtained with the addition of glycerol in the protein buffer. The N-terminal truncation dram…
bibliographic citation: Ker et al. (2017) Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase. PeerJ 5:e2961 https://doi.org/10.7717/peerj.2961
date submitted: 2016-07-19
date accepted: 2017-01-05
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ker
  given name: De-Sheng
author list: Agent
  family name: Pang
  given name: Sze Lei
author list: Agent
  family name: Othman
  given name: Noor Farhan
author list: Agent
  family name: Kumaran
  given name: Sekar
author list: Agent
  family name: Tan
  given name: Ee Fun
author list: Agent
  family name: Krishnan
  given name: Thiba
author list: Agent
  family name: Chan
  given name: Kok Gan
author list: Agent
  family name: Othman
  given name: Roohaida
author list: Agent
  family name: Hassan
  given name: Maizom
author list: Agent
  family name: Ng
  given name: Chyan Leong
doi: 10.7717/peerj.2961
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Ker et al.
attribution name: Ker et al.

Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids
type: item
type: AcademicArticle
description: Background Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production. Methods In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference. Results A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites. Discussion This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.
format: application/pdf
format: text/html
creator: Kok-Keong Loke
creator: Reyhaneh Rahnamaie-Tajadod
creator: Chean-Chean Yeoh
creator: Hoe-Han Goh
creator: Zeti-Azura Mohamed-Hussein
creator: Zamri Zainal
creator: Ismanizan Ismail
creator: Normah Mohd Noor
subject: Bioinformatics
subject: Biotechnology
subject: Genomics
description: doi:10.7717/peerj.2938
publisher: PeerJ Inc.
rights: © 2017 Loke et al.
abstract: Background Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production. Methods In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference. Results A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites. Discussion This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.
bibliographic citation: Loke et al. (2017) Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids. PeerJ 5:e2938 https://doi.org/10.7717/peerj.2938
date submitted: 2016-06-15
date accepted: 2016-12-23
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loke
  given name: Kok-Keong
author list: Agent
  family name: Rahnamaie-Tajadod
  given name: Reyhaneh
author list: Agent
  family name: Yeoh
  given name: Chean-Chean
author list: Agent
  family name: Goh
  given name: Hoe-Han
author list: Agent
  family name: Mohamed-Hussein
  given name: Zeti-Azura
author list: Agent
  family name: Zainal
  given name: Zamri
author list: Agent
  family name: Ismail
  given name: Ismanizan
author list: Agent
  family name: Mohd Noor
  given name: Normah
doi: 10.7717/peerj.2938
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Loke et al.
attribution name: Loke et al.

Evidence for high inter-generational individual quality in yellow-eyed penguins
type: item
type: AcademicArticle
description: Longitudinal studies focusing on lifetime reproductive success (LRS) have been used to measure individual breeding performance and identify commonalities among successful breeders. By extending the focus to subsequent generations we identify a proportion of high-quality individuals that contribute disproportionately to the population over multiple generations. We used 23 years of yellow-eyed penguin (Megadyptes antipodes) breeding data from one breeding area to identify the proportion of individual birds that raised successful breeders, which in turn raised offspring. We explored which life-history components influenced LRS, as this knowledge would enable conservation resources to be focused on high-performing individuals in this endangered population. From 2,147 birds marked as chicks, 370 (17.2%) survived to adulthood and recruited to their natal location, of which 219 (10.2%) fledged offspring: 124 (56.6%) of the 219 birds produced offspring that recruited as breeders. Only 102 birds (4.8% of 2,147) fledged first-generation offspring that in turn fledged offspring (second-generation offspring, or grand-offspring). We found that ∼25% of the birds that survived to breed had above-average LRS as well as above-average numbers of grand-offspring, and were more likely to have produced first-generation chicks that recruited and also produced above-average numbers of second-generation chicks. Our findings suggest that there is a core of “super-breeders” that contribute disproportionately to the population over successive generations. Lifespan and age-at-first-breeding were correlated with LRS. We suggest that traits of birds relating to longevity, health (e.g., immunocompetence) and fitness could be examined to identify potential links with high LRS and inter-generational fecundity. “Super-breeders” appear to consistently achieve high LRS and long lifespans in a stochastic environment, demonstrating greater resilience in the face of extreme events.
format: application/pdf
format: text/html
creator: Aviva M. Stein
creator: Melanie J. Young
creator: John T. Darby
creator: Philip J. Seddon
creator: Yolanda van Heezik
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2935
publisher: PeerJ Inc.
rights: © 2017 Stein et al.
abstract: Longitudinal studies focusing on lifetime reproductive success (LRS) have been used to measure individual breeding performance and identify commonalities among successful breeders. By extending the focus to subsequent generations we identify a proportion of high-quality individuals that contribute disproportionately to the population over multiple generations. We used 23 years of yellow-eyed penguin (Megadyptes antipodes) breeding data from one breeding area to identify the proportion of individual birds that raised successful breeders, which in turn raised offspring. We explored which life-history components influenced LRS, as this knowledge would enable conservation resources to be focused on high-performing individuals in this endangered population. From 2,147 birds marked as chicks, 370 (17.2%) survived to adulthood and recruited to their natal location, of which 219 (10.2%) fledged offspring: 124 (56.6%) of the 219 birds produced offspring that recruited as breeders. Only 102 birds (4.8% of 2,147) fledged first-generation offspring that in turn fledged offspring (second-generation offspring, or grand-offspring). We found that ∼25% of the birds that survived to breed had above-average LRS as well as above-average numbers of grand-offspring, and were more likely to have produced first-generation chicks that recruited and also produced above-average numbers of second-generation chicks. Our findings suggest that there is a core of “super-breeders” that contribute disproportionately to the population over successive generations. Lifespan and age-at-first-breeding were correlated with LRS. We suggest that traits of birds relating to longevity, health (e.g., immunocompetence) and fitness could be examined to identify potential links with high LRS and inter-generational fecundity. “Super-breeders” appear to consistently achieve high LRS and long lifespans in a stochastic environment, demonstrating greater resilience in the face of extreme events.
bibliographic citation: Stein et al. (2017) Evidence for high inter-generational individual quality in yellow-eyed penguins. PeerJ 5:e2935 https://doi.org/10.7717/peerj.2935
date submitted: 2016-08-22
date accepted: 2016-12-22
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stein
  given name: Aviva M.
author list: Agent
  family name: Young
  given name: Melanie J.
author list: Agent
  family name: Darby
  given name: John T.
author list: Agent
  family name: Seddon
  given name: Philip J.
author list: Agent
  family name: van Heezik
  given name: Yolanda
doi: 10.7717/peerj.2935
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Stein et al.
attribution name: Stein et al.

