PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities
items: Creating functional groups of marine fish from categorical traits
items: Epidemiological and genetic characteristics of swine pseudorabies virus in mainland China between 2012 and 2017
items: Non-sutural basicranium-derived cells undergo a unique mineralization pathway via a cartilage intermediate in vitro
items: The effectiveness of Payments for Ecosystem Services at delivering improvements in water quality: lessons for experiments at the landscape scale
items: Surgical antibiotic prophylaxis use and infection prevalence in non-cosmetic breast surgery procedures at a tertiary hospital in Western Australia—a retrospective study
items: Molecular characterization of the giant freshwater prawn (Macrobrachium rosenbergii) beta-actin gene promoter
items: The influence of Neanderthal alleles on cytotoxic response
items: Non-visual exploration of novel objects increases the levels of plasticity factors in the rat primary visual cortex
items: Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) parasitizing the gills of Congolese cichlids from northern Lake Tanganyika

Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities
type: item
type: AcademicArticle
description: The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
format: application/pdf
format: text/html
creator: Ella T. Sieradzki
creator: Jed A. Fuhrman
creator: Sara Rivero-Calle
creator: Laura Gómez-Consarnau
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.5798
publisher: PeerJ Inc.
rights: © 2018 Sieradzki et al.
abstract: The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
bibliographic citation: Sieradzki et al. (2018) Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PeerJ 6:e5798 https://doi.org/10.7717/peerj.5798
date submitted: 2018-05-21
date accepted: 2018-09-20
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sieradzki
  given name: Ella T.
author list: Agent
  family name: Fuhrman
  given name: Jed A.
author list: Agent
  family name: Rivero-Calle
  given name: Sara
author list: Agent
  family name: Gómez-Consarnau
  given name: Laura
doi: 10.7717/peerj.5798
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Sieradzki et al.
attribution name: Sieradzki et al.

Creating functional groups of marine fish from categorical traits
type: item
type: AcademicArticle
description: Background Functional groups serve two important functions in ecology: they allow for simplification of ecosystem models and can aid in understanding diversity. Despite their important applications, there has not been a universally accepted method of how to define them. A common approach is to cluster species on a set of traits, validated through visual confirmation of resulting groups based primarily on expert opinion. The goal of this research is to determine a suitable procedure for creating and evaluating functional groups that arise from clustering nominal traits. Methods To do so, we produced a species by trait matrix of 22 traits from 116 fish species from Tasman Bay and Golden Bay, New Zealand. Data collected from photographs and published literature were predominantly nominal, and a small number of continuous traits were discretized. Some data were missing, so the benefit of imputing data was assessed using four approaches on data with known missing values. Hierarchical clustering is utilised to search for underlying data structure in the data that may represent functional groups. Within this clustering paradigm there are a number of distance matrices and linkage methods available, several combinations of which we test. The resulting clusters are evaluated using internal metrics developed specifically for nominal clustering. This revealed the choice of number of clusters, distance matrix and linkage method greatly affected the overall within- and between- cluster variability. We visualise the clustering in two dimensions and the stability of clusters is assessed through bootstrapping. Results Missing data imputation showed up to 90% accuracy using polytomous imputation, so was used to impute the real missing data. A division of the species information into three functional groups was the most separated, compact and stable result. Increasing the number of clusters increased the inconsistency of group membership, and selection of the appropriate distance matr…
format: application/pdf
format: text/html
creator: Monique A. Ladds
creator: Nokuthaba Sibanda
creator: Richard Arnold
creator: Matthew R. Dunn
subject: Ecology
subject: Marine Biology
subject: Statistics
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.5795
publisher: PeerJ Inc.
rights: © 2018 Ladds et al.
