PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Correlations between personality traits and specific groups of alpha waves in the human EEG
items: Lateral presentation of faces alters overall viewing strategy
items: https://peerj.com/articles/2239
items: The final spawning ground of Tachypleus gigas (Müller, 1785) on the east Peninsular Malaysia is at risk: a call for action
items: Reconstitution of the complete rupture in musculotendinous junction using skeletal muscle-derived multipotent stem cell sheet-pellets as a “bio-bond”
items: Love the one you’re with: replicate viral adaptations converge on the same phenotypic change
items: Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures
items: Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
items: Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics
items: Enhanced functional connectivity properties of human brains during in-situ nature experience

Correlations between personality traits and specific groups of alpha waves in the human EEG
type: item
type: AcademicArticle
description: Background. Different individuals have alpha waves with different wavelengths. The distribution of the wavelengths is assumed to be bell-shaped and smooth. Although this view is generally accepted, it is still just an assumption and has never been critically tested. When exploring the relationship between alpha waves and personality traits, it makes a huge difference if the distribution of the alpha waves is smooth or if specific groups of alpha waves can be demonstrated. Previous studies have not considered the possibility that specific groups of alpha waves may exist. Methods. Computerized EEGs have become standard, but wavelength measurements are problematic when based on averaging procedures using the Fourier transformation because such procedures cause a large systematic error. If the actual wavelength is of interest, it is necessary to go back to basic physiology and use raw EEG signals. In the present study, measurements were made directly from sequences of alpha waves where every wave could be identified. Personality dimensions were measured using an inventory derived from the International Personality Item Pool. Results. Recordings from 200 healthy individuals revealed that there are three main groups of alpha waves. These groups had frequencies around 8, 10, and 12 waves per second. The middle group had a bimodal distribution, and a subdivision gave a total of four alpha groups. In the center of each group, the degree of extraversion was high and the degree of neuroticism was low. Many small differences in personality traits were found when the centers were compared with one another. This gave four personality profiles that resemble the four classical temperaments. When people in the surrounding zones were compared with those in the centers, relatively large differences in personality traits were found. Conclusions. Specific groups of alpha waves exist, and these groups have to be taken into account when correlations are made to personality dimensions and …
format: application/pdf
format: text/html
creator: Tomas Johannisson
subject: Neuroscience
subject: Anatomy and Physiology
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2245
publisher: PeerJ Inc.
rights: © 2016 Johannisson
abstract: Background. Different individuals have alpha waves with different wavelengths. The distribution of the wavelengths is assumed to be bell-shaped and smooth. Although this view is generally accepted, it is still just an assumption and has never been critically tested. When exploring the relationship between alpha waves and personality traits, it makes a huge difference if the distribution of the alpha waves is smooth or if specific groups of alpha waves can be demonstrated. Previous studies have not considered the possibility that specific groups of alpha waves may exist. Methods. Computerized EEGs have become standard, but wavelength measurements are problematic when based on averaging procedures using the Fourier transformation because such procedures cause a large systematic error. If the actual wavelength is of interest, it is necessary to go back to basic physiology and use raw EEG signals. In the present study, measurements were made directly from sequences of alpha waves where every wave could be identified. Personality dimensions were measured using an inventory derived from the International Personality Item Pool. Results. Recordings from 200 healthy individuals revealed that there are three main groups of alpha waves. These groups had frequencies around 8, 10, and 12 waves per second. The middle group had a bimodal distribution, and a subdivision gave a total of four alpha groups. In the center of each group, the degree of extraversion was high and the degree of neuroticism was low. Many small differences in personality traits were found when the centers were compared with one another. This gave four personality profiles that resemble the four classical temperaments. When people in the surrounding zones were compared with those in the centers, relatively large differences in personality traits were found. Conclusions. Specific groups of alpha waves exist, and these groups have to be taken into account when correlations are made to personality dimensions and …
bibliographic citation: Johannisson (2016) Correlations between personality traits and specific groups of alpha waves in the human EEG. PeerJ 4:e2245 https://doi.org/10.7717/peerj.2245
date submitted: 2016-03-16
date accepted: 2016-06-22
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johannisson
  given name: Tomas
doi: 10.7717/peerj.2245
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Johannisson
attribution name: Johannisson

Lateral presentation of faces alters overall viewing strategy
type: item
type: AcademicArticle
description: Eye tracking has been used during face categorisation and identification tasks to identify perceptually salient facial features and infer underlying cognitive processes. However, viewing patterns are influenced by a variety of gaze biases, drawing fixations to the centre of a screen and horizontally to the left side of face images (left-gaze bias). In order to investigate potential interactions between gaze biases uniquely associated with facial expression processing, and those associated with screen location, face stimuli were presented in three possible screen positions to the left, right and centre. Comparisons of fixations between screen locations highlight a significant impact of the screen centre bias, pulling fixations towards the centre of the screen and modifying gaze biases generally observed during facial categorisation tasks. A left horizontal bias for fixations was found to be independent of screen position but interacting with screen centre bias, drawing fixations to the left hemi-face rather than just to the left of the screen. Implications for eye tracking studies utilising centrally presented faces are discussed.
