PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The neuroprotective effect of nicotine in Parkinson’s disease models is associated with inhibiting PARP-1 and caspase-3 cleavage
items: Range expansion of a fouling species indirectly impacts local species interactions
items: Decreased quality of life and treatment satisfaction in patients with latent autoimmune diabetes of the adult
items: Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes
items: lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway
items: MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients
items: Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils
items: How to normalize metatranscriptomic count data for differential expression analysis
items: Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis
items: Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI

The neuroprotective effect of nicotine in Parkinson’s disease models is associated with inhibiting PARP-1 and caspase-3 cleavage
type: item
type: AcademicArticle
description: Clinical evidence points to neuroprotective effects of smoking in Parkinson’s disease (PD), but the molecular mechanisms remain unclear. We investigated the pharmacological pathways involved in these neuroprotective effects, which could provide novel ideas for developing targeted neuroprotective treatments for PD. We used the ETC complex I inhibitor methylpyridinium ion (MPP+) to induce cell death in SH-SY5Y cells as a cellular model for PD and found that nicotine inhibits cell death. Using choline as a nicotinic acetylcholine receptor (nAChR) agonist, we found that nAChR stimulation was sufficient to protect SH-SY5Y cells against cell death from MPP+. Blocking α7 nAChR with methyllycaconitine (MLA) prevented the protective effects of nicotine, demonstrating that these receptors are necessary for the neuroprotective effects of nicotine. The neuroprotective effect of nicotine involves other pathways relevant to PD. Cleaved Poly (ADP-ribose) polymerase-1 (PARP-1) and cleaved caspase-3 were decreased by nicotine in 6-hydroxydopamine (6-OHDA) lesioned mice and in MPP+-treated SH-SY5Y cells. In conclusion, our data indicate that nicotine likely exerts neuroprotective effects in PD through the α7 nAChR and downstream pathways including PARP-1 and caspase-3. This knowledge could be pursued in future research to develop neuroprotective treatments for PD.
format: application/pdf
format: text/html
creator: Justin Y.D. Lu
creator: Ping Su
creator: James E.M. Barber
creator: Joanne E. Nash
creator: Anh D. Le
creator: Fang Liu
creator: Albert H.C. Wong
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
subject: Neurology
subject: Pharmacology
description: doi:10.7717/peerj.3933
publisher: PeerJ Inc.
rights: © 2017 Lu et al.
abstract: Clinical evidence points to neuroprotective effects of smoking in Parkinson’s disease (PD), but the molecular mechanisms remain unclear. We investigated the pharmacological pathways involved in these neuroprotective effects, which could provide novel ideas for developing targeted neuroprotective treatments for PD. We used the ETC complex I inhibitor methylpyridinium ion (MPP+) to induce cell death in SH-SY5Y cells as a cellular model for PD and found that nicotine inhibits cell death. Using choline as a nicotinic acetylcholine receptor (nAChR) agonist, we found that nAChR stimulation was sufficient to protect SH-SY5Y cells against cell death from MPP+. Blocking α7 nAChR with methyllycaconitine (MLA) prevented the protective effects of nicotine, demonstrating that these receptors are necessary for the neuroprotective effects of nicotine. The neuroprotective effect of nicotine involves other pathways relevant to PD. Cleaved Poly (ADP-ribose) polymerase-1 (PARP-1) and cleaved caspase-3 were decreased by nicotine in 6-hydroxydopamine (6-OHDA) lesioned mice and in MPP+-treated SH-SY5Y cells. In conclusion, our data indicate that nicotine likely exerts neuroprotective effects in PD through the α7 nAChR and downstream pathways including PARP-1 and caspase-3. This knowledge could be pursued in future research to develop neuroprotective treatments for PD.
bibliographic citation: Lu et al. (2017) The neuroprotective effect of nicotine in Parkinson’s disease models is associated with inhibiting PARP-1 and caspase-3 cleavage. PeerJ 5:e3933 https://doi.org/10.7717/peerj.3933
date submitted: 2017-05-24
date accepted: 2017-09-26
issued: 2017-10-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Justin Y.D.
author list: Agent
  family name: Su
  given name: Ping
author list: Agent
  family name: Barber
  given name: James E.M.
author list: Agent
  family name: Nash
  given name: Joanne E.
author list: Agent
  family name: Le
  given name: Anh D.
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Wong
  given name: Albert H.C.
doi: 10.7717/peerj.3933
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-19
copyright: ©2017 Lu et al.
attribution name: Lu et al.