abstract: Background Functional groups serve two important functions in ecology: they allow for simplification of ecosystem models and can aid in understanding diversity. Despite their important applications, there has not been a universally accepted method of how to define them. A common approach is to cluster species on a set of traits, validated through visual confirmation of resulting groups based primarily on expert opinion. The goal of this research is to determine a suitable procedure for creating and evaluating functional groups that arise from clustering nominal traits. Methods To do so, we produced a species by trait matrix of 22 traits from 116 fish species from Tasman Bay and Golden Bay, New Zealand. Data collected from photographs and published literature were predominantly nominal, and a small number of continuous traits were discretized. Some data were missing, so the benefit of imputing data was assessed using four approaches on data with known missing values. Hierarchical clustering is utilised to search for underlying data structure in the data that may represent functional groups. Within this clustering paradigm there are a number of distance matrices and linkage methods available, several combinations of which we test. The resulting clusters are evaluated using internal metrics developed specifically for nominal clustering. This revealed the choice of number of clusters, distance matrix and linkage method greatly affected the overall within- and between- cluster variability. We visualise the clustering in two dimensions and the stability of clusters is assessed through bootstrapping. Results Missing data imputation showed up to 90% accuracy using polytomous imputation, so was used to impute the real missing data. A division of the species information into three functional groups was the most separated, compact and stable result. Increasing the number of clusters increased the inconsistency of group membership, and selection of the appropriate distance matr…
bibliographic citation: Ladds et al. (2018) Creating functional groups of marine fish from categorical traits. PeerJ 6:e5795 https://doi.org/10.7717/peerj.5795
date submitted: 2018-06-13
date accepted: 2018-09-20
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ladds
  given name: Monique A.
author list: Agent
  family name: Sibanda
  given name: Nokuthaba
author list: Agent
  family name: Arnold
  given name: Richard
author list: Agent
  family name: Dunn
  given name: Matthew R.
doi: 10.7717/peerj.5795
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Ladds et al.
attribution name: Ladds et al.

Epidemiological and genetic characteristics of swine pseudorabies virus in mainland China between 2012 and 2017
type: item
type: AcademicArticle
description: The outbreak of pseudorabies (PR) in many Bartha-K61 vaccinated farms in China in late 2011 has seriously damaged the pig industry of one of the largest producers of pork products in the world. To understand the epidemiological characteristics of the pseudorabies virus (PRV) strains currently prevalent in China, a total of 16,256 samples collected from pig farms suspected of PRV infection in 27 Provinces of China between 2012 and 2017 were evaluated for detection of PRV. Since the extensive use of gE-deleted PRV vaccine in China, the PRV-gE was applied for determining wild-type virus infection by PCR. Of the 16,256 samples detected, approximately 1,345 samples were positive for the detection of PRV-gE, yielding an average positive rate of 8.27%. The positive rates of PRV detection from 2012 to 2017 were 11.92% (153/1284), 12.19% (225/1846), 6.70% (169/2523), 11.10% (269/2424), 5.57% (147/2640), and 6.90% (382/5539), respectively. To understand the genetic characteristics of the PRV strains currently circulating, 25 PRV strains isolated from those PRV-gE positive samples were selected for further investigation. Phylogenetic analysis based on gB, gC, and gE showed that PRV strains prevalent in China had a remarkably distinct evolutionary relationship with PRVs from other countries, which might explain the observation that Bartha-K61 vaccine was unable to provide full protection against emergent strains. Sequence alignments identified many amino acid changes within the gB, gC, and gE proteins of the PRVs circulating in China after the outbreak compared to those from other countries or those prevalent in China before the outbreak; those changes also might affect the protective efficacy of previously used vaccines in China, as well as being associated in part with the increased virulence of the current PRV epidemic strains in China.
format: application/pdf
format: text/html
creator: Ying Sun
creator: Wan Liang
creator: Qingyun Liu
creator: Tingting Zhao
creator: Hechao Zhu
creator: Lin Hua
creator: Zhong Peng
creator: Xibiao Tang
creator: Charles W. Stratton
creator: Danna Zhou
creator: Yongxiang Tian
creator: Huanchun Chen
creator: Bin Wu
subject: Microbiology
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.5785
publisher: PeerJ Inc.
rights: © 2018 Sun et al.
abstract: The outbreak of pseudorabies (PR) in many Bartha-K61 vaccinated farms in China in late 2011 has seriously damaged the pig industry of one of the largest producers of pork products in the world. To understand the epidemiological characteristics of the pseudorabies virus (PRV) strains currently prevalent in China, a total of 16,256 samples collected from pig farms suspected of PRV infection in 27 Provinces of China between 2012 and 2017 were evaluated for detection of PRV. Since the extensive use of gE-deleted PRV vaccine in China, the PRV-gE was applied for determining wild-type virus infection by PCR. Of the 16,256 samples detected, approximately 1,345 samples were positive for the detection of PRV-gE, yielding an average positive rate of 8.27%. The positive rates of PRV detection from 2012 to 2017 were 11.92% (153/1284), 12.19% (225/1846), 6.70% (169/2523), 11.10% (269/2424), 5.57% (147/2640), and 6.90% (382/5539), respectively. To understand the genetic characteristics of the PRV strains currently circulating, 25 PRV strains isolated from those PRV-gE positive samples were selected for further investigation. Phylogenetic analysis based on gB, gC, and gE showed that PRV strains prevalent in China had a remarkably distinct evolutionary relationship with PRVs from other countries, which might explain the observation that Bartha-K61 vaccine was unable to provide full protection against emergent strains. Sequence alignments identified many amino acid changes within the gB, gC, and gE proteins of the PRVs circulating in China after the outbreak compared to those from other countries or those prevalent in China before the outbreak; those changes also might affect the protective efficacy of previously used vaccines in China, as well as being associated in part with the increased virulence of the current PRV epidemic strains in China.