format: application/pdf
format: text/html
creator: Christopher J. Luke
creator: Petra M.J. Pollux
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2241
publisher: PeerJ Inc.
rights: © 2016 Luke and Pollux
abstract: Eye tracking has been used during face categorisation and identification tasks to identify perceptually salient facial features and infer underlying cognitive processes. However, viewing patterns are influenced by a variety of gaze biases, drawing fixations to the centre of a screen and horizontally to the left side of face images (left-gaze bias). In order to investigate potential interactions between gaze biases uniquely associated with facial expression processing, and those associated with screen location, face stimuli were presented in three possible screen positions to the left, right and centre. Comparisons of fixations between screen locations highlight a significant impact of the screen centre bias, pulling fixations towards the centre of the screen and modifying gaze biases generally observed during facial categorisation tasks. A left horizontal bias for fixations was found to be independent of screen position but interacting with screen centre bias, drawing fixations to the left hemi-face rather than just to the left of the screen. Implications for eye tracking studies utilising centrally presented faces are discussed.
bibliographic citation: Luke et al. (2016) Lateral presentation of faces alters overall viewing strategy. PeerJ 4:e2241 https://doi.org/10.7717/peerj.2241
date submitted: 2016-04-05
date accepted: 2016-06-21
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luke
  given name: Christopher J.
author list: Agent
  family name: Pollux
  given name: Petra M.J.
doi: 10.7717/peerj.2241
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Luke and Pollux
attribution name: Luke and Pollux

https://peerj.com/articles/2239
type: item
type: AcademicArticle
title: Equivalent intraperitoneal doses of ibuprofen supplemented in drinking water or in diet: a behavioral and biochemical assay using antinociceptive and thromboxane inhibitory dose–response curves in mice
description: Background. Ibuprofen is used chronically in different animal models of inflammation by administration in drinking water or in diet due to its short half-life. Though this practice has been used for years, ibuprofen doses were never assayed against parenteral dose–response curves. This study aims at identifying the equivalent intraperitoneal (i.p.) doses of ibuprofen, when it is administered in drinking water or in diet. Methods. Bioassays were performed using formalin test and incisional pain model for antinociceptive efficacy and serum TXB2 for eicosanoid inhibitory activity. The dose–response curve of i.p. administered ibuprofen was constructed for each test using 50, 75, 100 and 200 mg/kg body weight (b.w.). The dose–response curves were constructed of phase 2a of the formalin test (the most sensitive phase to COX inhibitory agents), the area under the ‘change in mechanical threshold’-time curve in the incisional pain model and serum TXB2 levels. The assayed ibuprofen concentrations administered in drinking water were 0.2, 0.35, 0.6 mg/ml and those administered in diet were 82, 263, 375 mg/kg diet. Results. The 3 concentrations applied in drinking water lay between 73.6 and 85.5 mg/kg b.w., i.p., in case of the formalin test; between 58.9 and 77.8 mg/kg b.w., i.p., in case of the incisional pain model; and between 71.8 and 125.8 mg/kg b.w., i.p., in case of serum TXB2 levels. The 3 concentrations administered in diet lay between 67.6 and 83.8 mg/kg b.w., i.p., in case of the formalin test; between 52.7 and 68.6 mg/kg b.w., i.p., in case of the incisional pain model; and between 63.6 and 92.5 mg/kg b.w., i.p., in case of serum TXB2 levels. Discussion. The increment in pharmacological effects of different doses of continuously administered ibuprofen in drinking water or diet do not parallel those of i.p. administered ibuprofen. It is therefore difficult to assume the equivalent parenteral daily doses based on mathematical calculations.
