PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The effect of pupil size and peripheral brightness on detection and discrimination performance
items: Effect of music listening on hypertonia in neurologically impaired patients—systematic review
items: The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis
items: Biomarker potential of repetitive-element transcriptome in lung cancer
items: Genetic characteristics of non-familial epilepsy
items: Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats
items: Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis
items: Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies
items: Epidemiology of multiple sclerosis and vitamin D levels in Lanzarote, Canary Islands, Spain
items: First evidence of underwater vocalisations in hunting penguins

The effect of pupil size and peripheral brightness on detection and discrimination performance
type: item
type: AcademicArticle
description: It is easier to read dark text on a bright background (positive polarity) than to read bright text on a dark background (negative polarity). This positive-polarity advantage is often linked to pupil size: A bright background induces small pupils, which in turn increases visual acuity. Here we report that pupil size, when manipulated through peripheral brightness, has qualitatively different effects on discrimination of fine stimuli in central vision and detection of faint stimuli in peripheral vision. Small pupils are associated with improved discrimination performance, consistent with the positive-polarity advantage, but only for very small stimuli that are at the threshold of visual acuity. In contrast, large pupils are associated with improved detection performance. These results are likely due to two pupil-size related factors: Small pupils increase visual acuity, which improves discrimination of fine stimuli; and large pupils increase light influx, which improves detection of faint stimuli. Light scatter is likely also a contributing factor: When a display is bright, light scatter creates a diffuse veil of retinal illumination that reduces perceived image contrast, thus impairing detection performance. We further found that pupil size was larger during the detection task than during the discrimination task, even though both tasks were equally difficult and similar in visual input; this suggests that the pupil may automatically assume an optimal size for the current task. Our results may explain why pupils dilate in response to arousal: This may reflect an increased emphasis on detection of unpredictable danger, which is crucially important in many situations that are characterized by high levels of arousal. Finally, we discuss the implications of our results for the ergonomics of display design.
format: application/pdf
format: text/html
creator: Sebastiaan Mathôt
creator: Yavor Ivanov
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8220
publisher: PeerJ Inc.
rights: © 2019 Mathôt and Ivanov
abstract: It is easier to read dark text on a bright background (positive polarity) than to read bright text on a dark background (negative polarity). This positive-polarity advantage is often linked to pupil size: A bright background induces small pupils, which in turn increases visual acuity. Here we report that pupil size, when manipulated through peripheral brightness, has qualitatively different effects on discrimination of fine stimuli in central vision and detection of faint stimuli in peripheral vision. Small pupils are associated with improved discrimination performance, consistent with the positive-polarity advantage, but only for very small stimuli that are at the threshold of visual acuity. In contrast, large pupils are associated with improved detection performance. These results are likely due to two pupil-size related factors: Small pupils increase visual acuity, which improves discrimination of fine stimuli; and large pupils increase light influx, which improves detection of faint stimuli. Light scatter is likely also a contributing factor: When a display is bright, light scatter creates a diffuse veil of retinal illumination that reduces perceived image contrast, thus impairing detection performance. We further found that pupil size was larger during the detection task than during the discrimination task, even though both tasks were equally difficult and similar in visual input; this suggests that the pupil may automatically assume an optimal size for the current task. Our results may explain why pupils dilate in response to arousal: This may reflect an increased emphasis on detection of unpredictable danger, which is crucially important in many situations that are characterized by high levels of arousal. Finally, we discuss the implications of our results for the ergonomics of display design.