bibliographic citation: Sun et al. (2018) Epidemiological and genetic characteristics of swine pseudorabies virus in mainland China between 2012 and 2017. PeerJ 6:e5785 https://doi.org/10.7717/peerj.5785
date submitted: 2018-07-19
date accepted: 2018-09-18
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Ying
author list: Agent
  family name: Liang
  given name: Wan
author list: Agent
  family name: Liu
  given name: Qingyun
author list: Agent
  family name: Zhao
  given name: Tingting
author list: Agent
  family name: Zhu
  given name: Hechao
author list: Agent
  family name: Hua
  given name: Lin
author list: Agent
  family name: Peng
  given name: Zhong
author list: Agent
  family name: Tang
  given name: Xibiao
author list: Agent
  family name: Stratton
  given name: Charles W.
author list: Agent
  family name: Zhou
  given name: Danna
author list: Agent
  family name: Tian
  given name: Yongxiang
author list: Agent
  family name: Chen
  given name: Huanchun
author list: Agent
  family name: Wu
  given name: Bin
doi: 10.7717/peerj.5785
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Sun et al.
attribution name: Sun et al.

Non-sutural basicranium-derived cells undergo a unique mineralization pathway via a cartilage intermediate in vitro
type: item
type: AcademicArticle
description: The basicranium serves as a key interface in the mammalian skull, interacting with the calvarium, facial skeleton and vertebral column. Despite its critical function, little is known about basicranial bone formation, particularly on a cellular level. The goal of this study was therefore to cultivate a better understanding of basicranial development by isolating and characterizing the osteogenic potential of cells from the neonatal murine cranial base. Osteoblast-like basicranial cells were isolated, seeded in multicellular aggregates (designated micromasses), and cultured in osteogenic medium in the presence or absence of bone morphogenetic protein-6 (BMP6). A minimal osteogenic response was observed in control osteogenic medium, while BMP6 treatment induced a chondrogenic response followed by up-regulation of osteogenic markers and extensive mineralization. This response appears to be distinct from prior analyses of the calvarium and long bones, as basicranial cells did not mineralize under standard osteogenic conditions, but rather required BMP6 to stimulate mineralization, which occurred via an endochondral-like process. These findings suggest that this site may be unique compared to other cranial elements as well as the limb skeleton, and we propose that the distinct characteristics of these cells may be a function of the distinct properties of the basicranium: endochondral ossification, dual embryology, and complex loading environment.
format: application/pdf
format: text/html
creator: Holly E. Weiss-Bilka
creator: Justin A. Brill
creator: Matthew J. Ravosa
subject: Developmental Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.5757
publisher: PeerJ Inc.
rights: © 2018 Weiss-Bilka et al.
abstract: The basicranium serves as a key interface in the mammalian skull, interacting with the calvarium, facial skeleton and vertebral column. Despite its critical function, little is known about basicranial bone formation, particularly on a cellular level. The goal of this study was therefore to cultivate a better understanding of basicranial development by isolating and characterizing the osteogenic potential of cells from the neonatal murine cranial base. Osteoblast-like basicranial cells were isolated, seeded in multicellular aggregates (designated micromasses), and cultured in osteogenic medium in the presence or absence of bone morphogenetic protein-6 (BMP6). A minimal osteogenic response was observed in control osteogenic medium, while BMP6 treatment induced a chondrogenic response followed by up-regulation of osteogenic markers and extensive mineralization. This response appears to be distinct from prior analyses of the calvarium and long bones, as basicranial cells did not mineralize under standard osteogenic conditions, but rather required BMP6 to stimulate mineralization, which occurred via an endochondral-like process. These findings suggest that this site may be unique compared to other cranial elements as well as the limb skeleton, and we propose that the distinct characteristics of these cells may be a function of the distinct properties of the basicranium: endochondral ossification, dual embryology, and complex loading environment.