format: application/pdf
format: text/html
creator: Raghda A.M. Salama
creator: Nesreen H. El Gayar
creator: Sonia S. Georgy
creator: May Hamza
subject: Biochemistry
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.2239
publisher: PeerJ Inc.
rights: © 2016 Salama et al.
abstract: Background. Ibuprofen is used chronically in different animal models of inflammation by administration in drinking water or in diet due to its short half-life. Though this practice has been used for years, ibuprofen doses were never assayed against parenteral dose–response curves. This study aims at identifying the equivalent intraperitoneal (i.p.) doses of ibuprofen, when it is administered in drinking water or in diet. Methods. Bioassays were performed using formalin test and incisional pain model for antinociceptive efficacy and serum TXB2 for eicosanoid inhibitory activity. The dose–response curve of i.p. administered ibuprofen was constructed for each test using 50, 75, 100 and 200 mg/kg body weight (b.w.). The dose–response curves were constructed of phase 2a of the formalin test (the most sensitive phase to COX inhibitory agents), the area under the ‘change in mechanical threshold’-time curve in the incisional pain model and serum TXB2 levels. The assayed ibuprofen concentrations administered in drinking water were 0.2, 0.35, 0.6 mg/ml and those administered in diet were 82, 263, 375 mg/kg diet. Results. The 3 concentrations applied in drinking water lay between 73.6 and 85.5 mg/kg b.w., i.p., in case of the formalin test; between 58.9 and 77.8 mg/kg b.w., i.p., in case of the incisional pain model; and between 71.8 and 125.8 mg/kg b.w., i.p., in case of serum TXB2 levels. The 3 concentrations administered in diet lay between 67.6 and 83.8 mg/kg b.w., i.p., in case of the formalin test; between 52.7 and 68.6 mg/kg b.w., i.p., in case of the incisional pain model; and between 63.6 and 92.5 mg/kg b.w., i.p., in case of serum TXB2 levels. Discussion. The increment in pharmacological effects of different doses of continuously administered ibuprofen in drinking water or diet do not parallel those of i.p. administered ibuprofen. It is therefore difficult to assume the equivalent parenteral daily doses based on mathematical calculations.
bibliographic citation: Salama et al. (2016) Equivalent intraperitoneal doses of ibuprofen supplemented in drinking water or in diet: a behavioral and biochemical assay using antinociceptive and thromboxane inhibitory dose–response curves in mice. PeerJ 4:e2239 https://doi.org/10.7717/peerj.2239
date submitted: 2016-03-27
date accepted: 2016-06-19
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salama
  given name: Raghda A.M.
author list: Agent
  family name: El Gayar
  given name: Nesreen H.
author list: Agent
  family name: Georgy
  given name: Sonia S.
author list: Agent
  family name: Hamza
  given name: May
doi: 10.7717/peerj.2239
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Salama et al.
attribution name: Salama et al.