bibliographic citation: Mathôt et al. (2019) The effect of pupil size and peripheral brightness on detection and discrimination performance. PeerJ 7:e8220 https://doi.org/10.7717/peerj.8220
date submitted: 2019-05-06
date accepted: 2019-11-15
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mathôt
  given name: Sebastiaan
author list: Agent
  family name: Ivanov
  given name: Yavor
doi: 10.7717/peerj.8220
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Mathôt and Ivanov
attribution name: Mathôt and Ivanov

Effect of music listening on hypertonia in neurologically impaired patients—systematic review
type: item
type: AcademicArticle
description: Background As music listening is able to induce self-perceived and physiological signs of relaxation, it might be an interesting tool to induce muscle relaxation in patients with hypertonia. To this date effective non-pharmacological rehabilitation strategies to treat hypertonia in neurologically impaired patients are lacking. Therefore the aim is to investigate the effectiveness of music listening on muscle activity and relaxation. Methodology The search strategy was performed by the PRISMA guidelines and registered in the PROSPERO database (no. 42019128511). Seven databases were systematically searched until March 2019. Six of the 1,684 studies met the eligibility criteria and were included in this review. Risk of bias was assessed by the PEDro scale. In total 171 patients with a variety of neurological conditions were included assessing hypertonia with both clinicall and biomechanical measures. Results The analysis showed that there was a large treatment effect of music listening on muscle performance (SMD 0.96, 95% CI [0.29–1.63], I2 = 10%, Z = 2.82, p = 0.005). Music can be used as either background music during rehabilitation (dual-task) or during rest (single-task) and musical preferences seem to play a major role in the observed treatment effect. Conclusions Although music listening is able to induce muscle relaxation, several gaps in the available literature were acknowledged. Future research is in need of an accurate and objective assessment of hypertonia.
format: application/pdf
format: text/html
creator: Tamaya Van Criekinge
creator: Kristiaan D’Août
creator: Jonathon O’Brien
creator: Eduardo Coutinho
subject: Neuroscience
subject: Kinesiology
subject: Neurology
description: doi:10.7717/peerj.8228
publisher: PeerJ Inc.
rights: © 2019 Van Criekinge et al.
abstract: Background As music listening is able to induce self-perceived and physiological signs of relaxation, it might be an interesting tool to induce muscle relaxation in patients with hypertonia. To this date effective non-pharmacological rehabilitation strategies to treat hypertonia in neurologically impaired patients are lacking. Therefore the aim is to investigate the effectiveness of music listening on muscle activity and relaxation. Methodology The search strategy was performed by the PRISMA guidelines and registered in the PROSPERO database (no. 42019128511). Seven databases were systematically searched until March 2019. Six of the 1,684 studies met the eligibility criteria and were included in this review. Risk of bias was assessed by the PEDro scale. In total 171 patients with a variety of neurological conditions were included assessing hypertonia with both clinicall and biomechanical measures. Results The analysis showed that there was a large treatment effect of music listening on muscle performance (SMD 0.96, 95% CI [0.29–1.63], I2 = 10%, Z = 2.82, p = 0.005). Music can be used as either background music during rehabilitation (dual-task) or during rest (single-task) and musical preferences seem to play a major role in the observed treatment effect. Conclusions Although music listening is able to induce muscle relaxation, several gaps in the available literature were acknowledged. Future research is in need of an accurate and objective assessment of hypertonia.
bibliographic citation: Van Criekinge et al. (2019) Effect of music listening on hypertonia in neurologically impaired patients—systematic review. PeerJ 7:e8228 https://doi.org/10.7717/peerj.8228
date submitted: 2019-07-23
date accepted: 2019-11-18
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Van Criekinge
  given name: Tamaya
author list: Agent
  family name: D’Août
  given name: Kristiaan
author list: Agent
  family name: O’Brien
  given name: Jonathon
author list: Agent
  family name: Coutinho
  given name: Eduardo
doi: 10.7717/peerj.8228
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Van Criekinge et al.
attribution name: Van Criekinge et al.

