PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Chemovariation and antibacterial activity of extracts and isolated compounds from species of Ixora and Greenea (Ixoroideae, Rubiaceae)
items: Accuracy of a deep convolutional neural network in detection of retinitis pigmentosa on ultrawide-field images
items: Metacommunity patterns of Amazonian Odonata: the role of environmental gradients and major rivers
items: Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia
items: Optimization of extraction conditions and determination of purine content in marine fish during boiling
items: Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States
items: Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis
items: Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis
items: Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway
items: Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem

Chemovariation and antibacterial activity of extracts and isolated compounds from species of Ixora and Greenea (Ixoroideae, Rubiaceae)
type: item
type: AcademicArticle
description: Background A large number of secondary metabolites can be obtained from plants used for traditional medicine in two related genera (Ixora and Greenea) in the subfamily Ixoroideae (Rubiaceae), but there are only a few detailed studies on their bioactivities. Therefore, the main goals of this study were to determine the antibacterial activities of lipophilic extracts from plants of some Ixora and Greenea species native to Thailand, and to isolate some pure compounds from those extracts. Moreover, we compared the occurrence of compounds in different plant parts of samples from different habitats to better understand their variation. Methods A total of 56 lipophilic extracts were obtained from the leaves, stem bark, and root bark of eight Ixora and two Greenea species collected at various locations in Thailand. Isolated compounds were identified using nuclear magnetic resonance. Antimicrobial activities were evaluated against four Gram-positive and nine Gram-negative human pathogenic bacterial strains. Results Extracts from I. javanica, I. nigricans, I. brunonis, and G. montana, along with isolated scopoletin, exhibited antibacterial activities against Gram-positive methicillin-resistant Staphylococcus aureus ATCC 43300, with minimum inhibitory concentration values ranging from 64 to 256 µg/mL. The occurrence of scopoletin, isofraxidin, and geniposidic acid in lipophilic extracts showed some variation among different plant parts and species. Conclusions Lipophilic extracts of Ixora and Greenea species have the potential to be developed as anti-Gram-positive agents, in particular to counter infections of methicillin-resistant S. aureus strains. The chemical profiles showed differences between floristic regions but similarity within the same plant parts.
format: application/pdf
format: text/html
creator: Raveevatoo Buathong
creator: Voradol Chamchumroon
creator: Johann Schinnerl
creator: Markus Bacher
creator: Wichai Santimaleeworagun
creator: Ekaphan Kraichak
creator: Srunya Vajrodaya
subject: Plant Science
subject: Taxonomy
subject: Pharmacology
description: doi:10.7717/peerj.6893
publisher: PeerJ Inc.
rights: © 2019 Buathong et al.
abstract: Background A large number of secondary metabolites can be obtained from plants used for traditional medicine in two related genera (Ixora and Greenea) in the subfamily Ixoroideae (Rubiaceae), but there are only a few detailed studies on their bioactivities. Therefore, the main goals of this study were to determine the antibacterial activities of lipophilic extracts from plants of some Ixora and Greenea species native to Thailand, and to isolate some pure compounds from those extracts. Moreover, we compared the occurrence of compounds in different plant parts of samples from different habitats to better understand their variation. Methods A total of 56 lipophilic extracts were obtained from the leaves, stem bark, and root bark of eight Ixora and two Greenea species collected at various locations in Thailand. Isolated compounds were identified using nuclear magnetic resonance. Antimicrobial activities were evaluated against four Gram-positive and nine Gram-negative human pathogenic bacterial strains. Results Extracts from I. javanica, I. nigricans, I. brunonis, and G. montana, along with isolated scopoletin, exhibited antibacterial activities against Gram-positive methicillin-resistant Staphylococcus aureus ATCC 43300, with minimum inhibitory concentration values ranging from 64 to 256 µg/mL. The occurrence of scopoletin, isofraxidin, and geniposidic acid in lipophilic extracts showed some variation among different plant parts and species. Conclusions Lipophilic extracts of Ixora and Greenea species have the potential to be developed as anti-Gram-positive agents, in particular to counter infections of methicillin-resistant S. aureus strains. The chemical profiles showed differences between floristic regions but similarity within the same plant parts.
