PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Phytobiomes are compositionally nested from the ground up
items: A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya
items: Vocal recognition of a nest-predator in black grouse
items: Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
items: Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students
items: Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
items: Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
items: Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna
items: Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand
items: Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken

Phytobiomes are compositionally nested from the ground up
type: item
type: AcademicArticle
description: Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
format: application/pdf
format: text/html
creator: Anthony S. Amend
creator: Gerald M. Cobian
creator: Aki J. Laruson
creator: Kristina Remple
creator: Sarah J. Tucker
creator: Kirsten E. Poff
creator: Carmen Antaky
creator: Andre Boraks
creator: Casey A. Jones
creator: Donna Kuehu
creator: Becca R. Lensing
creator: Mersedeh Pejhanmehr
creator: Daniel T. Richardson
creator: Paul P. Riley
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6609
publisher: PeerJ Inc.
rights: © 2019 Amend et al.
abstract: Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
bibliographic citation: Amend et al. (2019) Phytobiomes are compositionally nested from the ground up. PeerJ 7:e6609 https://doi.org/10.7717/peerj.6609
date submitted: 2018-11-26
date accepted: 2019-02-04
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amend
  given name: Anthony S.
author list: Agent
  family name: Cobian
  given name: Gerald M.
author list: Agent
  family name: Laruson
  given name: Aki J.
author list: Agent
  family name: Remple
  given name: Kristina
author list: Agent
  family name: Tucker
  given name: Sarah J.
author list: Agent
  family name: Poff
  given name: Kirsten E.
author list: Agent
  family name: Antaky
  given name: Carmen
author list: Agent
  family name: Boraks
  given name: Andre
author list: Agent
  family name: Jones
  given name: Casey A.
author list: Agent
  family name: Kuehu
  given name: Donna
author list: Agent
  family name: Lensing
  given name: Becca R.
author list: Agent
  family name: Pejhanmehr
  given name: Mersedeh
author list: Agent
  family name: Richardson
  given name: Daniel T.
author list: Agent
  family name: Riley
  given name: Paul P.
doi: 10.7717/peerj.6609
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Amend et al.
attribution name: Amend et al.

A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya
type: item
type: AcademicArticle
description: Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV …
format: application/pdf
format: text/html
creator: James M. Wainaina
creator: Elijah Ateka
creator: Timothy Makori
creator: Monica A. Kehoe
creator: Laura M. Boykin
subject: Agricultural Science
subject: Virology
description: doi:10.7717/peerj.6465
publisher: PeerJ Inc.
rights: © 2019 Wainana et al.
abstract: Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV …
bibliographic citation: Wainaina et al. (2019) A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ 7:e6465 https://doi.org/10.7717/peerj.6465
date submitted: 2018-07-17
date accepted: 2019-01-16
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wainaina
  given name: James M.
author list: Agent
  family name: Ateka
  given name: Elijah
author list: Agent
  family name: Makori
  given name: Timothy
author list: Agent
  family name: Kehoe
  given name: Monica A.
author list: Agent
  family name: Boykin
  given name: Laura M.
doi: 10.7717/peerj.6465
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: © 2019 Wainana et al.
attribution name: Wainana et al.