The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis
type: item
type: AcademicArticle
description: Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.
format: application/pdf
format: text/html
creator: Dan Chen
creator: Jing Liu
creator: Luca Bartolozzi
creator: Xia Wan
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8274
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.
bibliographic citation: Chen et al. (2019) The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis. PeerJ 7:e8274 https://doi.org/10.7717/peerj.8274
date submitted: 2019-02-19
date accepted: 2019-11-22
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Dan
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Bartolozzi
  given name: Luca
author list: Agent
  family name: Wan
  given name: Xia
doi: 10.7717/peerj.8274
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Biomarker potential of repetitive-element transcriptome in lung cancer
type: item
type: AcademicArticle
description: Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
format: application/pdf
format: text/html
creator: Macarena Arroyo
creator: Rocío Bautista
creator: Rafael Larrosa
creator: Manuel Ángel Cobo
creator: M. Gonzalo Claros
subject: Bioinformatics
subject: Genomics
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.8277
publisher: PeerJ Inc.
rights: © 2019 Arroyo et al.
abstract: Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
bibliographic citation: Arroyo et al. (2019) Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 7:e8277 https://doi.org/10.7717/peerj.8277
date submitted: 2019-10-02
date accepted: 2019-11-22
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arroyo
  given name: Macarena
author list: Agent
  family name: Bautista
  given name: Rocío
author list: Agent
  family name: Larrosa
  given name: Rafael
author list: Agent
  family name: Cobo
  given name: Manuel Ángel
author list: Agent
  family name: Claros
  given name: M. Gonzalo
doi: 10.7717/peerj.8277
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Arroyo et al.
attribution name: Arroyo et al.

Genetic characteristics of non-familial epilepsy
type: item
type: AcademicArticle
description: Background Knowledge of the genetic etiology of epilepsy can provide essential prognostic information and influence decisions regarding treatment and management, leading us into the era of precision medicine. However, the genetic basis underlying epileptogenesis or epilepsy pharmacoresistance is not well-understood, particularly in non-familial epilepsies with heterogeneous phenotypes that last until or start in adulthood. Methods We sought to determine the contribution of known epilepsy-associated genes (EAGs) to the causation of non-familial epilepsies with heterogeneous phenotypes and to the genetic basis underlying epilepsy pharmacoresistance. We performed a multi-center study for whole exome sequencing-based screening of 178 selected EAGs in 243 non-familial adult patients with primarily focal epilepsy (122 drug-resistant and 121 drug-responsive epilepsies). The pathogenicity of each variant was assessed through a customized stringent filtering process and classified according to the American College of Medical Genetics and Genomics guidelines. Results Possible causal genetic variants of epilepsy were uncovered in 13.2% of non-familial patients with primarily focal epilepsy. The diagnostic yield according to the seizure onset age was 25% (2/8) in the neonatal and infantile period, 11.1% (14/126) in childhood and 14.7% (16/109) in adulthood. The higher diagnostic yields were from ion channel-related genes and mTOR pathway-related genes, which does not significantly differ from the results of previous studies on familial or early-onset epilepsies. These potentially pathogenic variants, which were identified in genes that have been mainly associated with early-onset epilepsies with severe phenotypes, were also linked to epilepsies that start in or last until adulthood in this study. This finding suggested the presence of one or more disease-modifying factors that regulate the onset time or severity of epileptogenesis. The target hypothesis of epilepsy pharmacoresi…
format: application/pdf
format: text/html
creator: Kyung Wook Kang
creator: Wonkuk Kim
creator: Yong Won Cho
creator: Sang Kun Lee
creator: Ki-Young Jung
creator: Wonchul Shin
creator: Dong Wook Kim
creator: Won-Joo Kim
creator: Hyang Woon Lee
creator: Woojun Kim
creator: Keuntae Kim
creator: So-Hyun Lee
creator: Seok-Yong Choi
creator: Myeong-Kyu Kim
subject: Genetics
subject: Neurology
description: doi:10.7717/peerj.8278
publisher: PeerJ Inc.
rights: © 2019 Kang et al.