bibliographic citation: Buathong et al. (2019) Chemovariation and antibacterial activity of extracts and isolated compounds from species of Ixora and Greenea (Ixoroideae, Rubiaceae). PeerJ 7:e6893 https://doi.org/10.7717/peerj.6893
date submitted: 2018-11-11
date accepted: 2019-03-31
issued: 2019-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buathong
  given name: Raveevatoo
author list: Agent
  family name: Chamchumroon
  given name: Voradol
author list: Agent
  family name: Schinnerl
  given name: Johann
author list: Agent
  family name: Bacher
  given name: Markus
author list: Agent
  family name: Santimaleeworagun
  given name: Wichai
author list: Agent
  family name: Kraichak
  given name: Ekaphan
author list: Agent
  family name: Vajrodaya
  given name: Srunya
doi: 10.7717/peerj.6893
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-07
copyright: © 2019 Buathong et al.
attribution name: Buathong et al.

Accuracy of a deep convolutional neural network in detection of retinitis pigmentosa on ultrawide-field images
type: item
type: AcademicArticle
description: Evaluating the discrimination ability of a deep convolution neural network for ultrawide-field pseudocolor imaging and ultrawide-field autofluorescence of retinitis pigmentosa. In total, the 373 ultrawide-field pseudocolor and ultrawide-field autofluorescence images (150, retinitis pigmentosa; 223, normal) obtained from the patients who visited the Department of Ophthalmology, Tsukazaki Hospital were used. Training with a convolutional neural network on these learning data objects was conducted. We examined the K-fold cross validation (K = 5). The mean area under the curve of the ultrawide-field pseudocolor group was 0.998 (95% confidence interval (CI) [0.9953–1.0]) and that of the ultrawide-field autofluorescence group was 1.0 (95% CI [0.9994–1.0]). The sensitivity and specificity of the ultrawide-field pseudocolor group were 99.3% (95% CI [96.3%–100.0%]) and 99.1% (95% CI [96.1%–99.7%]), and those of the ultrawide-field autofluorescence group were 100% (95% CI [97.6%–100%]) and 99.5% (95% CI [96.8%–99.9%]), respectively. Heatmaps were in accordance with the clinician’s observations. Using the proposed deep neural network model, retinitis pigmentosa can be distinguished from healthy eyes with high sensitivity and specificity on ultrawide-field pseudocolor and ultrawide-field autofluorescence images.
format: application/pdf
format: text/html
creator: Hiroki Masumoto
creator: Hitoshi Tabuchi
creator: Shunsuke Nakakura
creator: Hideharu Ohsugi
creator: Hiroki Enno
creator: Naofumi Ishitobi
creator: Eiko Ohsugi
creator: Yoshinori Mitamura
subject: Ophthalmology
subject: Computational Science
description: doi:10.7717/peerj.6900
publisher: PeerJ Inc.
rights: © 2019 Masumoto et al.
abstract: Evaluating the discrimination ability of a deep convolution neural network for ultrawide-field pseudocolor imaging and ultrawide-field autofluorescence of retinitis pigmentosa. In total, the 373 ultrawide-field pseudocolor and ultrawide-field autofluorescence images (150, retinitis pigmentosa; 223, normal) obtained from the patients who visited the Department of Ophthalmology, Tsukazaki Hospital were used. Training with a convolutional neural network on these learning data objects was conducted. We examined the K-fold cross validation (K = 5). The mean area under the curve of the ultrawide-field pseudocolor group was 0.998 (95% confidence interval (CI) [0.9953–1.0]) and that of the ultrawide-field autofluorescence group was 1.0 (95% CI [0.9994–1.0]). The sensitivity and specificity of the ultrawide-field pseudocolor group were 99.3% (95% CI [96.3%–100.0%]) and 99.1% (95% CI [96.1%–99.7%]), and those of the ultrawide-field autofluorescence group were 100% (95% CI [97.6%–100%]) and 99.5% (95% CI [96.8%–99.9%]), respectively. Heatmaps were in accordance with the clinician’s observations. Using the proposed deep neural network model, retinitis pigmentosa can be distinguished from healthy eyes with high sensitivity and specificity on ultrawide-field pseudocolor and ultrawide-field autofluorescence images.