The final spawning ground of Tachypleus gigas (Müller, 1785) on the east Peninsular Malaysia is at risk: a call for action
type: item
type: AcademicArticle
description: Tanjung Selongor and Pantai Balok (State Pahang) are the only two places known for spawning activity of the Malaysian horseshoe crab - Tachypleus gigas (Müller, 1785) on the east coast of Peninsular Malaysia. While the former beach has been disturbed by several anthropogenic activities that ultimately brought an end to the spawning activity of T. gigas, the status of the latter remains uncertain. In the present study, the spawning behavior of T. gigas at Pantai Balok (Sites I-III) was observed over a period of thirty six months, in three phases, between 2009 and 2013. Every year, the crab’s nesting activity was found to be high during Southwest monsoon (May–September) followed by Northeast (November–March) and Inter monsoon (April and October) periods. In the meantime, the number of female T. gigas in 2009–2010 (Phase-1) was higher (38 crabs) than in 2010–2011 (Phase-2: 7 crabs) and 2012–2013 (Phase-3: 9 crabs) for which both increased overexploitation (for edible and fishmeal preparations) as well as anthropogenic disturbances in the vicinity (sand mining since 2009, land reclamation for wave breaker/parking lot constructions in 2011 and fishing jetty construction in 2013) are responsible. In this context, the physical infrastructure developments have altered the sediment close to nesting sites to be dominated by fine sand (2.5Xφ ) with moderately-well sorted (0.6–0.7σφ), very-coarse skewed (−2.4SKφ), and extremely leptokurtic (12.6Kφ) properties. Also, increased concentrations of Cadmium (from 4.2 to 13.6 mg kg−1) and Selenium (from 11.5 to 23.3 mg kg−1) in the sediment, and Sulphide (from 21 to 28 µg l−1) in the water were observed. In relation to the monsoonal changes affecting sheltered beach topography and sediment flux, the spawning crabs have shown a seasonal nest shifting behaviour in-between Sites I-III during 2009–2011. However, in 2012–2013, the crabs were mostly restricted to the areas (i.e., Sites I and II) with high oxygen (5.5–8.0 mg l−1) and moistur…
format: application/pdf
format: text/html
creator: Bryan Raveen Nelson
creator: Behara Satyanarayana
creator: Julia Hwei Zhong Moh
creator: Mhd Ikhwanuddin
creator: Anil Chatterji
creator: Faizah Shaharom
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.2232
publisher: PeerJ Inc.
rights: © 2016 Nelson et al.
abstract: Tanjung Selongor and Pantai Balok (State Pahang) are the only two places known for spawning activity of the Malaysian horseshoe crab - Tachypleus gigas (Müller, 1785) on the east coast of Peninsular Malaysia. While the former beach has been disturbed by several anthropogenic activities that ultimately brought an end to the spawning activity of T. gigas, the status of the latter remains uncertain. In the present study, the spawning behavior of T. gigas at Pantai Balok (Sites I-III) was observed over a period of thirty six months, in three phases, between 2009 and 2013. Every year, the crab’s nesting activity was found to be high during Southwest monsoon (May–September) followed by Northeast (November–March) and Inter monsoon (April and October) periods. In the meantime, the number of female T. gigas in 2009–2010 (Phase-1) was higher (38 crabs) than in 2010–2011 (Phase-2: 7 crabs) and 2012–2013 (Phase-3: 9 crabs) for which both increased overexploitation (for edible and fishmeal preparations) as well as anthropogenic disturbances in the vicinity (sand mining since 2009, land reclamation for wave breaker/parking lot constructions in 2011 and fishing jetty construction in 2013) are responsible. In this context, the physical infrastructure developments have altered the sediment close to nesting sites to be dominated by fine sand (2.5Xφ ) with moderately-well sorted (0.6–0.7σφ), very-coarse skewed (−2.4SKφ), and extremely leptokurtic (12.6Kφ) properties. Also, increased concentrations of Cadmium (from 4.2 to 13.6 mg kg−1) and Selenium (from 11.5 to 23.3 mg kg−1) in the sediment, and Sulphide (from 21 to 28 µg l−1) in the water were observed. In relation to the monsoonal changes affecting sheltered beach topography and sediment flux, the spawning crabs have shown a seasonal nest shifting behaviour in-between Sites I-III during 2009–2011. However, in 2012–2013, the crabs were mostly restricted to the areas (i.e., Sites I and II) with high oxygen (5.5–8.0 mg l−1) and moistur…
bibliographic citation: Nelson et al. (2016) The final spawning ground of Tachypleus gigas (Müller, 1785) on the east Peninsular Malaysia is at risk: a call for action. PeerJ 4:e2232 https://doi.org/10.7717/peerj.2232
date submitted: 2016-03-20
date accepted: 2016-06-17
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nelson
  given name: Bryan Raveen
author list: Agent
  family name: Satyanarayana
  given name: Behara
author list: Agent
  family name: Moh
  given name: Julia Hwei Zhong
author list: Agent
  family name: Ikhwanuddin
  given name: Mhd
author list: Agent
  family name: Chatterji
  given name: Anil
author list: Agent
  family name: Shaharom
  given name: Faizah
doi: 10.7717/peerj.2232
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Nelson et al.