bibliographic citation: Weiss-Bilka et al. (2018) Non-sutural basicranium-derived cells undergo a unique mineralization pathway via a cartilage intermediate in vitro. PeerJ 6:e5757 https://doi.org/10.7717/peerj.5757
date submitted: 2018-05-01
date accepted: 2018-09-14
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weiss-Bilka
  given name: Holly E.
author list: Agent
  family name: Brill
  given name: Justin A.
author list: Agent
  family name: Ravosa
  given name: Matthew J.
doi: 10.7717/peerj.5757
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Weiss-Bilka et al.
attribution name: Weiss-Bilka et al.

The effectiveness of Payments for Ecosystem Services at delivering improvements in water quality: lessons for experiments at the landscape scale
type: item
type: AcademicArticle
description: Background Randomised Control Trials (RCTs) are used in impact evaluation in a range of fields. However, despite calls for their greater use in environmental management, their use to evaluate landscape scale interventions remains rare. Payments for Ecosystem Services (PES) incentivise land users to manage land to provide environmental benefits. We present the first RCT evaluation of a PES program aiming to improve water quality. Watershared is a program which incentivises landowners to avoid deforestation and exclude cattle from riparian forests. Using this unusual landscape-scale experiment we explore the efficacy of Watershared at improving water quality, and draw lessons for future RCT evaluations of landscape-scale environmental management interventions. Methods One hundred and twenty-nine communities in the Bolivian Andes were randomly allocated to treatment (offered Watershared agreements) or control (not offered agreements) following baseline data collection (including Escherichia coli contamination in most communities) in 2010. We collected end-line data in 2015. Using our end-line data, we explored the extent to which variables associated with the intervention (e.g. cattle exclusion, absence of faeces) predict water quality locally. We then investigated the efficacy of the intervention at improving water quality at the landscape scale using the RCT. This analysis was done in two ways; for the subset of communities for which we have both baseline and end-line data from identical locations we used difference-in-differences (matching on baseline water quality), for all sites we compared control and treatment at end-line controlling for selected predictors of water quality. Results The presence of cattle faeces in water adversely affected water quality suggesting excluding cattle has a positive impact on water quality locally. However, both the matched difference-in-differences analysis and the comparison between treatment and control communities at end-line su…
format: application/pdf
format: text/html
creator: Edwin L. Pynegar
creator: Julia P.G. Jones
creator: James M. Gibbons
creator: Nigel M. Asquith
subject: Conservation Biology
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.5753
publisher: PeerJ Inc.
rights: © 2018 Pynegar et al.
abstract: Background Randomised Control Trials (RCTs) are used in impact evaluation in a range of fields. However, despite calls for their greater use in environmental management, their use to evaluate landscape scale interventions remains rare. Payments for Ecosystem Services (PES) incentivise land users to manage land to provide environmental benefits. We present the first RCT evaluation of a PES program aiming to improve water quality. Watershared is a program which incentivises landowners to avoid deforestation and exclude cattle from riparian forests. Using this unusual landscape-scale experiment we explore the efficacy of Watershared at improving water quality, and draw lessons for future RCT evaluations of landscape-scale environmental management interventions. Methods One hundred and twenty-nine communities in the Bolivian Andes were randomly allocated to treatment (offered Watershared agreements) or control (not offered agreements) following baseline data collection (including Escherichia coli contamination in most communities) in 2010. We collected end-line data in 2015. Using our end-line data, we explored the extent to which variables associated with the intervention (e.g. cattle exclusion, absence of faeces) predict water quality locally. We then investigated the efficacy of the intervention at improving water quality at the landscape scale using the RCT. This analysis was done in two ways; for the subset of communities for which we have both baseline and end-line data from identical locations we used difference-in-differences (matching on baseline water quality), for all sites we compared control and treatment at end-line controlling for selected predictors of water quality. Results The presence of cattle faeces in water adversely affected water quality suggesting excluding cattle has a positive impact on water quality locally. However, both the matched difference-in-differences analysis and the comparison between treatment and control communities at end-line su…
bibliographic citation: Pynegar et al. (2018) The effectiveness of Payments for Ecosystem Services at delivering improvements in water quality: lessons for experiments at the landscape scale. PeerJ 6:e5753 https://doi.org/10.7717/peerj.5753
date submitted: 2018-05-03
date accepted: 2018-09-14
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pynegar
  given name: Edwin L.
author list: Agent
  family name: Jones
  given name: Julia P.G.
author list: Agent
  family name: Gibbons
  given name: James M.
author list: Agent
  family name: Asquith
  given name: Nigel M.
doi: 10.7717/peerj.5753
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Pynegar et al.
attribution name: Pynegar et al.