bibliographic citation: Masumoto et al. (2019) Accuracy of a deep convolutional neural network in detection of retinitis pigmentosa on ultrawide-field images. PeerJ 7:e6900 https://doi.org/10.7717/peerj.6900
date submitted: 2018-12-05
date accepted: 2019-04-02
issued: 2019-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masumoto
  given name: Hiroki
author list: Agent
  family name: Tabuchi
  given name: Hitoshi
author list: Agent
  family name: Nakakura
  given name: Shunsuke
author list: Agent
  family name: Ohsugi
  given name: Hideharu
author list: Agent
  family name: Enno
  given name: Hiroki
author list: Agent
  family name: Ishitobi
  given name: Naofumi
author list: Agent
  family name: Ohsugi
  given name: Eiko
author list: Agent
  family name: Mitamura
  given name: Yoshinori
doi: 10.7717/peerj.6900
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-07
copyright: © 2019 Masumoto et al.
attribution name: Masumoto et al.

Metacommunity patterns of Amazonian Odonata: the role of environmental gradients and major rivers
type: item
type: AcademicArticle
description: Background We identified and classified damselfly (Zygoptera) and dragonfly (Anisoptera) metacommunities in Brazilian Amazonia, relating species distribution patterns to known biological gradients and biogeographical history. We expected a random distribution of both Zygoptera and Anisoptera within interfluves. At the Amazonian scale, we expected Anisoptera metacommunities to be randomly distributed due to their higher dispersal ability and large environmental tolerance. In contrast, we expected Zygoptera communities to exhibit a Clementsian pattern, limited by the large Amazonia rivers due to their low dispersal ability. Methods We used a dataset of 58 first-to-third order well-sampled streamlets in four Amazonian interfluves and applied an extension of the Elements of Metacommunity Structure (EMS) framework, in which we order Zygoptera and Anisoptera metacommunities by known spatial and biogeographic predictors. Results At the Amazonian scale, both Zygoptera and Anisoptera presented a Clementsian pattern, driven by the same environmental and biogeographical predictors, namely biogeographic region (interfluve), annual mean temperature, habitat integrity and annual precipitation. At the interfluve scale, results were less consistent and only partially support our hypothesis. Zygoptera metacommunities at Guiana and Anisoptera metacommunities at Tapajós were classified as random, suggesting that neutral processes gain importance at smaller spatial scales. Discussion Our findings were consistent with previous studies showing that environmental gradients and major rivers limit the distribution of Odonata communities, supporting that larger Amazonian rivers act as barriers for the dispersal of this group. In addition, the importance of habitat integrity indicates that intactness of riparian vegetation is an important filter shaping metacommunity structure of Amazonian stream Odonata.
format: application/pdf
format: text/html
creator: Fernanda Alves-Martins
creator: Leandro Schlemmer Brasil
creator: Leandro Juen
creator: Paulo De Marco Jr
creator: Juliana Stropp
creator: Joaquín Hortal
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.6472
publisher: PeerJ Inc.
rights: © 2019 Alves-Martins et al.
abstract: Background We identified and classified damselfly (Zygoptera) and dragonfly (Anisoptera) metacommunities in Brazilian Amazonia, relating species distribution patterns to known biological gradients and biogeographical history. We expected a random distribution of both Zygoptera and Anisoptera within interfluves. At the Amazonian scale, we expected Anisoptera metacommunities to be randomly distributed due to their higher dispersal ability and large environmental tolerance. In contrast, we expected Zygoptera communities to exhibit a Clementsian pattern, limited by the large Amazonia rivers due to their low dispersal ability. Methods We used a dataset of 58 first-to-third order well-sampled streamlets in four Amazonian interfluves and applied an extension of the Elements of Metacommunity Structure (EMS) framework, in which we order Zygoptera and Anisoptera metacommunities by known spatial and biogeographic predictors. Results At the Amazonian scale, both Zygoptera and Anisoptera presented a Clementsian pattern, driven by the same environmental and biogeographical predictors, namely biogeographic region (interfluve), annual mean temperature, habitat integrity and annual precipitation. At the interfluve scale, results were less consistent and only partially support our hypothesis. Zygoptera metacommunities at Guiana and Anisoptera metacommunities at Tapajós were classified as random, suggesting that neutral processes gain importance at smaller spatial scales. Discussion Our findings were consistent with previous studies showing that environmental gradients and major rivers limit the distribution of Odonata communities, supporting that larger Amazonian rivers act as barriers for the dispersal of this group. In addition, the importance of habitat integrity indicates that intactness of riparian vegetation is an important filter shaping metacommunity structure of Amazonian stream Odonata.