Vocal recognition of a nest-predator in black grouse
type: item
type: AcademicArticle
description: Corvids count among the important predators of bird nests. They are vocal animals and one can expect that birds threatened by their predation, such as black grouse, are sensitive to and recognize their calls. Within the framework of field studies, we noticed that adult black grouse were alerted by raven calls during periods outside the breeding season. Since black grouse are large, extremely precocial birds, this reaction can hardly be explained by sensitization specifically to the threat of nest predation by ravens. This surprising observation prompted us to study the phenomenon more systematically. According to our knowledge, the response of birds to corvid vocalization has been studied in altricial birds only. We tested whether the black grouse distinguishes and responds specifically to playback calls of the common raven. Black grouse recognized raven calls and were alerted, displaying typical neck stretching, followed by head scanning, and eventual escape. Surprisingly, males tended to react faster and exhibited a longer duration of vigilance behavior compared to females. Although raven calls are recognized by adult black grouse out of the nesting period, they are not directly endangered by the raven. We speculate that the responsiveness of adult grouse to raven calls might be explained as a learned response in juveniles from nesting hens that is then preserved in adults, or by a known association between the raven and the red fox. In that case, calls of the raven would be rather interpreted as a warning signal of probable proximity of the red fox.
format: application/pdf
format: text/html
creator: Richard Policht
creator: Vlastimil Hart
creator: Denis Goncharov
creator: Peter Surový
creator: Vladimír Hanzal
creator: Jaroslav Červený
creator: Hynek Burda
subject: Animal Behavior
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.6533
publisher: PeerJ Inc.
rights: © 2019 Policht et al.
abstract: Corvids count among the important predators of bird nests. They are vocal animals and one can expect that birds threatened by their predation, such as black grouse, are sensitive to and recognize their calls. Within the framework of field studies, we noticed that adult black grouse were alerted by raven calls during periods outside the breeding season. Since black grouse are large, extremely precocial birds, this reaction can hardly be explained by sensitization specifically to the threat of nest predation by ravens. This surprising observation prompted us to study the phenomenon more systematically. According to our knowledge, the response of birds to corvid vocalization has been studied in altricial birds only. We tested whether the black grouse distinguishes and responds specifically to playback calls of the common raven. Black grouse recognized raven calls and were alerted, displaying typical neck stretching, followed by head scanning, and eventual escape. Surprisingly, males tended to react faster and exhibited a longer duration of vigilance behavior compared to females. Although raven calls are recognized by adult black grouse out of the nesting period, they are not directly endangered by the raven. We speculate that the responsiveness of adult grouse to raven calls might be explained as a learned response in juveniles from nesting hens that is then preserved in adults, or by a known association between the raven and the red fox. In that case, calls of the raven would be rather interpreted as a warning signal of probable proximity of the red fox.
bibliographic citation: Policht et al. (2019) Vocal recognition of a nest-predator in black grouse. PeerJ 7:e6533 https://doi.org/10.7717/peerj.6533
date submitted: 2018-12-12
date accepted: 2019-01-26
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Policht
  given name: Richard
author list: Agent
  family name: Hart
  given name: Vlastimil
author list: Agent
  family name: Goncharov
  given name: Denis
author list: Agent
  family name: Surový
  given name: Peter
author list: Agent
  family name: Hanzal
  given name: Vladimír
author list: Agent
  family name: Červený
  given name: Jaroslav
author list: Agent
  family name: Burda
  given name: Hynek
doi: 10.7717/peerj.6533
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: ©2019 Policht et al.
attribution name: Policht et al.

Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
type: item
type: AcademicArticle
description: Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical event…
format: application/pdf
format: text/html
creator: María Eugenia Arnaudo
creator: Néstor Toledo
creator: Leopoldo Soibelzon
creator: Paula Bona
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6597
publisher: PeerJ Inc.
rights: © 2019 Arnaudo et al.
abstract: Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical event…
bibliographic citation: Arnaudo et al. (2019) Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia). PeerJ 7:e6597 https://doi.org/10.7717/peerj.6597
date submitted: 2018-03-08
date accepted: 2019-02-09
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arnaudo
  given name: María Eugenia
author list: Agent
  family name: Toledo
  given name: Néstor
author list: Agent
  family name: Soibelzon
  given name: Leopoldo
author list: Agent
  family name: Bona
  given name: Paula
doi: 10.7717/peerj.6597
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: ©2019 Arnaudo et al.
attribution name: Arnaudo et al.

Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students
type: item
type: AcademicArticle
description: Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.
format: application/pdf
format: text/html
creator: Michael William Smith
creator: David Abarca Rondero
subject: Cardiology
subject: Emergency and Critical Care
subject: Science and Medical Education
description: doi:10.7717/peerj.6632
publisher: PeerJ Inc.
rights: © 2019 Smith and Abarca Rondero
abstract: Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.
bibliographic citation: Smith et al. (2019) Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students. PeerJ 7:e6632 https://doi.org/10.7717/peerj.6632
date submitted: 2018-10-16
date accepted: 2019-02-16
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Michael William
author list: Agent
  family name: Abarca Rondero
  given name: David
doi: 10.7717/peerj.6632
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: © 2019 Smith and Abarca Rondero
attribution name: Smith and Abarca Rondero

Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
type: item
type: AcademicArticle
description: Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
format: application/pdf
format: text/html
creator: Nan Lu
creator: Wenjun Ma
creator: Donghua Han
creator: Ying Liu
creator: Zhi Wang
creator: Nan Wang
creator: Guijuan Yang
creator: Guanzheng Qu
creator: Qiuxia Wang
creator: Kun Zhao
creator: Junhui Wang
subject: Agricultural Science
subject: Forestry
description: doi:10.7717/peerj.6520
publisher: PeerJ Inc.
rights: © 2019 Lu et al.
abstract: Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
bibliographic citation: Lu et al. (2019) Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood. PeerJ 7:e6520 https://doi.org/10.7717/peerj.6520
date submitted: 2018-11-20
date accepted: 2019-01-22
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Nan
author list: Agent
  family name: Ma
  given name: Wenjun
author list: Agent
  family name: Han
  given name: Donghua
author list: Agent
  family name: Liu
  given name: Ying
author list: Agent
  family name: Wang
  given name: Zhi
author list: Agent
  family name: Wang
  given name: Nan
author list: Agent
  family name: Yang
  given name: Guijuan
author list: Agent
  family name: Qu
  given name: Guanzheng
author list: Agent
  family name: Wang
  given name: Qiuxia
author list: Agent
  family name: Zhao
  given name: Kun
author list: Agent
  family name: Wang
  given name: Junhui
doi: 10.7717/peerj.6520
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: ©2019 Lu et al.
attribution name: Lu et al.

Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
type: item
type: AcademicArticle
description: Background Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein–protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. Results To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the “Stage” of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
format: application/pdf
format: text/html
creator: Wang-Xiao Xia
creator: Qin Yu
creator: Gong-Hua Li
creator: Yao-Wen Liu
creator: Fu-Hui Xiao
creator: Li-Qin Yang
creator: Zia Ur Rahman
creator: Hao-Tian Wang
creator: Qing-Peng Kong
subject: Bioinformatics
subject: Genetics
subject: Oncology
description: doi:10.7717/peerj.6555
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: Background Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein–protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. Results To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the “Stage” of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
bibliographic citation: Xia et al. (2019) Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA. PeerJ 7:e6555 https://doi.org/10.7717/peerj.6555
date submitted: 2018-10-25
date accepted: 2019-02-02
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Wang-Xiao
author list: Agent
  family name: Yu
  given name: Qin
author list: Agent
  family name: Li
  given name: Gong-Hua
author list: Agent
  family name: Liu
  given name: Yao-Wen
author list: Agent
  family name: Xiao
  given name: Fu-Hui
author list: Agent
  family name: Yang
  given name: Li-Qin
author list: Agent
  family name: Rahman
  given name: Zia Ur
author list: Agent
  family name: Wang
  given name: Hao-Tian
author list: Agent
  family name: Kong
  given name: Qing-Peng
doi: 10.7717/peerj.6555
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna
type: item
type: AcademicArticle
