PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Ozymandias: a biodiversity knowledge graph
items: Genotypic variation in disease susceptibility among cultured stocks of elkhorn and staghorn corals
items: Efficacy and potential of phage therapy against multidrug resistant Shigella spp.
items: Enhancement of carbon monoxide concentration in atmosphere due to large scale forest fire of Uttarakhand
items: Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation
items: Cafeteria diet increased adiposity in comparison to high fat diet in young male rats
items: Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica
items: Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore
items: HERVs, immunity, and autoimmunity: understanding the connection
items: Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells

Ozymandias: a biodiversity knowledge graph
type: item
type: AcademicArticle
description: Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com.
format: application/pdf
format: text/html
creator: Roderic D.M. Page
subject: Biodiversity
subject: Bioinformatics
subject: Taxonomy
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6739
publisher: PeerJ Inc.
rights: © 2019 Page
abstract: Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com.
bibliographic citation: Page (2019) Ozymandias: a biodiversity knowledge graph. PeerJ 7:e6739 https://doi.org/10.7717/peerj.6739
date submitted: 2018-12-19
date accepted: 2019-03-07
issued: 2019-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Page
  given name: Roderic D.M.
doi: 10.7717/peerj.6739
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-08
copyright: ©2019 Page
attribution name: Page

Genotypic variation in disease susceptibility among cultured stocks of elkhorn and staghorn corals
type: item
type: AcademicArticle
description: Disease mortality has been a primary driver of population declines and the threatened status of the foundational Caribbean corals, Acropora palmata and A. cervicornis. There remain few tools to effectively manage coral disease. Substantial investment is flowing into in situ culture and population enhancement efforts, while disease takes a variable but sometimes high toll in restored populations. If genetic resistance to disease can be identified in these corals, it may be leveraged to improve resistance in restored populations and possibly lead to effective diagnostic tests and disease treatments. Using a standardized field protocol based on replicated direct-graft challenge assays, we quantified this important trait in cultured stocks from three field nurseries in the Florida Keys. Field tests of 12 genotypes of A. palmata and 31 genotypes of A. cervicornis revealed significant genotypic variation in disease susceptibility of both species measured both as risk of transmission (percent of exposed fragments that displayed tissue loss) and as the rate of tissue loss (cm2 d–1) in fragments with elicited lesions. These assay results provide a measure of relative disease resistance that can be incorporated, along with consideration of other important traits such as growth and reproductive success, into restoration strategies to yield more resilient populations.
format: application/pdf
format: text/html
creator: Margaret W. Miller
creator: Philip J. Colburn
creator: Emma Pontes
creator: Dana E. Williams
creator: Allan J. Bright
creator: Xaymara M. Serrano
creator: Esther C. Peters
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.6751
publisher: PeerJ Inc.
rights: © 2019
abstract: Disease mortality has been a primary driver of population declines and the threatened status of the foundational Caribbean corals, Acropora palmata and A. cervicornis. There remain few tools to effectively manage coral disease. Substantial investment is flowing into in situ culture and population enhancement efforts, while disease takes a variable but sometimes high toll in restored populations. If genetic resistance to disease can be identified in these corals, it may be leveraged to improve resistance in restored populations and possibly lead to effective diagnostic tests and disease treatments. Using a standardized field protocol based on replicated direct-graft challenge assays, we quantified this important trait in cultured stocks from three field nurseries in the Florida Keys. Field tests of 12 genotypes of A. palmata and 31 genotypes of A. cervicornis revealed significant genotypic variation in disease susceptibility of both species measured both as risk of transmission (percent of exposed fragments that displayed tissue loss) and as the rate of tissue loss (cm2 d–1) in fragments with elicited lesions. These assay results provide a measure of relative disease resistance that can be incorporated, along with consideration of other important traits such as growth and reproductive success, into restoration strategies to yield more resilient populations.
bibliographic citation: Miller et al. (2019) Genotypic variation in disease susceptibility among cultured stocks of elkhorn and staghorn corals. PeerJ 7:e6751 https://doi.org/10.7717/peerj.6751
date submitted: 2018-12-31
date accepted: 2019-03-05
issued: 2019-04-08
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Miller
  given name: Margaret W.
author list: Agent
  family name: Colburn
  given name: Philip J.
author list: Agent
  family name: Pontes
  given name: Emma
author list: Agent
  family name: Williams
  given name: Dana E.
author list: Agent
  family name: Bright
  given name: Allan J.
author list: Agent
  family name: Serrano
  given name: Xaymara M.
author list: Agent
  family name: Peters
  given name: Esther C.
doi: 10.7717/peerj.6751
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-08