bibliographic citation: Alves-Martins et al. (2019) Metacommunity patterns of Amazonian Odonata: the role of environmental gradients and major rivers. PeerJ 7:e6472 https://doi.org/10.7717/peerj.6472
date submitted: 2018-06-09
date accepted: 2019-01-18
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alves-Martins
  given name: Fernanda
author list: Agent
  family name: Brasil
  given name: Leandro Schlemmer
author list: Agent
  family name: Juen
  given name: Leandro
author list: Agent
  family name: De Marco Jr
  given name: Paulo
author list: Agent
  family name: Stropp
  given name: Juliana
author list: Agent
  family name: Hortal
  given name: Joaquín
doi: 10.7717/peerj.6472
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Alves-Martins et al.
attribution name: Alves-Martins et al.

Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia
type: item
type: AcademicArticle
description: The stomach bacterium Helicobacter pylori is one of the most prevalent pathogens in humans, closely linked with serious diseases such as gastric cancer. The microbe has been associated with its host for more than 100,000 years and escorted modern humans out of Africa. H. pylori is predominantly transmitted within families and dispersed globally, resulting in distinct phylogeographic patterns, which can be utilized to investigate migrations and bioturbation events in human history. Latin America was affected by several human migratory waves due to the Spanish colonisation that drastically changed the genetic load and composition of the bacteria and its host. Genetic evidence indicates that independent evolutionary lines of H. pylori have evolved in mestizos from Colombia and other countries in the region during more than 500 years since colonisation. The vacuolating cytotoxin VacA represents a major virulence factor of the pathogen comprising two domains, p33 and p55, the latter of which is essential for binding to the host epithelial cell. The evolution of the VacA toxin in Colombia has been strongly biased due to the effects of Spanish colonization. However, the variation patterns and microevolution of the p55 domain have not yet been described for this population. In the present study, we determined the genetic polymorphisms and deviations in the neutral model of molecular evolution in the p55 domain of 101 clinical H. pylori isolates collected in Bogotá, a city located in Andean mountains characterized by its high gastric cancer risk and its dominant mestizo population. The microevolutionary patterns of the p55 domain were shaped by recombination, purifying and episodic diversifying positive selection. Furthermore, amino acid positions 261 and 321 in the p55 domain of VacA show a high variability among mestizos clinical subsets, suggesting that natural selection in H. pylori may operate differentially in patients with different gastric diseases.
format: application/pdf
format: text/html
creator: Andrés J. Gutiérrez-Escobar
creator: María M. Bravo
creator: Orlando Acevedo
creator: Steffen Backert
subject: Bioinformatics
subject: Evolutionary Studies
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.6634
publisher: PeerJ Inc.
rights: © 2019 Gutiérrez-Escobar et al.
abstract: The stomach bacterium Helicobacter pylori is one of the most prevalent pathogens in humans, closely linked with serious diseases such as gastric cancer. The microbe has been associated with its host for more than 100,000 years and escorted modern humans out of Africa. H. pylori is predominantly transmitted within families and dispersed globally, resulting in distinct phylogeographic patterns, which can be utilized to investigate migrations and bioturbation events in human history. Latin America was affected by several human migratory waves due to the Spanish colonisation that drastically changed the genetic load and composition of the bacteria and its host. Genetic evidence indicates that independent evolutionary lines of H. pylori have evolved in mestizos from Colombia and other countries in the region during more than 500 years since colonisation. The vacuolating cytotoxin VacA represents a major virulence factor of the pathogen comprising two domains, p33 and p55, the latter of which is essential for binding to the host epithelial cell. The evolution of the VacA toxin in Colombia has been strongly biased due to the effects of Spanish colonization. However, the variation patterns and microevolution of the p55 domain have not yet been described for this population. In the present study, we determined the genetic polymorphisms and deviations in the neutral model of molecular evolution in the p55 domain of 101 clinical H. pylori isolates collected in Bogotá, a city located in Andean mountains characterized by its high gastric cancer risk and its dominant mestizo population. The microevolutionary patterns of the p55 domain were shaped by recombination, purifying and episodic diversifying positive selection. Furthermore, amino acid positions 261 and 321 in the p55 domain of VacA show a high variability among mestizos clinical subsets, suggesting that natural selection in H. pylori may operate differentially in patients with different gastric diseases.