abstract: Background Knowledge of the genetic etiology of epilepsy can provide essential prognostic information and influence decisions regarding treatment and management, leading us into the era of precision medicine. However, the genetic basis underlying epileptogenesis or epilepsy pharmacoresistance is not well-understood, particularly in non-familial epilepsies with heterogeneous phenotypes that last until or start in adulthood. Methods We sought to determine the contribution of known epilepsy-associated genes (EAGs) to the causation of non-familial epilepsies with heterogeneous phenotypes and to the genetic basis underlying epilepsy pharmacoresistance. We performed a multi-center study for whole exome sequencing-based screening of 178 selected EAGs in 243 non-familial adult patients with primarily focal epilepsy (122 drug-resistant and 121 drug-responsive epilepsies). The pathogenicity of each variant was assessed through a customized stringent filtering process and classified according to the American College of Medical Genetics and Genomics guidelines. Results Possible causal genetic variants of epilepsy were uncovered in 13.2% of non-familial patients with primarily focal epilepsy. The diagnostic yield according to the seizure onset age was 25% (2/8) in the neonatal and infantile period, 11.1% (14/126) in childhood and 14.7% (16/109) in adulthood. The higher diagnostic yields were from ion channel-related genes and mTOR pathway-related genes, which does not significantly differ from the results of previous studies on familial or early-onset epilepsies. These potentially pathogenic variants, which were identified in genes that have been mainly associated with early-onset epilepsies with severe phenotypes, were also linked to epilepsies that start in or last until adulthood in this study. This finding suggested the presence of one or more disease-modifying factors that regulate the onset time or severity of epileptogenesis. The target hypothesis of epilepsy pharmacoresi…
bibliographic citation: Kang et al. (2019) Genetic characteristics of non-familial epilepsy. PeerJ 7:e8278 https://doi.org/10.7717/peerj.8278
date submitted: 2019-06-25
date accepted: 2019-11-22
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Kyung Wook
author list: Agent
  family name: Kim
  given name: Wonkuk
author list: Agent
  family name: Cho
  given name: Yong Won
author list: Agent
  family name: Lee
  given name: Sang Kun
author list: Agent
  family name: Jung
  given name: Ki-Young
author list: Agent
  family name: Shin
  given name: Wonchul
author list: Agent
  family name: Kim
  given name: Dong Wook
author list: Agent
  family name: Kim
  given name: Won-Joo
author list: Agent
  family name: Lee
  given name: Hyang Woon
author list: Agent
  family name: Kim
  given name: Woojun
author list: Agent
  family name: Kim
  given name: Keuntae
author list: Agent
  family name: Lee
  given name: So-Hyun
author list: Agent
  family name: Choi
  given name: Seok-Yong
author list: Agent
  family name: Kim
  given name: Myeong-Kyu
doi: 10.7717/peerj.8278
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: © 2019 Kang et al.
attribution name: Kang et al.

Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats
type: item
type: AcademicArticle
description: Background Traumatic brain injury (TBI) is a common neurological emergency observed in hospitals. A considerable number of patients suffer from long-term disabilities after TBI. This study aimed to identify altered gene expression signatures and mechanisms related to TBI-induced chronic neuroinflammation and neurodegeneration. Methods An integrated analysis was performed using published RNA-sequencing studies to determine TBI-induced differentially expressed genes (DEGs). Based on the DEG data, functional annotation, signal-net, and transcription factor analyses were conducted to understand the mechanism of chronic neuroinflammation and neurodegeneration induced after TBI. Results Two datasets were obtained using the Gene Expression Omnibus database, of which, 6,513 DEGs were identified (6,464 upregulated and 49 downregulated). Positive regulation of biological process, positive regulation of cellular process, nucleus, and heterocyclic compound binding were Gene Ontology terms significantly enriched in post-TBI rat models. Leukocyte transendothelial migration, chemokine signaling pathway, neurotrophin signaling pathway, and longevity-regulating pathway were significantly enriched after TBI. With regard to the signal-net analysis, FOXO3, DGKZ and ILK were considered the most critical genes derived using high–betweenness centrality calculation. A total of 44 TFs, including FOXO1, SRY and KLF4, were predicted to play an important role in the upregulation of gene expression. Using integrated bioinformatics analysis, TBI was found to be associated with a significant inflammatory response and neurodegeneration. FOXO3, apolipoprotein (APOE), microtubule-associated protein tau (MAPT), and TREM2 were probably associated with the TBI pathological process. The mitochondrial electron transport chain may be associated with neurodegeneration in patients with TBI, serving as a potential therapeutic target.