FUCHS—towards full circular RNA characterization using RNAseq
type: item
type: AcademicArticle
description: Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5′ splice site is linked to an upstream 3′ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data—FUCHS: FUll CHaracterization of circular RNA using RNA-Sequencing. Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically >150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries. This new knowledge will enable the user to carry out differential motif enrichment and miRNA seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research.
format: application/pdf
format: text/html
creator: Franziska Metge
creator: Lisa F. Czaja-Hasse
creator: Richard Reinhardt
creator: Chistoph Dieterich
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.2934
publisher: PeerJ Inc.
rights: © 2017 Metge et al.
abstract: Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5′ splice site is linked to an upstream 3′ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data—FUCHS: FUll CHaracterization of circular RNA using RNA-Sequencing. Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically >150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries. This new knowledge will enable the user to carry out differential motif enrichment and miRNA seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research.
bibliographic citation: Metge et al. (2017) FUCHS—towards full circular RNA characterization using RNAseq. PeerJ 5:e2934 https://doi.org/10.7717/peerj.2934
date submitted: 2016-12-01
date accepted: 2016-12-22
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Metge
  given name: Franziska
author list: Agent
  family name: Czaja-Hasse
  given name: Lisa F.
author list: Agent
  family name: Reinhardt
  given name: Richard
author list: Agent
  family name: Dieterich
  given name: Chistoph
doi: 10.7717/peerj.2934
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Metge et al.
attribution name: Metge et al.

Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt
type: item
type: AcademicArticle
description: Amphibian populations are highly vulnerable to road mortality and habitat fragmentation caused by road networks. Wildlife road tunnels are considered the most promising road mitigation measure for amphibians yet generally remain inadequately monitored, resulting in mixed success rates in the short-term and uncertain conservation benefits in the long-term. We monitored a complex multi-tunnel and fence system over five years and investigated the impact of the scheme on movement patterns of two newt species, including the largest known UK population of the great crested newt (Triturus cristatus), a European Protected Species. We used a stage descriptive approach based on capture positions to quantify newt movement patterns. Newt species successfully used the mitigation but the system constituted a bottleneck to movements from the fences to the tunnels. Crossing rates varied widely among years and were skewed towards autumn dispersal rather than spring breeding migration. There was a substantial negative bias against adult male great crested newts using the system. This study indicates that road tunnels could partially mitigate wider connectivity loss and fragmentation at the landscape scale for newt species. However, the observed bottleneck effects and seasonal bias could have population-level effects which must be better understood, especially for small populations, so that improvements can be made. Current requirements for monitoring mitigation schemes post-implementation are probably too short to assess their effectiveness in maintaining connectivity and to adequately understand their population-level impacts.
format: application/pdf
format: text/html
creator: Cátia Matos
creator: Silviu Petrovan
creator: Alastair I. Ward
creator: Philip Wheeler
subject: Animal Behavior
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Mathematical Biology
description: doi:10.7717/peerj.2922
publisher: PeerJ Inc.
rights: © 2017 Matos et al.
abstract: Amphibian populations are highly vulnerable to road mortality and habitat fragmentation caused by road networks. Wildlife road tunnels are considered the most promising road mitigation measure for amphibians yet generally remain inadequately monitored, resulting in mixed success rates in the short-term and uncertain conservation benefits in the long-term. We monitored a complex multi-tunnel and fence system over five years and investigated the impact of the scheme on movement patterns of two newt species, including the largest known UK population of the great crested newt (Triturus cristatus), a European Protected Species. We used a stage descriptive approach based on capture positions to quantify newt movement patterns. Newt species successfully used the mitigation but the system constituted a bottleneck to movements from the fences to the tunnels. Crossing rates varied widely among years and were skewed towards autumn dispersal rather than spring breeding migration. There was a substantial negative bias against adult male great crested newts using the system. This study indicates that road tunnels could partially mitigate wider connectivity loss and fragmentation at the landscape scale for newt species. However, the observed bottleneck effects and seasonal bias could have population-level effects which must be better understood, especially for small populations, so that improvements can be made. Current requirements for monitoring mitigation schemes post-implementation are probably too short to assess their effectiveness in maintaining connectivity and to adequately understand their population-level impacts.
bibliographic citation: Matos et al. (2017) Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt. PeerJ 5:e2922 https://doi.org/10.7717/peerj.2922
date submitted: 2016-08-23
date accepted: 2016-12-19
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matos
  given name: Cátia
author list: Agent
  family name: Petrovan
  given name: Silviu
author list: Agent
  family name: Ward
  given name: Alastair I.
author list: Agent
  family name: Wheeler
  given name: Philip
doi: 10.7717/peerj.2922
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Matos et al.
attribution name: Matos et al.

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