Surgical antibiotic prophylaxis use and infection prevalence in non-cosmetic breast surgery procedures at a tertiary hospital in Western Australia—a retrospective study
type: item
type: AcademicArticle
description: Background Surgical site infections (SSIs) are a common complication following breast surgery procedures, despite being considered a clean surgery. The prevalence of SSIs can be minimised with the appropriate use of antibiotic prophylaxis as outlined in the Australian Therapeutic Guidelines (eTG). The aims of this study were to evaluate adherence to the eTG for antibiotic prophylaxis in breast surgery procedures at a Western Australian teaching hospital following an update of the guidelines in 2014 and examine the impact of prophylactic antibiotics on SSI incidence and length of hospital stay. Method A retrospective cross-sectional study which reviewed medical records from a random sample of 250 patients selected from 973 patients who underwent breast surgical procedures between February 2015 and March 2017. Results Overall adherence to current eTG occurred in 49.2% (123/250) of operations. Pre-operative and post-operative antibiotics were prescribed in 98.4% (246/250) and 11.2% (28/250) operations respectively. Adherence rates to three specific elements of the eTG (drug prescribed, drug dosage and timing of administration) were 91.6% (229/250), 53.6% (134/250) and 86.4% (216/250) respectively. For the 14.4% (36/250) patients with relevant drug allergies, there was zero adherence to the eTG. Overall recorded SSI prevalence was low at 5.2% (13/250). The mean length of stay in patients (2.3 ± 1.7 days) was not influenced by level of eTG adherence (p = 0.131) or SSIs (p = 0.306). Conclusion These data demonstrate a significant improvement in overall adherence to the eTG from 13.3% to 49.2% (p = < 0.001). The level of detected SSIs in this study was low. Further improvement is necessary with respect to prescribing appropriate antibiotic dosages and for those with allergies.
format: application/pdf
format: text/html
creator: Ainslie Lavers
creator: Wai Siong Yip
creator: Bruce Sunderland
creator: Richard Parsons
creator: Sarah Mackenzie
creator: Jason Seet
creator: Petra Czarniak
subject: Evidence Based Medicine
subject: Infectious Diseases
subject: Internal Medicine
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.5724
publisher: PeerJ Inc.
rights: © 2018 Lavers et al.
abstract: Background Surgical site infections (SSIs) are a common complication following breast surgery procedures, despite being considered a clean surgery. The prevalence of SSIs can be minimised with the appropriate use of antibiotic prophylaxis as outlined in the Australian Therapeutic Guidelines (eTG). The aims of this study were to evaluate adherence to the eTG for antibiotic prophylaxis in breast surgery procedures at a Western Australian teaching hospital following an update of the guidelines in 2014 and examine the impact of prophylactic antibiotics on SSI incidence and length of hospital stay. Method A retrospective cross-sectional study which reviewed medical records from a random sample of 250 patients selected from 973 patients who underwent breast surgical procedures between February 2015 and March 2017. Results Overall adherence to current eTG occurred in 49.2% (123/250) of operations. Pre-operative and post-operative antibiotics were prescribed in 98.4% (246/250) and 11.2% (28/250) operations respectively. Adherence rates to three specific elements of the eTG (drug prescribed, drug dosage and timing of administration) were 91.6% (229/250), 53.6% (134/250) and 86.4% (216/250) respectively. For the 14.4% (36/250) patients with relevant drug allergies, there was zero adherence to the eTG. Overall recorded SSI prevalence was low at 5.2% (13/250). The mean length of stay in patients (2.3 ± 1.7 days) was not influenced by level of eTG adherence (p = 0.131) or SSIs (p = 0.306). Conclusion These data demonstrate a significant improvement in overall adherence to the eTG from 13.3% to 49.2% (p = < 0.001). The level of detected SSIs in this study was low. Further improvement is necessary with respect to prescribing appropriate antibiotic dosages and for those with allergies.