bibliographic citation: Gutiérrez-Escobar et al. (2019) Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia. PeerJ 7:e6634 https://doi.org/10.7717/peerj.6634
date submitted: 2018-09-07
date accepted: 2019-02-18
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gutiérrez-Escobar
  given name: Andrés J.
author list: Agent
  family name: Bravo
  given name: María M.
author list: Agent
  family name: Acevedo
  given name: Orlando
author list: Agent
  family name: Backert
  given name: Steffen
doi: 10.7717/peerj.6634
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Gutiérrez-Escobar et al.
attribution name: Gutiérrez-Escobar et al.

Optimization of extraction conditions and determination of purine content in marine fish during boiling
type: item
type: AcademicArticle
description: Background Gout is the second most common metabolic disease affecting human health. The disease of gout is closely related to the level of uric acid, which is the end-product of human purine metabolism. Moreover, food is the main way of external ingestion of purine. Method A simple and time-saving method was developed to extract purines like adenine, hypoxanthine, guanine, and xanthine from marine fish by single factor design combined with Box–Behnken. The contents of these purines in the edible parts and internal organs of marine fish, as well as Scophthalmus maximus, were determined by high-performance liquid chromatography to investigate the relationship between the boiling process and purine content. Result The mixed-acid method was chosen for the extraction of purine bases and the extraction conditions were as follows: mixture acid 90.00% TFA/80.00% FA (v/v, 1:1); hydrolysis temperature 90.00 °C; time 10.00 min; liquid-to-solid ratio 30:1. The total purine content of the edible parts (eyes, dorsal muscles, abdominal muscles, and skin) was the highest in Scophthalmus maximus, followed by sphyraena, Sardinella, Trichiurus lepturus, Scomberomorus niphonius, Pleuronectiformes, Sea catfish, Anguillidae, and Rajiformes. Moreover, boiling significantly reduced the purine content in the marine fish because of the transfer of the purines to the cooking liquid during boiling. Scophthalmus maximus, Sphyraena, and Sardinella were regard as high-purine marine fish, which we should eat less. We also confirmed that boiling significantly transferred purine bases from fish to cooking liquid. Thus, boiling could reduce the purine content of fish, thereby reducing the risk of hyperuricemia and gout.
format: application/pdf
format: text/html
creator: Tingting Li
creator: Likun Ren
creator: Dangfeng Wang
creator: Minjie Song
creator: Qiuying Li
creator: Jianrong Li
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
description: doi:10.7717/peerj.6690
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Gout is the second most common metabolic disease affecting human health. The disease of gout is closely related to the level of uric acid, which is the end-product of human purine metabolism. Moreover, food is the main way of external ingestion of purine. Method A simple and time-saving method was developed to extract purines like adenine, hypoxanthine, guanine, and xanthine from marine fish by single factor design combined with Box–Behnken. The contents of these purines in the edible parts and internal organs of marine fish, as well as Scophthalmus maximus, were determined by high-performance liquid chromatography to investigate the relationship between the boiling process and purine content. Result The mixed-acid method was chosen for the extraction of purine bases and the extraction conditions were as follows: mixture acid 90.00% TFA/80.00% FA (v/v, 1:1); hydrolysis temperature 90.00 °C; time 10.00 min; liquid-to-solid ratio 30:1. The total purine content of the edible parts (eyes, dorsal muscles, abdominal muscles, and skin) was the highest in Scophthalmus maximus, followed by sphyraena, Sardinella, Trichiurus lepturus, Scomberomorus niphonius, Pleuronectiformes, Sea catfish, Anguillidae, and Rajiformes. Moreover, boiling significantly reduced the purine content in the marine fish because of the transfer of the purines to the cooking liquid during boiling. Scophthalmus maximus, Sphyraena, and Sardinella were regard as high-purine marine fish, which we should eat less. We also confirmed that boiling significantly transferred purine bases from fish to cooking liquid. Thus, boiling could reduce the purine content of fish, thereby reducing the risk of hyperuricemia and gout.