Range expansion of a fouling species indirectly impacts local species interactions
type: item
type: AcademicArticle
description: We investigated how recent changes in the distribution and abundance of a fouling organism affected the strength of interactions between a commercially important foundation species and a common predator. Increases in the abundance of boring sponges that bioerode the calcified shells of oysters and other shelled organisms have been attributed to increased salinization of estuarine ecosystems. We tested the hypothesis that fouling by boring sponges will change the interaction strength between oysters and a common predator (stone crabs). We generated five oyster density treatments crossed with two sponge treatments (sponge and no sponge). We contrasted the interaction strength between stone crabs and fouled and non-fouled oysters by comparing the parameters of fitted functional response curves based on Rogers random predation model. We found that fouled oysters suffered higher predation from stone crabs, and that the increased predation risk stemmed from a reduction in the handling time needed to consume the fouled oysters. These findings highlight the importance of understanding the effects of abiotic changes on both the composition of ecological communities, and on the strengths of direct and indirect interactions among species. Global climate change is altering local ecosystems in complex ways, and the success of restoration, management, and mitigation strategies for important species requires a better appreciation for how these effects cascade through ecosystems.
format: application/pdf
format: text/html
creator: Cori J. Speights
creator: Michael W. McCoy
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3911
publisher: PeerJ Inc.
rights: © 2017 Speights and McCoy
abstract: We investigated how recent changes in the distribution and abundance of a fouling organism affected the strength of interactions between a commercially important foundation species and a common predator. Increases in the abundance of boring sponges that bioerode the calcified shells of oysters and other shelled organisms have been attributed to increased salinization of estuarine ecosystems. We tested the hypothesis that fouling by boring sponges will change the interaction strength between oysters and a common predator (stone crabs). We generated five oyster density treatments crossed with two sponge treatments (sponge and no sponge). We contrasted the interaction strength between stone crabs and fouled and non-fouled oysters by comparing the parameters of fitted functional response curves based on Rogers random predation model. We found that fouled oysters suffered higher predation from stone crabs, and that the increased predation risk stemmed from a reduction in the handling time needed to consume the fouled oysters. These findings highlight the importance of understanding the effects of abiotic changes on both the composition of ecological communities, and on the strengths of direct and indirect interactions among species. Global climate change is altering local ecosystems in complex ways, and the success of restoration, management, and mitigation strategies for important species requires a better appreciation for how these effects cascade through ecosystems.
bibliographic citation: Speights et al. (2017) Range expansion of a fouling species indirectly impacts local species interactions. PeerJ 5:e3911 https://doi.org/10.7717/peerj.3911
date submitted: 2017-06-30
date accepted: 2017-09-19
issued: 2017-10-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Speights
  given name: Cori J.
author list: Agent
  family name: McCoy
  given name: Michael W.
doi: 10.7717/peerj.3911
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-19
copyright: ©2017 Speights and McCoy
attribution name: Speights and McCoy