format: application/pdf
format: text/html
creator: Jianwei Zhao
creator: Chen Xu
creator: Heli Cao
creator: Lin Zhang
creator: Xuyang Wang
creator: Shiwen Chen
subject: Bioinformatics
subject: Emergency and Critical Care
subject: Neurology
description: doi:10.7717/peerj.8324
publisher: PeerJ Inc.
rights: © 2019 Zhao et al.
abstract: Background Traumatic brain injury (TBI) is a common neurological emergency observed in hospitals. A considerable number of patients suffer from long-term disabilities after TBI. This study aimed to identify altered gene expression signatures and mechanisms related to TBI-induced chronic neuroinflammation and neurodegeneration. Methods An integrated analysis was performed using published RNA-sequencing studies to determine TBI-induced differentially expressed genes (DEGs). Based on the DEG data, functional annotation, signal-net, and transcription factor analyses were conducted to understand the mechanism of chronic neuroinflammation and neurodegeneration induced after TBI. Results Two datasets were obtained using the Gene Expression Omnibus database, of which, 6,513 DEGs were identified (6,464 upregulated and 49 downregulated). Positive regulation of biological process, positive regulation of cellular process, nucleus, and heterocyclic compound binding were Gene Ontology terms significantly enriched in post-TBI rat models. Leukocyte transendothelial migration, chemokine signaling pathway, neurotrophin signaling pathway, and longevity-regulating pathway were significantly enriched after TBI. With regard to the signal-net analysis, FOXO3, DGKZ and ILK were considered the most critical genes derived using high–betweenness centrality calculation. A total of 44 TFs, including FOXO1, SRY and KLF4, were predicted to play an important role in the upregulation of gene expression. Using integrated bioinformatics analysis, TBI was found to be associated with a significant inflammatory response and neurodegeneration. FOXO3, apolipoprotein (APOE), microtubule-associated protein tau (MAPT), and TREM2 were probably associated with the TBI pathological process. The mitochondrial electron transport chain may be associated with neurodegeneration in patients with TBI, serving as a potential therapeutic target.
bibliographic citation: Zhao et al. (2019) Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats. PeerJ 7:e8324 https://doi.org/10.7717/peerj.8324
date submitted: 2019-09-13
date accepted: 2019-12-01
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Jianwei
author list: Agent
  family name: Xu
  given name: Chen
author list: Agent
  family name: Cao
  given name: Heli
author list: Agent
  family name: Zhang
  given name: Lin
author list: Agent
  family name: Wang
  given name: Xuyang
author list: Agent
  family name: Chen
  given name: Shiwen
doi: 10.7717/peerj.8324
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: © 2019 Zhao et al.
attribution name: Zhao et al.

Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis
type: item
type: AcademicArticle
description: Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens inclu…
format: application/pdf
format: text/html
creator: Ahmad Bazli Ramzi
creator: Muhammad Lutfi Che Me
creator: Ummul Syafiqah Ruslan
creator: Syarul Nataqain Baharum
creator: Nor Azlan Nor Muhammad
subject: Agricultural Science
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
description: doi:10.7717/peerj.8065
publisher: PeerJ Inc.
rights: © 2019 Ramzi et al.
abstract: Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens inclu…
bibliographic citation: Ramzi et al. (2019) Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ 7:e8065 https://doi.org/10.7717/peerj.8065
date submitted: 2019-01-05
date accepted: 2019-10-20
issued: 2019-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramzi
  given name: Ahmad Bazli
author list: Agent
  family name: Che Me
  given name: Muhammad Lutfi
author list: Agent
  family name: Ruslan
  given name: Ummul Syafiqah
author list: Agent
  family name: Baharum
  given name: Syarul Nataqain
author list: Agent
  family name: Nor Muhammad
  given name: Nor Azlan
doi: 10.7717/peerj.8065
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-18
copyright: ©2019 Ramzi et al.
attribution name: Ramzi et al.

Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies
type: item
type: AcademicArticle
description: Improved understanding of properties that mediate protein solubility and resistance to aggregation are important for developing biopharmaceuticals, and more generally in biotechnology and synthetic biology. Recent acquisition of large datasets for antibody biophysical properties enables the search for predictive models. In this report, machine learning methods are used to derive models for 12 biophysical properties. A physicochemical perspective is maintained in analysing the models, leading to the observation that models cluster largely according to charge (cross-interaction measurements) and hydrophobicity (self-interaction methods). These two properties also overlap in some cases, for example in a new interpretation of variation in hydrophobic interaction chromatography. Since the models are developed from differences of antibody variable loops, the next stage is to extend models to more diverse protein sets. Availability The web application for the sequence-based algorithms are available on the protein-sol webserver, at https://protein-sol.manchester.ac.uk/abpred, with models and virtualisation software available at https://protein-sol.manchester.ac.uk/software.
format: application/pdf
format: text/html
creator: Max Hebditch
creator: Jim Warwicker
subject: Biochemistry
subject: Bioinformatics
subject: Biophysics
subject: Biotechnology
subject: Computational Biology
description: doi:10.7717/peerj.8199
publisher: PeerJ Inc.
rights: © 2019 Hebditch and Warwicker
abstract: Improved understanding of properties that mediate protein solubility and resistance to aggregation are important for developing biopharmaceuticals, and more generally in biotechnology and synthetic biology. Recent acquisition of large datasets for antibody biophysical properties enables the search for predictive models. In this report, machine learning methods are used to derive models for 12 biophysical properties. A physicochemical perspective is maintained in analysing the models, leading to the observation that models cluster largely according to charge (cross-interaction measurements) and hydrophobicity (self-interaction methods). These two properties also overlap in some cases, for example in a new interpretation of variation in hydrophobic interaction chromatography. Since the models are developed from differences of antibody variable loops, the next stage is to extend models to more diverse protein sets. Availability The web application for the sequence-based algorithms are available on the protein-sol webserver, at https://protein-sol.manchester.ac.uk/abpred, with models and virtualisation software available at https://protein-sol.manchester.ac.uk/software.
bibliographic citation: Hebditch et al. (2019) Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies. PeerJ 7:e8199 https://doi.org/10.7717/peerj.8199
date submitted: 2019-08-28
date accepted: 2019-11-13
issued: 2019-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hebditch
  given name: Max
author list: Agent
  family name: Warwicker
  given name: Jim
doi: 10.7717/peerj.8199
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-18
copyright: ©2019 Hebditch and Warwicker
attribution name: Hebditch and Warwicker

Epidemiology of multiple sclerosis and vitamin D levels in Lanzarote, Canary Islands, Spain
type: item
type: AcademicArticle
description: Background Low levels of 25-hydroxyvitamin D (25(OH)D) have been described as one of the possible environmental factors involved in multiple sclerosis (MS) etiopathogenesis. Objectives To study epidemiology of MS and 25(OH)D serum levels of patients in Lanzarote (29°02′06″N), a region with high ultraviolet radiation values during the whole year which is located far apart from Iberian Peninsula (36°–43°N), but without genetic/ethnic differences with it. Methods Incidence in Lanzarote was assessed according to McDonald 2005 criteria between January 2008 and December 2015 and prevalence date was 12/31/15. For 25(OH)D serum levels analyses, samples from 60 MS patients and 60 healthy donors (HD) were collected monthly in a one-year prospective study. Results The prevalence of MS in Lanzarote was 50.0/100,000 and the incidence per year was 2.5/100,000. Median 25(OH)D levels values were 29.1 ng/ml for MS patients (maximum = 36.1 ng/ml, minimum = 22.5 ng/ml) and 27.1 ng/ml for HD (maximum = 34.8 ng/ml, minimum = 22.8 ng/ml). There were no significant differences between 25(OH)D serum levels between MS patients and HD. Conclusions Lanzarote possesses lower prevalence and incidence values than peninsular Spain. Moreover, 25(OH)D serum levels do not differ between MS patients and HD.