bibliographic citation: Li et al. (2019) Optimization of extraction conditions and determination of purine content in marine fish during boiling. PeerJ 7:e6690 https://doi.org/10.7717/peerj.6690
date submitted: 2018-12-07
date accepted: 2019-02-27
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Tingting
author list: Agent
  family name: Ren
  given name: Likun
author list: Agent
  family name: Wang
  given name: Dangfeng
author list: Agent
  family name: Song
  given name: Minjie
author list: Agent
  family name: Li
  given name: Qiuying
author list: Agent
  family name: Li
  given name: Jianrong
doi: 10.7717/peerj.6690
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: © 2019 Li et al.
attribution name: Li et al.

Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States
type: item
type: AcademicArticle
description: Background Coagulase negative Staphylococcus (CNS) species are currently the most prevalent intra-mammary pathogens causing subclinical mastitis and occasional clinical mastitis or persistent infection in lactating dairy cattle. More than 10 CNS species have been identified, but they are generally managed as one group on most dairies in the United States. However, improved management decisions and treatment outcomes may be achieved with better understanding of the prevalent species, pathogenicity and strain diversity within and across dairies. Methodology A total of 604 CNS isolates were cultured from milk samples collected during a dry-cow treatment clinical trial conducted on 6 dairy herds in 4 states in the US. All the study cows were randomized to receive 1 of the 3 different intra-mammary antimicrobial infusions (Quatermaster, Spectramast DC or ToMorrow Dry Cow) at dry-off. Milk samples were collected at dry-off, calving (0–6 days in milk, DIM), post-calving (7–13 DIM) and at mastitis events within the first 100 DIM. The CNS isolates were identified to species level by partial sequencing of the rpoβ gene, and genetic relatedness within species was investigated by phylogenetic analysis of the pulse-field gel electrophoresis profiles of the isolates. Results The major CNS species identified were S. chromogenes (48.3%), S. haemolyticus (17.9%), S. simulans and S. epidermidis (each at 6.5%). Other CNS species identified at lower frequencies included S. hominis, S. auricularis, S. sciuri, S. spp KS-SP, S. capitis, S. cohnii, S. warneri, S. pasteuri, S. xylosus, S. hyicus, S. equorum, S. microti, S. rostri, S. gallinarum, S. saprophyticus and S. succinus. Phylogenetic analyses of the major species types demonstrated an association between genetic relatedness and epidemiological distributions of S. chromogenes, S. simulans, S. haemolyticus and S. auricularis. Additionally, identical strains of S. chromogenes and S. simulans were isolated from the same udder quarter of…
format: application/pdf
format: text/html
creator: Stephen N. Jenkins
creator: Emmanuel Okello
creator: Paul V. Rossitto
creator: Terry W. Lehenbauer
creator: John Champagne
creator: Maria C.T. Penedo
creator: Andréia G. Arruda
creator: Sandra Godden
creator: Paul Rapnicki
creator: Patrick J. Gorden
creator: Leo L. Timms
creator: Sharif S. Aly
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.6749
publisher: PeerJ Inc.
rights: © 2019 Jenkins et al.