attribution name: Nelson et al.

Reconstitution of the complete rupture in musculotendinous junction using skeletal muscle-derived multipotent stem cell sheet-pellets as a “bio-bond”
type: item
type: AcademicArticle
description: Background. Significant and/or complete rupture in the musculotendinous junction (MTJ) is a challenging lesion to treat because of the lack of reliable suture methods. Skeletal muscle-derived multipotent stem cell (Sk-MSC) sheet-pellets, which are able to reconstitute peripheral nerve and muscular/vascular tissues with robust connective tissue networks, have been applied as a “bio-bond”. Methods. Sk-MSC sheet-pellets, derived from GFP transgenic-mice after 7 days of expansion culture, were detached with EDTA to maintain cell–cell connections. A completely ruptured MTJ model was prepared in the right tibialis anterior (TA) of the recipient mice, and was covered with sheet-pellets. The left side was preserved as a contralateral control. The control group received the same amount of the cell-free medium. The sheet-pellet transplantation (SP) group was further divided into two groups; as the short term (4–8 weeks) and long term (14–18 weeks) recovery group. At each time point after transplantation, tetanic tension output was measured through the electrical stimulation of the sciatic nerve. The behavior of engrafted GFP+ tissues and cells was analyzed by fluorescence immunohistochemistry. Results. The SP short term recovery group showed average 64% recovery of muscle mass, and 36% recovery of tetanic tension output relative to the contralateral side. Then, the SP long term recovery group showed increased recovery of average muscle mass (77%) and tetanic tension output (49%). However, the control group showed no recovery of continuity between muscle and tendon, and demonstrated increased muscle atrophy, with coalescence to the tibia during 4–8 weeks after operation. Histological evidence also supported the above functional recovery of SP group. Engrafted Sk-MSCs primarily formed the connective tissues and muscle fibers, including nerve-vascular networks, and bridged the ruptured tendon–muscle fiber units, with differentiation into skeletal muscle cells, Schwann cells, vas…
format: application/pdf
format: text/html
creator: Hiroyuki Hashimoto
creator: Tetsuro Tamaki
creator: Maki Hirata
creator: Yoshiyasu Uchiyama
creator: Masato Sato
creator: Joji Mochida
subject: Cell Biology
subject: Anatomy and Physiology
subject: Orthopedics
subject: Translational Medicine
description: doi:10.7717/peerj.2231
publisher: PeerJ Inc.
rights: © 2016 Hashimoto et al.