Decreased quality of life and treatment satisfaction in patients with latent autoimmune diabetes of the adult
type: item
type: AcademicArticle
description: Objectives Our main aim was to assess the quality of life (QoL) and treatment satisfaction (TS) of subjects with LADA (latent autoimmune diabetes of the adult) and compare these measures with those of patients with other diabetes types, i.e., type 1 (T1DM) and type 2 diabetes mellitus (T2DM). Methods This was a cross-sectional study with a total of 48 patients with LADA, 297 patients with T2DM and 124 with T1DM. The Audit of Diabetes-Dependent Quality of Life (ADDQoL-19) questionnaire and the Diabetes Treatment Satisfaction Questionnaire (DTSQ) were administered. Relevant clinical variables were also assessed. The data analysis included comparisons between groups and multivariate linear models. Results The LADA patients presented lower diabetes-specific QoL (p = 0.045) and average weighted impact scores (p = 0.007) than the T2DM patients. The subgroup of LADA patients with diabetic retinopathy (DR) who were treated with insulin had a lower ADDQoL average weighted impact score than the other diabetic groups. Although the overall measure of TS was not different between the LADA and T2DM (p = 0.389) and T1DM (p = 0.091) groups, the patients with LADA showed a poorer hyperglycemic frequency perception than the T2DM patients (p < 0.001) and an improved frequency of hypoglycemic perception compared with the T1DM patients (p = 0.021). Conclusions The current findings suggest a poorer quality of life, especially in terms of DR and insulin treatment, among patients with LADA compared with those with T1DM and T2DM. Hyperglycemia frequency perception was also poorer in the LADA patients than in the T1DM and T2DM patients. Further research with prospective studies and a large number of patients is necessary.
format: application/pdf
format: text/html
creator: Minerva Granado-Casas
creator: Montserrat Martínez-Alonso
creator: Nuria Alcubierre
creator: Anna Ramírez-Morros
creator: Marta Hernández
creator: Esmeralda Castelblanco
creator: Joan Torres-Puiggros
creator: Didac Mauricio
subject: Diabetes and Endocrinology
subject: Nursing
subject: Public Health
description: doi:10.7717/peerj.3928
publisher: PeerJ Inc.
rights: © 2017 Granado-Casas et al.
abstract: Objectives Our main aim was to assess the quality of life (QoL) and treatment satisfaction (TS) of subjects with LADA (latent autoimmune diabetes of the adult) and compare these measures with those of patients with other diabetes types, i.e., type 1 (T1DM) and type 2 diabetes mellitus (T2DM). Methods This was a cross-sectional study with a total of 48 patients with LADA, 297 patients with T2DM and 124 with T1DM. The Audit of Diabetes-Dependent Quality of Life (ADDQoL-19) questionnaire and the Diabetes Treatment Satisfaction Questionnaire (DTSQ) were administered. Relevant clinical variables were also assessed. The data analysis included comparisons between groups and multivariate linear models. Results The LADA patients presented lower diabetes-specific QoL (p = 0.045) and average weighted impact scores (p = 0.007) than the T2DM patients. The subgroup of LADA patients with diabetic retinopathy (DR) who were treated with insulin had a lower ADDQoL average weighted impact score than the other diabetic groups. Although the overall measure of TS was not different between the LADA and T2DM (p = 0.389) and T1DM (p = 0.091) groups, the patients with LADA showed a poorer hyperglycemic frequency perception than the T2DM patients (p < 0.001) and an improved frequency of hypoglycemic perception compared with the T1DM patients (p = 0.021). Conclusions The current findings suggest a poorer quality of life, especially in terms of DR and insulin treatment, among patients with LADA compared with those with T1DM and T2DM. Hyperglycemia frequency perception was also poorer in the LADA patients than in the T1DM and T2DM patients. Further research with prospective studies and a large number of patients is necessary.
bibliographic citation: Granado-Casas et al. (2017) Decreased quality of life and treatment satisfaction in patients with latent autoimmune diabetes of the adult. PeerJ 5:e3928 https://doi.org/10.7717/peerj.3928
date submitted: 2017-05-02
date accepted: 2017-09-26
issued: 2017-10-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Granado-Casas
  given name: Minerva
author list: Agent
  family name: Martínez-Alonso
  given name: Montserrat
author list: Agent
  family name: Alcubierre
  given name: Nuria
author list: Agent
  family name: Ramírez-Morros
  given name: Anna
author list: Agent
  family name: Hernández
  given name: Marta
author list: Agent
  family name: Castelblanco
  given name: Esmeralda
author list: Agent
  family name: Torres-Puiggros
  given name: Joan
author list: Agent
  family name: Mauricio
  given name: Didac
doi: 10.7717/peerj.3928
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-18
copyright: ©2017 Granado-Casas et al.
attribution name: Granado-Casas et al.

Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes
type: item
type: AcademicArticle
description: The invasion of Indo-Pacific lionfish is one of the most pressing concerns in the context of coral reef conservation throughout the Caribbean. Invasive lionfish threaten Caribbean fish communities by feeding on a wide range of native prey species, some of which have high ecological and economic value. In Roatan (Honduras) a local non-governmental organisation (i.e. Roatan Marine Park) trains residents and tourists in the use of spears to remove invasive lionfish. Here, we assess the effectiveness of local removal efforts in reducing lionfish populations. We ask whether reefs subject to relatively frequent removals support more diverse and abundant native fish assemblages compared to sites were no removals take place. Lionfish biomass, as well as density and diversity of native prey species were quantified on reefs subject to regular and no removal efforts. Reefs subject to regular lionfish removals (two to three removals month−1) with a mean catch per unit effort of 2.76 ± 1.72 lionfish fisher−1 h−1 had 95% lower lionfish biomass compared to non-removal sites. Sites subject to lionfish removals supported 30% higher densities of native prey-sized fishes compared to sites subject to no removal efforts. We found no evidence that species richness and diversity of native fish communities differ between removal and non-removal sites. We conclude that opportunistic voluntary removals are an effective management intervention to reduce lionfish populations locally and might alleviate negative impacts of lionfish predation. We recommend that local management and the diving industry cooperate to cost-effectively extend the spatial scale at which removal regimes are currently sustained.
format: application/pdf
format: text/html
creator: Friederike Peiffer
creator: Sonia Bejarano
creator: Giacomo Palavicini de Witte
creator: Christian Wild
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.3818
publisher: PeerJ Inc.
rights: © 2017 Peiffer et al.
abstract: The invasion of Indo-Pacific lionfish is one of the most pressing concerns in the context of coral reef conservation throughout the Caribbean. Invasive lionfish threaten Caribbean fish communities by feeding on a wide range of native prey species, some of which have high ecological and economic value. In Roatan (Honduras) a local non-governmental organisation (i.e. Roatan Marine Park) trains residents and tourists in the use of spears to remove invasive lionfish. Here, we assess the effectiveness of local removal efforts in reducing lionfish populations. We ask whether reefs subject to relatively frequent removals support more diverse and abundant native fish assemblages compared to sites were no removals take place. Lionfish biomass, as well as density and diversity of native prey species were quantified on reefs subject to regular and no removal efforts. Reefs subject to regular lionfish removals (two to three removals month−1) with a mean catch per unit effort of 2.76 ± 1.72 lionfish fisher−1 h−1 had 95% lower lionfish biomass compared to non-removal sites. Sites subject to lionfish removals supported 30% higher densities of native prey-sized fishes compared to sites subject to no removal efforts. We found no evidence that species richness and diversity of native fish communities differ between removal and non-removal sites. We conclude that opportunistic voluntary removals are an effective management intervention to reduce lionfish populations locally and might alleviate negative impacts of lionfish predation. We recommend that local management and the diving industry cooperate to cost-effectively extend the spatial scale at which removal regimes are currently sustained.
bibliographic citation: Peiffer et al. (2017) Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes. PeerJ 5:e3818 https://doi.org/10.7717/peerj.3818
date submitted: 2017-04-08
date accepted: 2017-08-26
issued: 2017-10-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peiffer
  given name: Friederike
author list: Agent
  family name: Bejarano
  given name: Sonia
author list: Agent
  family name: Palavicini de Witte
  given name: Giacomo
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.3818
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-18
copyright: © 2017 Peiffer et al.
attribution name: Peiffer et al.

lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway
type: item
type: AcademicArticle
description: Increased levels of long noncoding RNA H19 (H19) have been observed in many inflammatory and organ fibrosis diseases including ulcerative colitis, osteoarthritis, liver fibrosis, renal fibrosis and pulmonary fibrosis. However, the role of H19 in bovine mastitis and mastitis-caused fibrosis is still unclear. In our study, H19 was characterized as a novel regulator of EMT induced by transforming growth factor-β1 (TGF-β1) in bovine mammary alveolar cell-T (MAC-T) cell line. We found that H19 was highly expressed in bovine mastitis tissues and inflammatory MAC-T cells induced by virulence factors of pathogens. TGF-β1 was also highly expressed in inflammatory MAC-T cells, and exogenous TGF-β1 could induce EMT, enhance extracellular matrix protein expression, and upregulate H19 expression in epithelial cells. Stable expression of H19 significantly promotes EMT progression and expression of ECM protein induced by TGF-β1 in MAC-T cells. Furthermore, by using a specific inhibitor of the PI3K/AKT pathway, we demonstrated that TGF-β1 upregulated H19 expression through PI3K/AKT pathway. All these observations imply that the lncRNA H19 modulated TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT signaling pathway, which suggests that mammary epithelial cells might be one source for myofibroblasts in vivo in the mammary glands under an inflammatory condition, thereby contributing to mammary gland fibrosis.
format: application/pdf
format: text/html
creator: Wei Yang
creator: Xuezhong Li
creator: Shaopei Qi
creator: Xueru Li
creator: Kun Zhou
creator: Suzhu Qing
creator: Yong Zhang
creator: Ming-Qing Gao
subject: Biochemistry
subject: Cell Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.3950
publisher: PeerJ Inc.
rights: © 2017 Yang et al.
abstract: Increased levels of long noncoding RNA H19 (H19) have been observed in many inflammatory and organ fibrosis diseases including ulcerative colitis, osteoarthritis, liver fibrosis, renal fibrosis and pulmonary fibrosis. However, the role of H19 in bovine mastitis and mastitis-caused fibrosis is still unclear. In our study, H19 was characterized as a novel regulator of EMT induced by transforming growth factor-β1 (TGF-β1) in bovine mammary alveolar cell-T (MAC-T) cell line. We found that H19 was highly expressed in bovine mastitis tissues and inflammatory MAC-T cells induced by virulence factors of pathogens. TGF-β1 was also highly expressed in inflammatory MAC-T cells, and exogenous TGF-β1 could induce EMT, enhance extracellular matrix protein expression, and upregulate H19 expression in epithelial cells. Stable expression of H19 significantly promotes EMT progression and expression of ECM protein induced by TGF-β1 in MAC-T cells. Furthermore, by using a specific inhibitor of the PI3K/AKT pathway, we demonstrated that TGF-β1 upregulated H19 expression through PI3K/AKT pathway. All these observations imply that the lncRNA H19 modulated TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT signaling pathway, which suggests that mammary epithelial cells might be one source for myofibroblasts in vivo in the mammary glands under an inflammatory condition, thereby contributing to mammary gland fibrosis.
bibliographic citation: Yang et al. (2017) lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway. PeerJ 5:e3950 https://doi.org/10.7717/peerj.3950
date submitted: 2017-07-25
date accepted: 2017-10-01
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Wei
author list: Agent
  family name: Li
  given name: Xuezhong
author list: Agent
  family name: Qi
  given name: Shaopei
author list: Agent
  family name: Li
  given name: Xueru
author list: Agent
  family name: Zhou
  given name: Kun
author list: Agent
  family name: Qing
  given name: Suzhu
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Gao
  given name: Ming-Qing
doi: 10.7717/peerj.3950
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Yang et al.
attribution name: Yang et al.

MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients
type: item
type: AcademicArticle
description: Background/Aim Strabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene. Methods From Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT), TDT allowing for errors (TDTae), and linkage analysis under dominant and recessive inheritance. Results The SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2), on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2), on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis. Conclusions This study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population.
format: application/pdf
format: text/html
creator: Jingjing Zhang
creator: Toshihiko Matsuo
subject: Genetics
subject: Genomics
subject: Ophthalmology
subject: Medical Genetics
description: doi:10.7717/peerj.3935
publisher: PeerJ Inc.
rights: © 2017 Zhang and Matsuo
abstract: Background/Aim Strabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene. Methods From Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT), TDT allowing for errors (TDTae), and linkage analysis under dominant and recessive inheritance. Results The SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2), on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2), on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis. Conclusions This study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population.
bibliographic citation: Zhang et al. (2017) MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients. PeerJ 5:e3935 https://doi.org/10.7717/peerj.3935
date submitted: 2017-06-02
date accepted: 2017-09-26
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jingjing
author list: Agent
  family name: Matsuo
  given name: Toshihiko
doi: 10.7717/peerj.3935
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Zhang and Matsuo
attribution name: Zhang and Matsuo