bibliographic citation: Lavers et al. (2018) Surgical antibiotic prophylaxis use and infection prevalence in non-cosmetic breast surgery procedures at a tertiary hospital in Western Australia—a retrospective study. PeerJ 6:e5724 https://doi.org/10.7717/peerj.5724
date submitted: 2018-03-27
date accepted: 2018-09-11
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lavers
  given name: Ainslie
author list: Agent
  family name: Yip
  given name: Wai Siong
author list: Agent
  family name: Sunderland
  given name: Bruce
author list: Agent
  family name: Parsons
  given name: Richard
author list: Agent
  family name: Mackenzie
  given name: Sarah
author list: Agent
  family name: Seet
  given name: Jason
author list: Agent
  family name: Czarniak
  given name: Petra
doi: 10.7717/peerj.5724
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Lavers et al.
attribution name: Lavers et al.

Molecular characterization of the giant freshwater prawn (Macrobrachium rosenbergii) beta-actin gene promoter
type: item
type: AcademicArticle
description: Constitutive promoters are important tools for gene function studies and transgenesis. The Beta-actin (actb1) gene promoter has been isolated from many species but remains to be cloned from the giant freshwater prawn (Macrobrachium rosenbergii). In this study, we cloned and characterized the Mractb1 gene promoter. Two alternative promoters were identified for the Mractb1 gene, which direct the generation of two transcripts with different 5′ untranslated regions. Three CpG islands were predicted in the upstream sequence, which are intimately related to transcription initiation and promoter activity. In addition to the CCAAT-box and the CArG-box, molecular dissection of the flanking sequence revealed the existence of one negative and two positive elements in the upstream region and the first intron. Finally, the Mractb1 promoter demonstrated comparative activity to the carp (Cyprinus carpio) actb1 promoter. Our investigations provide a valuable genetic tool for gene function studies and shed light on the regulation of the Mractb1 gene.
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creator: Junjun Yan
creator: Qiang Gao
creator: Zongbin Cui
creator: Guoliang Yang
creator: Yong Long
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.5701
publisher: PeerJ Inc.
rights: © 2018 Yan et al.
abstract: Constitutive promoters are important tools for gene function studies and transgenesis. The Beta-actin (actb1) gene promoter has been isolated from many species but remains to be cloned from the giant freshwater prawn (Macrobrachium rosenbergii). In this study, we cloned and characterized the Mractb1 gene promoter. Two alternative promoters were identified for the Mractb1 gene, which direct the generation of two transcripts with different 5′ untranslated regions. Three CpG islands were predicted in the upstream sequence, which are intimately related to transcription initiation and promoter activity. In addition to the CCAAT-box and the CArG-box, molecular dissection of the flanking sequence revealed the existence of one negative and two positive elements in the upstream region and the first intron. Finally, the Mractb1 promoter demonstrated comparative activity to the carp (Cyprinus carpio) actb1 promoter. Our investigations provide a valuable genetic tool for gene function studies and shed light on the regulation of the Mractb1 gene.
bibliographic citation: Yan et al. (2018) Molecular characterization of the giant freshwater prawn (Macrobrachium rosenbergii) beta-actin gene promoter. PeerJ 6:e5701 https://doi.org/10.7717/peerj.5701
date submitted: 2018-07-09
date accepted: 2018-09-06
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Junjun
author list: Agent
  family name: Gao
  given name: Qiang
author list: Agent
  family name: Cui
  given name: Zongbin
author list: Agent
  family name: Yang
  given name: Guoliang
author list: Agent
  family name: Long
  given name: Yong
doi: 10.7717/peerj.5701
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Yan et al.
attribution name: Yan et al.

The influence of Neanderthal alleles on cytotoxic response
type: item
type: AcademicArticle
description: Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children’s Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.
format: application/pdf
format: text/html
creator: Farida S. Akhtari
creator: Tammy M. Havener
creator: Masahide Fukudo
creator: John R. Jack
creator: Howard L. McLeod
creator: Tim Wiltshire
creator: Alison A. Motsinger-Reif
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.5691
publisher: PeerJ Inc.
rights: © 2018 Akhtari et al.
abstract: Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children’s Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.
bibliographic citation: Akhtari et al. (2018) The influence of Neanderthal alleles on cytotoxic response. PeerJ 6:e5691 https://doi.org/10.7717/peerj.5691
date submitted: 2018-02-20
date accepted: 2018-09-04
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Akhtari
  given name: Farida S.
author list: Agent
  family name: Havener
  given name: Tammy M.
author list: Agent
  family name: Fukudo
  given name: Masahide
author list: Agent
  family name: Jack
  given name: John R.
author list: Agent
  family name: McLeod
  given name: Howard L.
author list: Agent
  family name: Wiltshire
  given name: Tim
author list: Agent
  family name: Motsinger-Reif
  given name: Alison A.
doi: 10.7717/peerj.5691
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Akhtari et al.
attribution name: Akhtari et al.