abstract: Background. Significant and/or complete rupture in the musculotendinous junction (MTJ) is a challenging lesion to treat because of the lack of reliable suture methods. Skeletal muscle-derived multipotent stem cell (Sk-MSC) sheet-pellets, which are able to reconstitute peripheral nerve and muscular/vascular tissues with robust connective tissue networks, have been applied as a “bio-bond”. Methods. Sk-MSC sheet-pellets, derived from GFP transgenic-mice after 7 days of expansion culture, were detached with EDTA to maintain cell–cell connections. A completely ruptured MTJ model was prepared in the right tibialis anterior (TA) of the recipient mice, and was covered with sheet-pellets. The left side was preserved as a contralateral control. The control group received the same amount of the cell-free medium. The sheet-pellet transplantation (SP) group was further divided into two groups; as the short term (4–8 weeks) and long term (14–18 weeks) recovery group. At each time point after transplantation, tetanic tension output was measured through the electrical stimulation of the sciatic nerve. The behavior of engrafted GFP+ tissues and cells was analyzed by fluorescence immunohistochemistry. Results. The SP short term recovery group showed average 64% recovery of muscle mass, and 36% recovery of tetanic tension output relative to the contralateral side. Then, the SP long term recovery group showed increased recovery of average muscle mass (77%) and tetanic tension output (49%). However, the control group showed no recovery of continuity between muscle and tendon, and demonstrated increased muscle atrophy, with coalescence to the tibia during 4–8 weeks after operation. Histological evidence also supported the above functional recovery of SP group. Engrafted Sk-MSCs primarily formed the connective tissues and muscle fibers, including nerve-vascular networks, and bridged the ruptured tendon–muscle fiber units, with differentiation into skeletal muscle cells, Schwann cells, vas…
bibliographic citation: Hashimoto et al. (2016) Reconstitution of the complete rupture in musculotendinous junction using skeletal muscle-derived multipotent stem cell sheet-pellets as a “bio-bond”. PeerJ 4:e2231 https://doi.org/10.7717/peerj.2231
date submitted: 2016-01-23
date accepted: 2016-06-16
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hashimoto
  given name: Hiroyuki
author list: Agent
  family name: Tamaki
  given name: Tetsuro
author list: Agent
  family name: Hirata
  given name: Maki
author list: Agent
  family name: Uchiyama
  given name: Yoshiyasu
author list: Agent
  family name: Sato
  given name: Masato
author list: Agent
  family name: Mochida
  given name: Joji
doi: 10.7717/peerj.2231
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Hashimoto et al.
attribution name: Hashimoto et al.

Love the one you’re with: replicate viral adaptations converge on the same phenotypic change
type: item
type: AcademicArticle
description: Parallelism is important because it reveals how inherently stochastic adaptation is. Even as we come to better understand evolutionary forces, stochasticity limits how well we can predict evolutionary outcomes. Here we sought to quantify parallelism and some of its underlying causes by adapting a bacteriophage (ID11) with nine different first-step mutations, each with eight-fold replication, for 100 passages. This was followed by whole-genome sequencing five isolates from each endpoint. A large amount of variation arose—281 mutational events occurred representing 112 unique mutations. At least 41% of the mutations and 77% of the events were adaptive. Within wells, populations generally experienced complex interference dynamics. The genome locations and counts of mutations were highly uneven: mutations were concentrated in two regulatory elements and three genes and, while 103 of the 112 (92%) of the mutations were observed in ≤4 wells, a few mutations arose many times. 91% of the wells and 81% of the isolates had a mutation in the D-promoter. Parallelism was moderate compared to previous experiments with this system. On average, wells shared 27% of their mutations at the DNA level and 38% when the definition of parallel change is expanded to include the same regulatory feature or residue. About half of the parallelism came from D-promoter mutations. Background had a small but significant effect on parallelism. Similarly, an analyses of epistasis between mutations and their ancestral background was significant, but the result was mostly driven by four individual mutations. A second analysis of epistasis focused on de novo mutations revealed that no isolate ever had more than one D-promoter mutation and that 56 of the 65 isolates lacking a D-promoter mutation had a mutation in genes D and/or E. We assayed time to lysis in four of these mutually exclusive mutations (the two most frequent D-promoter and two in gene D) across four genetic backgrounds. In all cases lysis …
format: application/pdf
format: text/html
creator: Craig R. Miller
creator: Anna C. Nagel
creator: LuAnn Scott
creator: Matt Settles
creator: Paul Joyce
creator: Holly A. Wichman
subject: Evolutionary Studies
subject: Genetics
subject: Virology
description: doi:10.7717/peerj.2227
publisher: PeerJ Inc.
rights: © 2016 Miller et al.