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils
type: item
type: AcademicArticle
description: In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.
format: application/pdf
format: text/html
creator: Craig Anderson
creator: Mike Beare
creator: Hannah L. Buckley
creator: Gavin Lear
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.3930
publisher: PeerJ Inc.
rights: © 2017 Anderson et al.
abstract: In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.
bibliographic citation: Anderson et al. (2017) Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils. PeerJ 5:e3930 https://doi.org/10.7717/peerj.3930
date submitted: 2017-07-26
date accepted: 2017-09-26
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Craig
author list: Agent
  family name: Beare
  given name: Mike
author list: Agent
  family name: Buckley
  given name: Hannah L.
author list: Agent
  family name: Lear
  given name: Gavin
doi: 10.7717/peerj.3930
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Anderson et al.
attribution name: Anderson et al.

How to normalize metatranscriptomic count data for differential expression analysis
type: item
type: AcademicArticle
description: Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and…
format: application/pdf
format: text/html
creator: Heiner Klingenberg
creator: Peter Meinicke
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.3859
publisher: PeerJ Inc.
rights: © 2017 Klingenberg and Meinicke
abstract: Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and…
bibliographic citation: Klingenberg et al. (2017) How to normalize metatranscriptomic count data for differential expression analysis. PeerJ 5:e3859 https://doi.org/10.7717/peerj.3859
date submitted: 2017-05-10
date accepted: 2017-09-06
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klingenberg
  given name: Heiner
author list: Agent
  family name: Meinicke
  given name: Peter
doi: 10.7717/peerj.3859
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Klingenberg and Meinicke
attribution name: Klingenberg and Meinicke

Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis
type: item
type: AcademicArticle
description: Background The study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives. Methods Eight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis. Results A total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress. Discussion EDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health. PROSPERO Registration Number CRD42014010806.
format: application/pdf
format: text/html
creator: Sarah E. Golding
creator: Claire Horsfield
creator: Annette Davies
creator: Bernadette Egan
creator: Martyn Jones
creator: Mary Raleigh
creator: Patricia Schofield
creator: Allison Squires
creator: Kath Start
creator: Tom Quinn
creator: Mark Cropley
subject: Emergency and Critical Care
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3735
publisher: PeerJ Inc.
rights: © 2017 Golding et al.
abstract: Background The study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives. Methods Eight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis. Results A total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress. Discussion EDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health. PROSPERO Registration Number CRD42014010806.
bibliographic citation: Golding et al. (2017) Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis. PeerJ 5:e3735 https://doi.org/10.7717/peerj.3735
date submitted: 2017-04-08
date accepted: 2017-08-04
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Golding
  given name: Sarah E.
author list: Agent
  family name: Horsfield
  given name: Claire
author list: Agent
  family name: Davies
  given name: Annette
author list: Agent
  family name: Egan
  given name: Bernadette
author list: Agent
  family name: Jones
  given name: Martyn
author list: Agent
  family name: Raleigh
  given name: Mary
author list: Agent
  family name: Schofield
  given name: Patricia
author list: Agent
  family name: Squires
  given name: Allison
author list: Agent
  family name: Start
  given name: Kath
author list: Agent
  family name: Quinn
  given name: Tom
author list: Agent
  family name: Cropley
  given name: Mark
doi: 10.7717/peerj.3735
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Golding et al.
attribution name: Golding et al.

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI
type: item
type: AcademicArticle
description: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
format: application/pdf
format: text/html
creator: Miranda H. Hengy
creator: Dean J. Horton
creator: Donald G. Uzarski
creator: Deric R. Learman
subject: Biodiversity
subject: Ecology
subject: Environmental Sciences
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.3937
publisher: PeerJ Inc.
rights: © 2017 Hengy et al.
abstract: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
bibliographic citation: Hengy et al. (2017) Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI. PeerJ 5:e3937 https://doi.org/10.7717/peerj.3937
date submitted: 2017-06-13
date accepted: 2017-09-26
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hengy
  given name: Miranda H.
author list: Agent
  family name: Horton
  given name: Dean J.
author list: Agent
  family name: Uzarski
  given name: Donald G.
author list: Agent
  family name: Learman
  given name: Deric R.
doi: 10.7717/peerj.3937
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Hengy et al.
attribution name: Hengy et al.

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