format: application/pdf
format: text/html
creator: Silvia Pérez-Pérez
creator: Pablo Eguia del Rio
creator: María Inmaculada Domínguez-Mozo
creator: María Ángel García-Martínez
creator: María Francisca Zapata-Ramos
creator: Maria Jose Torrejon
creator: Rafael Arroyo
creator: Roberto Alvarez-Lafuente
subject: Epidemiology
subject: Neurology
subject: Public Health
description: doi:10.7717/peerj.8235
publisher: PeerJ Inc.
rights: © 2019 Pérez-Pérez et al.
abstract: Background Low levels of 25-hydroxyvitamin D (25(OH)D) have been described as one of the possible environmental factors involved in multiple sclerosis (MS) etiopathogenesis. Objectives To study epidemiology of MS and 25(OH)D serum levels of patients in Lanzarote (29°02′06″N), a region with high ultraviolet radiation values during the whole year which is located far apart from Iberian Peninsula (36°–43°N), but without genetic/ethnic differences with it. Methods Incidence in Lanzarote was assessed according to McDonald 2005 criteria between January 2008 and December 2015 and prevalence date was 12/31/15. For 25(OH)D serum levels analyses, samples from 60 MS patients and 60 healthy donors (HD) were collected monthly in a one-year prospective study. Results The prevalence of MS in Lanzarote was 50.0/100,000 and the incidence per year was 2.5/100,000. Median 25(OH)D levels values were 29.1 ng/ml for MS patients (maximum = 36.1 ng/ml, minimum = 22.5 ng/ml) and 27.1 ng/ml for HD (maximum = 34.8 ng/ml, minimum = 22.8 ng/ml). There were no significant differences between 25(OH)D serum levels between MS patients and HD. Conclusions Lanzarote possesses lower prevalence and incidence values than peninsular Spain. Moreover, 25(OH)D serum levels do not differ between MS patients and HD.
bibliographic citation: Pérez-Pérez et al. (2019) Epidemiology of multiple sclerosis and vitamin D levels in Lanzarote, Canary Islands, Spain. PeerJ 7:e8235 https://doi.org/10.7717/peerj.8235
date submitted: 2019-08-06
date accepted: 2019-11-18
issued: 2019-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pérez-Pérez
  given name: Silvia
author list: Agent
  family name: Eguia del Rio
  given name: Pablo
author list: Agent
  family name: Domínguez-Mozo
  given name: María Inmaculada
author list: Agent
  family name: García-Martínez
  given name: María Ángel
author list: Agent
  family name: Zapata-Ramos
  given name: María Francisca
author list: Agent
  family name: Torrejon
  given name: Maria Jose
author list: Agent
  family name: Arroyo
  given name: Rafael
author list: Agent
  family name: Alvarez-Lafuente
  given name: Roberto
doi: 10.7717/peerj.8235
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-18
copyright: ©2019 Pérez-Pérez et al.
attribution name: Pérez-Pérez et al.