abstract: Parallelism is important because it reveals how inherently stochastic adaptation is. Even as we come to better understand evolutionary forces, stochasticity limits how well we can predict evolutionary outcomes. Here we sought to quantify parallelism and some of its underlying causes by adapting a bacteriophage (ID11) with nine different first-step mutations, each with eight-fold replication, for 100 passages. This was followed by whole-genome sequencing five isolates from each endpoint. A large amount of variation arose—281 mutational events occurred representing 112 unique mutations. At least 41% of the mutations and 77% of the events were adaptive. Within wells, populations generally experienced complex interference dynamics. The genome locations and counts of mutations were highly uneven: mutations were concentrated in two regulatory elements and three genes and, while 103 of the 112 (92%) of the mutations were observed in ≤4 wells, a few mutations arose many times. 91% of the wells and 81% of the isolates had a mutation in the D-promoter. Parallelism was moderate compared to previous experiments with this system. On average, wells shared 27% of their mutations at the DNA level and 38% when the definition of parallel change is expanded to include the same regulatory feature or residue. About half of the parallelism came from D-promoter mutations. Background had a small but significant effect on parallelism. Similarly, an analyses of epistasis between mutations and their ancestral background was significant, but the result was mostly driven by four individual mutations. A second analysis of epistasis focused on de novo mutations revealed that no isolate ever had more than one D-promoter mutation and that 56 of the 65 isolates lacking a D-promoter mutation had a mutation in genes D and/or E. We assayed time to lysis in four of these mutually exclusive mutations (the two most frequent D-promoter and two in gene D) across four genetic backgrounds. In all cases lysis …
bibliographic citation: Miller et al. (2016) Love the one you’re with: replicate viral adaptations converge on the same phenotypic change. PeerJ 4:e2227 https://doi.org/10.7717/peerj.2227
date submitted: 2016-04-22
date accepted: 2016-06-16
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miller
  given name: Craig R.
author list: Agent
  family name: Nagel
  given name: Anna C.
author list: Agent
  family name: Scott
  given name: LuAnn
author list: Agent
  family name: Settles
  given name: Matt
author list: Agent
  family name: Joyce
  given name: Paul
author list: Agent
  family name: Wichman
  given name: Holly A.
doi: 10.7717/peerj.2227
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Miller et al.
attribution name: Miller et al.

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures
type: item
type: AcademicArticle
description: Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.
format: application/pdf
format: text/html
creator: Kok-Gan Chan
creator: Kumutha Priya
creator: Chien-Yi Chang
creator: Ahmad Yamin Abdul Rahman
creator: Kok Keng Tee
creator: Wai-Fong Yin
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2223
publisher: PeerJ Inc.
rights: © 2016 Chan et al.
abstract: Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.
bibliographic citation: Chan et al. (2016) Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures. PeerJ 4:e2223 https://doi.org/10.7717/peerj.2223
date submitted: 2016-01-19
date accepted: 2016-06-15
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chan
  given name: Kok-Gan
author list: Agent
  family name: Priya
  given name: Kumutha
author list: Agent
  family name: Chang
  given name: Chien-Yi
author list: Agent
  family name: Abdul Rahman
  given name: Ahmad Yamin
author list: Agent
  family name: Tee
  given name: Kok Keng
author list: Agent
  family name: Yin
  given name: Wai-Fong
doi: 10.7717/peerj.2223
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: © 2016 Chan et al.
attribution name: Chan et al.

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
type: item
type: AcademicArticle
description: Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
format: application/pdf
format: text/html
creator: Edward W. Davis II
creator: Alexandra J. Weisberg
creator: Javier F. Tabima
creator: Niklaus J. Grunwald
creator: Jeff H. Chang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.2222
publisher: PeerJ Inc.
rights: © 2016 Davis II et al.
abstract: Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
bibliographic citation: Davis II et al. (2016) Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ 4:e2222 https://doi.org/10.7717/peerj.2222
date submitted: 2016-04-29
date accepted: 2016-06-15
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davis II
  given name: Edward W.
author list: Agent
  family name: Weisberg
  given name: Alexandra J.
author list: Agent
  family name: Tabima
  given name: Javier F.
author list: Agent
  family name: Grunwald
  given name: Niklaus J.
author list: Agent
  family name: Chang
  given name: Jeff H.
doi: 10.7717/peerj.2222
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Davis II et al.
attribution name: Davis II et al.

Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics
type: item
type: AcademicArticle
description: Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the jui…
format: application/pdf
format: text/html
creator: Juan J. Martinez-Nicolas
creator: Pablo Melgarejo
creator: Pilar Legua
creator: Francisco Garcia-Sanchez
creator: Francisca Hernández
subject: Agricultural Science
subject: Biodiversity
subject: Plant Science
description: doi:10.7717/peerj.2214
publisher: PeerJ Inc.
rights: © 2016 Martinez-Nicolas et al.
abstract: Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the jui…
bibliographic citation: Martinez-Nicolas et al. (2016) Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics. PeerJ 4:e2214 https://doi.org/10.7717/peerj.2214
date submitted: 2016-02-20
date accepted: 2016-06-14
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Nicolas
  given name: Juan J.
author list: Agent
  family name: Melgarejo
  given name: Pablo
author list: Agent
  family name: Legua
  given name: Pilar
author list: Agent
  family name: Garcia-Sanchez
  given name: Francisco
author list: Agent
  family name: Hernández
  given name: Francisca
doi: 10.7717/peerj.2214
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Martinez-Nicolas et al.
attribution name: Martinez-Nicolas et al.

Enhanced functional connectivity properties of human brains during in-situ nature experience
type: item
type: AcademicArticle
description: In this study, we investigated the impacts of in-situ nature and urban exposure on human brain activities and their dynamics. We randomly assigned 32 healthy right-handed college students (mean age = 20.6 years, SD = 1.6; 16 males) to a 20 min in-situ sitting exposure in either a nature (n = 16) or urban environment (n = 16) and measured their Electroencephalography (EEG) signals. Analyses revealed that a brief in-situ restorative nature experience may induce more efficient and stronger brain connectivity with enhanced small-world properties compared with a stressful urban experience. The enhanced small-world properties were found to be correlated with “coherent” experience measured by Perceived Restorativeness Scale (PRS). Exposure to nature also induces stronger long-term correlated activity across different brain regions with a right lateralization. These findings may advance our understanding of the functional activities during in-situ environmental exposures and imply that a nature or nature-like environment may potentially benefit cognitive processes and mental well-being.
format: application/pdf
format: text/html
creator: Zheng Chen
creator: Yujia He
creator: Yuguo Yu
subject: Computational Biology
subject: Neuroscience
description: doi:10.7717/peerj.2210
publisher: PeerJ Inc.
rights: © 2016 Chen et al.
abstract: In this study, we investigated the impacts of in-situ nature and urban exposure on human brain activities and their dynamics. We randomly assigned 32 healthy right-handed college students (mean age = 20.6 years, SD = 1.6; 16 males) to a 20 min in-situ sitting exposure in either a nature (n = 16) or urban environment (n = 16) and measured their Electroencephalography (EEG) signals. Analyses revealed that a brief in-situ restorative nature experience may induce more efficient and stronger brain connectivity with enhanced small-world properties compared with a stressful urban experience. The enhanced small-world properties were found to be correlated with “coherent” experience measured by Perceived Restorativeness Scale (PRS). Exposure to nature also induces stronger long-term correlated activity across different brain regions with a right lateralization. These findings may advance our understanding of the functional activities during in-situ environmental exposures and imply that a nature or nature-like environment may potentially benefit cognitive processes and mental well-being.
bibliographic citation: Chen et al. (2016) Enhanced functional connectivity properties of human brains during in-situ nature experience. PeerJ 4:e2210 https://doi.org/10.7717/peerj.2210
date submitted: 2016-03-10
date accepted: 2016-06-13
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Zheng
author list: Agent
  family name: He
  given name: Yujia
author list: Agent
  family name: Yu
  given name: Yuguo
doi: 10.7717/peerj.2210
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: © 2016 Chen et al.
attribution name: Chen et al.

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