abstract: Background Coagulase negative Staphylococcus (CNS) species are currently the most prevalent intra-mammary pathogens causing subclinical mastitis and occasional clinical mastitis or persistent infection in lactating dairy cattle. More than 10 CNS species have been identified, but they are generally managed as one group on most dairies in the United States. However, improved management decisions and treatment outcomes may be achieved with better understanding of the prevalent species, pathogenicity and strain diversity within and across dairies. Methodology A total of 604 CNS isolates were cultured from milk samples collected during a dry-cow treatment clinical trial conducted on 6 dairy herds in 4 states in the US. All the study cows were randomized to receive 1 of the 3 different intra-mammary antimicrobial infusions (Quatermaster, Spectramast DC or ToMorrow Dry Cow) at dry-off. Milk samples were collected at dry-off, calving (0–6 days in milk, DIM), post-calving (7–13 DIM) and at mastitis events within the first 100 DIM. The CNS isolates were identified to species level by partial sequencing of the rpoβ gene, and genetic relatedness within species was investigated by phylogenetic analysis of the pulse-field gel electrophoresis profiles of the isolates. Results The major CNS species identified were S. chromogenes (48.3%), S. haemolyticus (17.9%), S. simulans and S. epidermidis (each at 6.5%). Other CNS species identified at lower frequencies included S. hominis, S. auricularis, S. sciuri, S. spp KS-SP, S. capitis, S. cohnii, S. warneri, S. pasteuri, S. xylosus, S. hyicus, S. equorum, S. microti, S. rostri, S. gallinarum, S. saprophyticus and S. succinus. Phylogenetic analyses of the major species types demonstrated an association between genetic relatedness and epidemiological distributions of S. chromogenes, S. simulans, S. haemolyticus and S. auricularis. Additionally, identical strains of S. chromogenes and S. simulans were isolated from the same udder quarter of…
bibliographic citation: Jenkins et al. (2019) Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States. PeerJ 7:e6749 https://doi.org/10.7717/peerj.6749
date submitted: 2018-10-08
date accepted: 2019-03-08
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jenkins
  given name: Stephen N.
author list: Agent
  family name: Okello
  given name: Emmanuel
author list: Agent
  family name: Rossitto
  given name: Paul V.
author list: Agent
  family name: Lehenbauer
  given name: Terry W.
author list: Agent
  family name: Champagne
  given name: John
author list: Agent
  family name: Penedo
  given name: Maria C.T.
author list: Agent
  family name: Arruda
  given name: Andréia G.
author list: Agent
  family name: Godden
  given name: Sandra
author list: Agent
  family name: Rapnicki
  given name: Paul
author list: Agent
  family name: Gorden
  given name: Patrick J.
author list: Agent
  family name: Timms
  given name: Leo L.
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.6749
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Jenkins et al.
attribution name: Jenkins et al.

Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis
type: item
type: AcademicArticle
description: Introduction A hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis. Methods A total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population. Results In total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low FSTvalues obtained from pairwise FST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (al…
format: application/pdf
format: text/html
creator: Huijuan Chen
creator: Dengqiang Wang
creator: Xinbin Duan
creator: Shaoping Liu
creator: Daqing Chen
creator: Yun Li
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genetics
subject: Freshwater Biology
description: doi:10.7717/peerj.6836
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Introduction A hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis. Methods A total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population. Results In total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low FSTvalues obtained from pairwise FST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (al…
bibliographic citation: Chen et al. (2019) Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis. PeerJ 7:e6836 https://doi.org/10.7717/peerj.6836
date submitted: 2018-08-26
date accepted: 2019-03-23
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Huijuan
author list: Agent
  family name: Wang
  given name: Dengqiang
author list: Agent
  family name: Duan
  given name: Xinbin
author list: Agent
  family name: Liu
  given name: Shaoping
author list: Agent
  family name: Chen
  given name: Daqing
author list: Agent
  family name: Li
  given name: Yun
doi: 10.7717/peerj.6836
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis
type: item
type: AcademicArticle
description: Objectives This study aims to evaluate the changes of development trends and research hotspots of biomaterials research from 2013 to 2017, which can identify the general information of papers and explore the changes of research content, thus providing perspectives for the development of biomaterials in China and other countries. Methods Data of the paper were retrieved from the Web of Science Core Collection, and then analyzed by the bibliometric and CiteSpace visualization analysis. Results It was found that a total of 3,839 related papers had been published from the year 2013 to 2017. The analysis of the articles showed that the annual quantity and quality of the articles in the biomaterials research have been increasing since 2013, and the Wang L / Chinese Academy of Sciences were the most productive author/institution. Meanwhile, the keywords “in vitro”, “scaffold”, “nanoparticle” , “mechanical property”, and “biocompatibility” have the relatively higher frequency, and the keywords “apatite”, “deposition”, and “surface modification” have the strongest burst citation. Conclusions After statistics and analysis, we found that biomaterials is a promising research field. The study may be helpful in understanding research trends in this field.
format: application/pdf
format: text/html
creator: Dandan Hou
creator: Xuewei Bi
creator: Zhinan Mao
creator: Yubo Fan
creator: Xiangming Hu
creator: Xiaoming Li
subject: Bioengineering
subject: Bioinformatics
description: doi:10.7717/peerj.6859
publisher: PeerJ Inc.