First evidence of underwater vocalisations in hunting penguins
type: item
type: AcademicArticle
description: Seabirds are highly vocal on land where acoustic communication plays a crucial role in reproduction. Yet, seabirds spend most of their life at sea. They have developed a number of morphological, physiological and behavioural adaptations to forage in the marine environment. The use of acoustic signals at sea could potentially enhance seabirds’ foraging success, but remains largely unexplored. Penguins emit vocalisations from the sea surface when commuting, a behaviour possibly associated with group formation at sea. Still, they are unique in their exceptional diving abilities and feed entirely underwater. Other air-breathing marine predators that feed under water, like cetaceans, pinnipeds and marine turtles, are known to emit sound underwater, but such behaviour has not yet been described in seabirds. We aimed to assess the potential prevalence and diversity of vocalisations emitted underwater by penguins. We chose three study species from three different genera, and equipped foraging adults with video cameras with built-in microphones. We recorded a total of 203 underwater vocalisation from all three species during 4 h 43 min of underwater footage. Vocalisations were very short in duration (0.06 s on average), with a frequency of maximum amplitude averaging 998 Hz, 1097 Hz and 680 Hz for King, Gentoo and Macaroni penguins, respectively. All vocalisations were emitted during feeding dives and more than 50% of them were directly associated with hunting behaviour, preceeded by an acceleration (by 2.2 s on average) and/or followed by a prey capture attempt (after 0.12 s on average). The function of these vocalisations remain speculative. Although it seems to be related to hunting behaviour, these novel observations warrant further investigation.
format: application/pdf
format: text/html
creator: Andréa Thiebault
creator: Isabelle Charrier
creator: Thierry Aubin
creator: David B. Green
creator: Pierre A. Pistorius
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.8240
publisher: PeerJ Inc.
rights: © 2019 Thiebault et al.
abstract: Seabirds are highly vocal on land where acoustic communication plays a crucial role in reproduction. Yet, seabirds spend most of their life at sea. They have developed a number of morphological, physiological and behavioural adaptations to forage in the marine environment. The use of acoustic signals at sea could potentially enhance seabirds’ foraging success, but remains largely unexplored. Penguins emit vocalisations from the sea surface when commuting, a behaviour possibly associated with group formation at sea. Still, they are unique in their exceptional diving abilities and feed entirely underwater. Other air-breathing marine predators that feed under water, like cetaceans, pinnipeds and marine turtles, are known to emit sound underwater, but such behaviour has not yet been described in seabirds. We aimed to assess the potential prevalence and diversity of vocalisations emitted underwater by penguins. We chose three study species from three different genera, and equipped foraging adults with video cameras with built-in microphones. We recorded a total of 203 underwater vocalisation from all three species during 4 h 43 min of underwater footage. Vocalisations were very short in duration (0.06 s on average), with a frequency of maximum amplitude averaging 998 Hz, 1097 Hz and 680 Hz for King, Gentoo and Macaroni penguins, respectively. All vocalisations were emitted during feeding dives and more than 50% of them were directly associated with hunting behaviour, preceeded by an acceleration (by 2.2 s on average) and/or followed by a prey capture attempt (after 0.12 s on average). The function of these vocalisations remain speculative. Although it seems to be related to hunting behaviour, these novel observations warrant further investigation.
bibliographic citation: Thiebault et al. (2019) First evidence of underwater vocalisations in hunting penguins. PeerJ 7:e8240 https://doi.org/10.7717/peerj.8240
date submitted: 2019-10-01
date accepted: 2019-11-19
issued: 2019-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thiebault
  given name: Andréa
author list: Agent
  family name: Charrier
  given name: Isabelle
author list: Agent
  family name: Aubin
  given name: Thierry
author list: Agent
  family name: Green
  given name: David B.
author list: Agent
  family name: Pistorius
  given name: Pierre A.
doi: 10.7717/peerj.8240
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-18
copyright: © 2019 Thiebault et al.
attribution name: Thiebault et al.

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