Non-visual exploration of novel objects increases the levels of plasticity factors in the rat primary visual cortex
type: item
type: AcademicArticle
description: Background Historically, the primary sensory areas of the cerebral cortex have been exclusively associated with the processing of a single sensory modality. Yet the presence of tactile responses in the primary visual (V1) cortex has challenged this view, leading to the notion that primary sensory areas engage in cross-modal processing, and that the associated circuitry is modifiable by such activity. To explore this notion, here we assessed whether the exploration of novel objects in the dark induces the activation of plasticity markers in the V1 cortex of rats. Methods Adult rats were allowed to freely explore for 20 min a completely dark box with four novel objects of different shapes and textures. Animals were euthanized either 1 (n = 5) or 3 h (n = 5) after exploration. A control group (n = 5) was placed for 20 min in the same environment, but without the objects. Frontal sections of the brains were submitted to immunohistochemistry to measure protein levels of egr-1 and c-fos, and phosphorylated calcium-dependent kinase (pCaKMII) in V1 cortex. Results The amount of neurons labeled with monoclonal antibodies against c-fos, egr-1 or pCaKMII increased significantly in V1 cortex after one hour of exploration in the dark. Three hours after exploration, the number of labeled neurons decreased to basal levels. Conclusions Our results suggest that non-visual exploration induces the activation of immediate-early genes in V1 cortex, which is suggestive of cross-modal processing in this area. Besides, the increase in the number of neurons labeled with pCaKMII may signal a condition promoting synaptic plasticity.
format: application/pdf
format: text/html
creator: Catia M. Pereira
creator: Marco Aurelio M. Freire
creator: José R. Santos
creator: Joanilson S. Guimarães
creator: Gabriella Dias-Florencio
creator: Sharlene Santos
creator: Antonio Pereira
creator: Sidarta Ribeiro
subject: Neuroscience
description: doi:10.7717/peerj.5678
publisher: PeerJ Inc.
rights: © 2018 Pereira et al.
abstract: Background Historically, the primary sensory areas of the cerebral cortex have been exclusively associated with the processing of a single sensory modality. Yet the presence of tactile responses in the primary visual (V1) cortex has challenged this view, leading to the notion that primary sensory areas engage in cross-modal processing, and that the associated circuitry is modifiable by such activity. To explore this notion, here we assessed whether the exploration of novel objects in the dark induces the activation of plasticity markers in the V1 cortex of rats. Methods Adult rats were allowed to freely explore for 20 min a completely dark box with four novel objects of different shapes and textures. Animals were euthanized either 1 (n = 5) or 3 h (n = 5) after exploration. A control group (n = 5) was placed for 20 min in the same environment, but without the objects. Frontal sections of the brains were submitted to immunohistochemistry to measure protein levels of egr-1 and c-fos, and phosphorylated calcium-dependent kinase (pCaKMII) in V1 cortex. Results The amount of neurons labeled with monoclonal antibodies against c-fos, egr-1 or pCaKMII increased significantly in V1 cortex after one hour of exploration in the dark. Three hours after exploration, the number of labeled neurons decreased to basal levels. Conclusions Our results suggest that non-visual exploration induces the activation of immediate-early genes in V1 cortex, which is suggestive of cross-modal processing in this area. Besides, the increase in the number of neurons labeled with pCaKMII may signal a condition promoting synaptic plasticity.
bibliographic citation: Pereira et al. (2018) Non-visual exploration of novel objects increases the levels of plasticity factors in the rat primary visual cortex. PeerJ 6:e5678 https://doi.org/10.7717/peerj.5678
date submitted: 2018-04-11
date accepted: 2018-08-29
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pereira
  given name: Catia M.
author list: Agent
  family name: Freire
  given name: Marco Aurelio M.
author list: Agent
  family name: Santos
  given name: José R.
author list: Agent
  family name: Guimarães
  given name: Joanilson S.
author list: Agent
  family name: Dias-Florencio
  given name: Gabriella
author list: Agent
  family name: Santos
  given name: Sharlene
author list: Agent
  family name: Pereira
  given name: Antonio
author list: Agent
  family name: Ribeiro
  given name: Sidarta
doi: 10.7717/peerj.5678
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: ©2018 Pereira et al.
attribution name: Pereira et al.

Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) parasitizing the gills of Congolese cichlids from northern Lake Tanganyika
type: item
type: AcademicArticle
description: Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) isolated from the gills of six cichlid host species belonging to four tribes and sampled from the Congolese coastline of Lake Tanganyika (LT) are described: Cichlidogyrus adkoningsi sp. nov. from Cyphotilapia frontosa (tribe Cyphotilapiini); C. koblmuelleri sp. nov. from Cardiopharynx schoutedeni (Ectodini); C. habluetzeli sp. nov. from C. schoutedeni and C. frontosa; C. antoineparisellei sp. nov. from Interochromis loocki (Tropheini); C. masilyai sp. nov. from Petrochromis orthognathus (Tropheini); C. salzburgeri sp. nov. from P. trewavasae, and C. sergemorandi sp. nov. from Tylochromis polylepis (Tylochromini). This study represents the first parasitological examination of cyphotilapiine cichlid hosts. Representatives of the Tanganyikan ectodine, tropheine, and tylochromine cichlids previously sampled from various localities in the lake yielded nine, twelve, and two described species of Cichlidogyrus, respectively. The study further includes a morphological characterization of the male copulatory organ of six undescribed species of Cichlidogyrus found on the gills of the tropheines I. loocki and P. orthognathus, and on those of Callochromis melanostigma and Xenotilapia flavipinnis (both Ectodini). Geographical variation in the monogenean fauna of I. loocki was observed. The most closely related cichlid species investigated in this study harboured Cichlidogyrus spp. exhibiting some similarities in their sclerotized structures. Thus, our paper provides additional evidence of the high species richness of Cichlidogyrus and the link with their hosts’s phylogenetic affinities in LT.
format: application/pdf
format: text/html
creator: Chahrazed Rahmouni
creator: Maarten P.M. Vanhove
creator: Andrea Šimková
subject: Biodiversity
subject: Parasitology
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.5604
publisher: PeerJ Inc.
rights: © 2018 Rahmouni et al.
abstract: Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) isolated from the gills of six cichlid host species belonging to four tribes and sampled from the Congolese coastline of Lake Tanganyika (LT) are described: Cichlidogyrus adkoningsi sp. nov. from Cyphotilapia frontosa (tribe Cyphotilapiini); C. koblmuelleri sp. nov. from Cardiopharynx schoutedeni (Ectodini); C. habluetzeli sp. nov. from C. schoutedeni and C. frontosa; C. antoineparisellei sp. nov. from Interochromis loocki (Tropheini); C. masilyai sp. nov. from Petrochromis orthognathus (Tropheini); C. salzburgeri sp. nov. from P. trewavasae, and C. sergemorandi sp. nov. from Tylochromis polylepis (Tylochromini). This study represents the first parasitological examination of cyphotilapiine cichlid hosts. Representatives of the Tanganyikan ectodine, tropheine, and tylochromine cichlids previously sampled from various localities in the lake yielded nine, twelve, and two described species of Cichlidogyrus, respectively. The study further includes a morphological characterization of the male copulatory organ of six undescribed species of Cichlidogyrus found on the gills of the tropheines I. loocki and P. orthognathus, and on those of Callochromis melanostigma and Xenotilapia flavipinnis (both Ectodini). Geographical variation in the monogenean fauna of I. loocki was observed. The most closely related cichlid species investigated in this study harboured Cichlidogyrus spp. exhibiting some similarities in their sclerotized structures. Thus, our paper provides additional evidence of the high species richness of Cichlidogyrus and the link with their hosts’s phylogenetic affinities in LT.
bibliographic citation: Rahmouni et al. (2018) Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) parasitizing the gills of Congolese cichlids from northern Lake Tanganyika. PeerJ 6:e5604 https://doi.org/10.7717/peerj.5604
date submitted: 2018-03-02
date accepted: 2018-08-16
issued: 2018-10-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahmouni
  given name: Chahrazed
author list: Agent
  family name: Vanhove
  given name: Maarten P.M.
author list: Agent
  family name: Šimková
  given name: Andrea
doi: 10.7717/peerj.5604
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-23
copyright: © 2018 Rahmouni et al.
attribution name: Rahmouni et al.

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