rights: © 2019 Hou et al.
abstract: Objectives This study aims to evaluate the changes of development trends and research hotspots of biomaterials research from 2013 to 2017, which can identify the general information of papers and explore the changes of research content, thus providing perspectives for the development of biomaterials in China and other countries. Methods Data of the paper were retrieved from the Web of Science Core Collection, and then analyzed by the bibliometric and CiteSpace visualization analysis. Results It was found that a total of 3,839 related papers had been published from the year 2013 to 2017. The analysis of the articles showed that the annual quantity and quality of the articles in the biomaterials research have been increasing since 2013, and the Wang L / Chinese Academy of Sciences were the most productive author/institution. Meanwhile, the keywords “in vitro”, “scaffold”, “nanoparticle” , “mechanical property”, and “biocompatibility” have the relatively higher frequency, and the keywords “apatite”, “deposition”, and “surface modification” have the strongest burst citation. Conclusions After statistics and analysis, we found that biomaterials is a promising research field. The study may be helpful in understanding research trends in this field.
bibliographic citation: Hou et al. (2019) Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis. PeerJ 7:e6859 https://doi.org/10.7717/peerj.6859
date submitted: 2019-01-03
date accepted: 2019-03-21
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Dandan
author list: Agent
  family name: Bi
  given name: Xuewei
author list: Agent
  family name: Mao
  given name: Zhinan
author list: Agent
  family name: Fan
  given name: Yubo
author list: Agent
  family name: Hu
  given name: Xiangming
author list: Agent
  family name: Li
  given name: Xiaoming
doi: 10.7717/peerj.6859
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Hou et al.
attribution name: Hou et al.

Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway
type: item
type: AcademicArticle
description: The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating th…
format: application/pdf
format: text/html
creator: Ruoxi Yu
creator: Zhi Li
creator: Chuang Zhang
creator: Huicong Song
creator: Mingming Deng
creator: Liping Sun
creator: Ling Xu
creator: Xiaofang Che
creator: Xuejun Hu
creator: Xiujuan Qu
creator: Yunpeng Liu
creator: Ye Zhang
subject: Bioinformatics
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.6885
publisher: PeerJ Inc.
rights: © 2019 Yu et al.
abstract: The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating th…
bibliographic citation: Yu et al. (2019) Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway. PeerJ 7:e6885 https://doi.org/10.7717/peerj.6885
date submitted: 2018-11-22
date accepted: 2019-03-31
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Ruoxi
author list: Agent
  family name: Li
  given name: Zhi
author list: Agent
  family name: Zhang
  given name: Chuang
author list: Agent
  family name: Song
  given name: Huicong
author list: Agent
  family name: Deng
  given name: Mingming
author list: Agent
  family name: Sun
  given name: Liping
author list: Agent
  family name: Xu
  given name: Ling
author list: Agent
  family name: Che
  given name: Xiaofang
author list: Agent
  family name: Hu
  given name: Xuejun
author list: Agent
  family name: Qu
  given name: Xiujuan
author list: Agent
  family name: Liu
  given name: Yunpeng
author list: Agent
  family name: Zhang
  given name: Ye
doi: 10.7717/peerj.6885
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Yu et al.
attribution name: Yu et al.

Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem
type: item
type: AcademicArticle
description: Background Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance. Methods We analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively. Results Site effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness. Conclusions There was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems.
format: application/pdf
format: text/html
creator: Daniel J. McGlinn
creator: Michael W. Palmer
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6738
publisher: PeerJ Inc.
rights: © 2019 McGlinn and Palmer
abstract: Background Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance. Methods We analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively. Results Site effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness. Conclusions There was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems.
bibliographic citation: McGlinn et al. (2019) Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem. PeerJ 7:e6738 https://doi.org/10.7717/peerj.6738
date submitted: 2017-05-23
date accepted: 2019-03-06
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGlinn
  given name: Daniel J.
author list: Agent
  family name: Palmer
  given name: Michael W.
doi: 10.7717/peerj.6738
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 McGlinn and Palmer
attribution name: McGlinn and Palmer

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