description: Dibutyl phthalate (DBP) poses a severe threat to aquatic ecosystems, introducing hazards to both aquatic species and human health. The ecotoxic effects of DBP on aquatic organisms have not been fully investigated. This study investigates acute toxicity, oxidative damage, and antioxidant enzyme parameters in neonate and adult Daphnia magna exposed to DBP. The obtained results show comparable DBP toxic responses in neonates and adults. The median lethal concentrations (LC50) of DBP in neonates exposed for 24 and 48 h were 3.48 and 2.83 mg/L, respectively. The LC50 of adults for the same DBP exposure durations were 4.92 and 4.31 mg/L, respectively. Increased hydrogen peroxide and malondialdehyde were found in neonates and adults at both 24 and 48 h, while the total antioxidant capacity decreased. Superoxide dismutase activity increased significantly in neonates and adults exposed to 0.5 mg/L DBP, and subsequently diminished at higher DBP concentrations and prolonged exposure. Catalase and glutathione S-transferases activities both decreased markedly in neonates and adults. The changes observed were found to be time and concentration dependent. Overall, these data indicated that the acute toxic effects of DBP exposure on neonates were more pronounced than in adults, and oxidative injury may be the main mechanism of DBP toxicity. These results provide a functional link for lipid peroxidation, antioxidant capacity, and antioxidant enzyme levels in the Daphnia magna response to DBP exposure.
format: application/pdf
format: text/html
creator: Chenchen Shen
creator: Jie Wei
creator: Tianyi Wang
creator: Yuan Wang
subject: Ecotoxicology
subject: Freshwater Biology
description: doi:10.7717/peerj.6584
publisher: PeerJ Inc.
rights: © 2019 Shen et al.
abstract: Dibutyl phthalate (DBP) poses a severe threat to aquatic ecosystems, introducing hazards to both aquatic species and human health. The ecotoxic effects of DBP on aquatic organisms have not been fully investigated. This study investigates acute toxicity, oxidative damage, and antioxidant enzyme parameters in neonate and adult Daphnia magna exposed to DBP. The obtained results show comparable DBP toxic responses in neonates and adults. The median lethal concentrations (LC50) of DBP in neonates exposed for 24 and 48 h were 3.48 and 2.83 mg/L, respectively. The LC50 of adults for the same DBP exposure durations were 4.92 and 4.31 mg/L, respectively. Increased hydrogen peroxide and malondialdehyde were found in neonates and adults at both 24 and 48 h, while the total antioxidant capacity decreased. Superoxide dismutase activity increased significantly in neonates and adults exposed to 0.5 mg/L DBP, and subsequently diminished at higher DBP concentrations and prolonged exposure. Catalase and glutathione S-transferases activities both decreased markedly in neonates and adults. The changes observed were found to be time and concentration dependent. Overall, these data indicated that the acute toxic effects of DBP exposure on neonates were more pronounced than in adults, and oxidative injury may be the main mechanism of DBP toxicity. These results provide a functional link for lipid peroxidation, antioxidant capacity, and antioxidant enzyme levels in the Daphnia magna response to DBP exposure.
bibliographic citation: Shen et al. (2019) Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna. PeerJ 7:e6584 https://doi.org/10.7717/peerj.6584
date submitted: 2018-11-25
date accepted: 2019-02-06
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Chenchen
author list: Agent
  family name: Wei
  given name: Jie
author list: Agent
  family name: Wang
  given name: Tianyi
author list: Agent
  family name: Wang
  given name: Yuan
doi: 10.7717/peerj.6584
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Shen et al.
attribution name: Shen et al.

Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand
type: item
type: AcademicArticle
description: Background Staphylococcus spp. are major cause of bovine mastitis (BM) worldwide leading to economic damage to dairy farms and public health threat. Recently, a newly emerged Staphylococcus argenteus has been found as a human and animal pathogen. Molecular characteristics, virulence and antibiotic resistant phenotypes of bacteria causing BM in Thailand are rare. This study aimed to investigated Staphylococcus spp. associated with subclinical bovine mastitis (SCM) in Thailand. Methods Milk samples were collected from 224 cows of 52 dairy herds in four central and northeast provinces. Total somatic cell counts (SCC) and California mastitis test (CMT) were used to identify SCM cows. Milk samples were cultured for Staphylococcus spp. Coagulase-positive isolates were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Organisms suspected as S. argenteus were verified by detecting nonribosomal peptide synthetase gene. All isolates were checked for antibiograms and the presence of various virulence genes. Results From the 224 milk samples of 224 cows, 132 (59%) were positive for SCM by SCC and CMT and 229 staphylococcal isolates were recovered. They were 32 coagulase-positive (24 S. aureus and eight S. argenteus) and 197 coagulase-negative. PFGE of the S. aureus and S. argenteus revealed 11 clusters and a non-typeable pattern. MLST of representatives of the 11 PFGE clusters, three PFGE non-typeable S. aureus isolates from different locations and S. argenteus showed 12 sequence types. The eight S. argenteus isolates belonged to ST1223 (three isolates), ST2250 (two isolates), and ST2793 (two isolates). The antimicrobial tests identified 11 (46%) methicillin-resistant S. aureus and 25 (13%) methicillin-resistant coagulase-negative isolates, while seven S. argenteus were methicillin-susceptible and one isolate was methicillin-resistant. All of the 229 isolates were multiply resistant to other antibiotics. The most prevalent virulence gen…
format: application/pdf
format: text/html
creator: Natapol Pumipuntu
creator: Witawat Tunyong
creator: Narisara Chantratita
creator: Pornphan Diraphat
creator: Pornpan Pumirat
creator: Nitat Sookrung
creator: Wanpen Chaicumpa
creator: Nitaya Indrawattana
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.6587
publisher: PeerJ Inc.
rights: © 2019 Pumipuntu et al.
abstract: Background Staphylococcus spp. are major cause of bovine mastitis (BM) worldwide leading to economic damage to dairy farms and public health threat. Recently, a newly emerged Staphylococcus argenteus has been found as a human and animal pathogen. Molecular characteristics, virulence and antibiotic resistant phenotypes of bacteria causing BM in Thailand are rare. This study aimed to investigated Staphylococcus spp. associated with subclinical bovine mastitis (SCM) in Thailand. Methods Milk samples were collected from 224 cows of 52 dairy herds in four central and northeast provinces. Total somatic cell counts (SCC) and California mastitis test (CMT) were used to identify SCM cows. Milk samples were cultured for Staphylococcus spp. Coagulase-positive isolates were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Organisms suspected as S. argenteus were verified by detecting nonribosomal peptide synthetase gene. All isolates were checked for antibiograms and the presence of various virulence genes. Results From the 224 milk samples of 224 cows, 132 (59%) were positive for SCM by SCC and CMT and 229 staphylococcal isolates were recovered. They were 32 coagulase-positive (24 S. aureus and eight S. argenteus) and 197 coagulase-negative. PFGE of the S. aureus and S. argenteus revealed 11 clusters and a non-typeable pattern. MLST of representatives of the 11 PFGE clusters, three PFGE non-typeable S. aureus isolates from different locations and S. argenteus showed 12 sequence types. The eight S. argenteus isolates belonged to ST1223 (three isolates), ST2250 (two isolates), and ST2793 (two isolates). The antimicrobial tests identified 11 (46%) methicillin-resistant S. aureus and 25 (13%) methicillin-resistant coagulase-negative isolates, while seven S. argenteus were methicillin-susceptible and one isolate was methicillin-resistant. All of the 229 isolates were multiply resistant to other antibiotics. The most prevalent virulence gen…
bibliographic citation: Pumipuntu et al. (2019) Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand. PeerJ 7:e6587 https://doi.org/10.7717/peerj.6587
date submitted: 2018-11-12
date accepted: 2019-02-10
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pumipuntu
  given name: Natapol
author list: Agent
  family name: Tunyong
  given name: Witawat
author list: Agent
  family name: Chantratita
  given name: Narisara
author list: Agent
  family name: Diraphat
  given name: Pornphan
author list: Agent
  family name: Pumirat
  given name: Pornpan
author list: Agent
  family name: Sookrung
  given name: Nitat
author list: Agent
  family name: Chaicumpa
  given name: Wanpen
author list: Agent
  family name: Indrawattana
  given name: Nitaya
doi: 10.7717/peerj.6587
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Pumipuntu et al.
attribution name: Pumipuntu et al.

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken
type: item
type: AcademicArticle
description: The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillat…
format: application/pdf
format: text/html
creator: Anne-Sophie Charlotte Hieke
creator: Shawna Marie Hubert
creator: Giridhar Athrey
subject: Agricultural Science
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6592
publisher: PeerJ Inc.
rights: © 2019 Hieke et al.
abstract: The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillat…
bibliographic citation: Hieke et al. (2019) Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken. PeerJ 7:e6592 https://doi.org/10.7717/peerj.6592
date submitted: 2018-08-09
date accepted: 2019-02-09
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hieke
  given name: Anne-Sophie Charlotte
author list: Agent
  family name: Hubert
  given name: Shawna Marie
author list: Agent
  family name: Athrey
  given name: Giridhar
doi: 10.7717/peerj.6592
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Hieke et al.
attribution name: Hieke et al.

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