Efficacy and potential of phage therapy against multidrug resistant Shigella spp.
type: item
type: AcademicArticle
description: Shigella-infected bacillary dysentery or commonly known as Shigellosis is a leading cause of morbidity and mortality worldwide. The gradual emergence of multidrug resistant Shigella spp. has triggered the search for alternatives to conventional antibiotics. Phage therapy could be one such suitable alternative, given its proven long term safety profile as well as the rapid expansion of phage therapy research. To be successful, phage therapy will need an adequate regulatory framework, effective strategies, the proper selection of appropriate phages, early solutions to overcome phage therapy limitations, the implementation of safety protocols, and finally improved public awareness. To achieve all these criteria and successfully apply phage therapy against multidrug resistant shigellosis, a comprehensive study is required. In fact, a variety of phage-based approaches and products including single phages, phage cocktails, mutated phages, genetically engineered phages, and combinations of phages with antibiotics have already been carried out to test the applications of phage therapy against multidrug resistant Shigella. This review provides a broad survey of phage treatments from past to present, focusing on the history, applications, limitations and effective solutions related to, as well as the prospects for, the use of phage therapy against multidrug resistant Shigella spp. and other multidrug resistant bacterial pathogens.
format: application/pdf
format: text/html
creator: Swee-Seong Tang
creator: Sudhangshu Kumar Biswas
creator: Wen Siang Tan
creator: Ananda Kumar Saha
creator: Bey-Fen Leo
subject: Microbiology
description: doi:10.7717/peerj.6225
publisher: PeerJ Inc.
rights: © 2019 Tang et al.
abstract: Shigella-infected bacillary dysentery or commonly known as Shigellosis is a leading cause of morbidity and mortality worldwide. The gradual emergence of multidrug resistant Shigella spp. has triggered the search for alternatives to conventional antibiotics. Phage therapy could be one such suitable alternative, given its proven long term safety profile as well as the rapid expansion of phage therapy research. To be successful, phage therapy will need an adequate regulatory framework, effective strategies, the proper selection of appropriate phages, early solutions to overcome phage therapy limitations, the implementation of safety protocols, and finally improved public awareness. To achieve all these criteria and successfully apply phage therapy against multidrug resistant shigellosis, a comprehensive study is required. In fact, a variety of phage-based approaches and products including single phages, phage cocktails, mutated phages, genetically engineered phages, and combinations of phages with antibiotics have already been carried out to test the applications of phage therapy against multidrug resistant Shigella. This review provides a broad survey of phage treatments from past to present, focusing on the history, applications, limitations and effective solutions related to, as well as the prospects for, the use of phage therapy against multidrug resistant Shigella spp. and other multidrug resistant bacterial pathogens.
bibliographic citation: Tang et al. (2019) Efficacy and potential of phage therapy against multidrug resistant Shigella spp.. PeerJ 7:e6225 https://doi.org/10.7717/peerj.6225
date submitted: 2017-10-12
date accepted: 2018-12-04
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Swee-Seong
author list: Agent
  family name: Biswas
  given name: Sudhangshu Kumar
author list: Agent
  family name: Tan
  given name: Wen Siang
author list: Agent
  family name: Saha
  given name: Ananda Kumar
author list: Agent
  family name: Leo
  given name: Bey-Fen
doi: 10.7717/peerj.6225
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Tang et al.
attribution name: Tang et al.

Enhancement of carbon monoxide concentration in atmosphere due to large scale forest fire of Uttarakhand
type: item
type: AcademicArticle
description: The richly forested Indian state of Uttarakhand experienced widespread forest fires in April to May 2016. The current study examines dispersion of carbon monoxide (CO) from the source regions of forest fire to distant places, using the Lagrangian particle dispersion model, FLEXPART. Atmospheric Infrared Sounder (AIRS) observations revealed that CO columnar concentrations had increased by almost 28 percentage during 24 April to 02 May 2016 with respect to the previous non-burning period of April 2016 at Uttarakhand. It is also seen that there is considerable enhancement of 45 percentage in average columnar concentration of CO during the burning period, compared to that in the previous 5 years as observed by AIRS. In the present study, concentrations of CO at different pressure levels and columnar CO over Uttarakhand during the forest fire event have been simulated using FLEXPART. The area averaged profile of model derived CO has been compared with the profile from AIRS onboard Aqua. Comparison between model derived columnar CO and satellite observations shows good agreement with coefficient of correlation (r) approximately 0.91 over the burnt areas. Further analysis using FLEXPART reveals that the transport of pollutants is towards north-eastern and eastern regions from the locations of forest fire events. Model derived vertical distribution of CO over Tibet, which is situated at the north-east of Uttarakhand, shows significant increase of CO concentration at higher altitudes around 3 km from the mean sea level during the fire event. FLEXPART results show that the emissions from the Uttarakhand fires were transported to Tibet during the study period.
format: application/pdf
format: text/html
creator: Jaya Thakur
creator: Prajesh Thever
creator: Biswadip Gharai
creator: MVR Sesha Sai
creator: VNRao Pamaraju
subject: Atmospheric Chemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.6507
publisher: PeerJ Inc.
rights: © 2019 Thakur et al.
abstract: The richly forested Indian state of Uttarakhand experienced widespread forest fires in April to May 2016. The current study examines dispersion of carbon monoxide (CO) from the source regions of forest fire to distant places, using the Lagrangian particle dispersion model, FLEXPART. Atmospheric Infrared Sounder (AIRS) observations revealed that CO columnar concentrations had increased by almost 28 percentage during 24 April to 02 May 2016 with respect to the previous non-burning period of April 2016 at Uttarakhand. It is also seen that there is considerable enhancement of 45 percentage in average columnar concentration of CO during the burning period, compared to that in the previous 5 years as observed by AIRS. In the present study, concentrations of CO at different pressure levels and columnar CO over Uttarakhand during the forest fire event have been simulated using FLEXPART. The area averaged profile of model derived CO has been compared with the profile from AIRS onboard Aqua. Comparison between model derived columnar CO and satellite observations shows good agreement with coefficient of correlation (r) approximately 0.91 over the burnt areas. Further analysis using FLEXPART reveals that the transport of pollutants is towards north-eastern and eastern regions from the locations of forest fire events. Model derived vertical distribution of CO over Tibet, which is situated at the north-east of Uttarakhand, shows significant increase of CO concentration at higher altitudes around 3 km from the mean sea level during the fire event. FLEXPART results show that the emissions from the Uttarakhand fires were transported to Tibet during the study period.
bibliographic citation: Thakur et al. (2019) Enhancement of carbon monoxide concentration in atmosphere due to large scale forest fire of Uttarakhand. PeerJ 7:e6507 https://doi.org/10.7717/peerj.6507
date submitted: 2018-02-17
date accepted: 2019-01-24
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thakur
  given name: Jaya
author list: Agent
  family name: Thever
  given name: Prajesh
author list: Agent
  family name: Gharai
  given name: Biswadip
author list: Agent
  family name: Sesha Sai
  given name: MVR
author list: Agent
  family name: Pamaraju
  given name: VNRao
doi: 10.7717/peerj.6507
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Thakur et al.
attribution name: Thakur et al.

Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation
type: item
type: AcademicArticle
description: Pathologically relevant behaviors of Vibrio, such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of Vibrio. Here, we reported the potential molecular interaction of fatty acids identified in vibriosis-resistant grouper with LuxP. Fatty acid, 4-oxodocosahexaenoic acid (4R8) showed significant binding affinity toward LuxP (−6.0 kcal/mol) based on molecular docking analysis. The dynamic behavior of the protein–ligand complex was illustrated by molecular dynamic simulations. The fluctuation of the protein backbone, the stability of ligand binding, and hydrogen bond interactions were assessed, suggesting 4R8 possesses potential interaction with LuxP, which was supported by the low binding free energy (−29.144 kJ/mol) calculated using the molecular mechanics Poisson–Boltzmann surface area.
format: application/pdf
format: text/html
creator: Chen-Fei Low
creator: Mohd Shahir Shamsir
creator: Zeti-Azura Mohamed-Hussein
creator: Syarul Nataqain Baharum
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Biotechnology
description: doi:10.7717/peerj.6568
publisher: PeerJ Inc.
rights: © 2019 Low et al.
abstract: Pathologically relevant behaviors of Vibrio, such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of Vibrio. Here, we reported the potential molecular interaction of fatty acids identified in vibriosis-resistant grouper with LuxP. Fatty acid, 4-oxodocosahexaenoic acid (4R8) showed significant binding affinity toward LuxP (−6.0 kcal/mol) based on molecular docking analysis. The dynamic behavior of the protein–ligand complex was illustrated by molecular dynamic simulations. The fluctuation of the protein backbone, the stability of ligand binding, and hydrogen bond interactions were assessed, suggesting 4R8 possesses potential interaction with LuxP, which was supported by the low binding free energy (−29.144 kJ/mol) calculated using the molecular mechanics Poisson–Boltzmann surface area.
bibliographic citation: Low et al. (2019) Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation. PeerJ 7:e6568 https://doi.org/10.7717/peerj.6568
date submitted: 2018-10-23
date accepted: 2019-02-05
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Low
  given name: Chen-Fei
author list: Agent
  family name: Shamsir
  given name: Mohd Shahir
author list: Agent
  family name: Mohamed-Hussein
  given name: Zeti-Azura
author list: Agent
  family name: Baharum
  given name: Syarul Nataqain
doi: 10.7717/peerj.6568
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: © 2019 Low et al.
attribution name: Low et al.

Cafeteria diet increased adiposity in comparison to high fat diet in young male rats
type: item
type: AcademicArticle
description: Background Dietary intervention studies in animal models of obesity are crucial to elucidate the mechanistic effects of specific nutrients and diets. Although several models of diet induced obesity have been examined in rodents to assess obesity, there are few studies that have researched influence of different high fat and/or westernized diets. The aim of this study was to compare a high fat diet and a cafeteria diet on obesity related biochemical and physiological parameters in young male rats. Methods Five week old Wistar male rats were fed a control chow diet (C), butter-based high fat diet (HF) or cafeteria diet (CAF) for twelve weeks. In HF, 40% of energy came from fat and this ratio was 46% in CAF. CAF composed of highly energetic and palatable human foods along with chow diet. At the end of the feeding protocol all animals were culled using CO2 asphyxia and cervical dislocation after an overnight fasting. Results Total energy and fat intake of CAF was significantly higher than C and HF. CAF was more effective in inducing obesity, as demonstrated by increased weight gain, Lee index, fat depot weights and total body fat in comparison to C and HF. Despite increased adiposity in CAF, plasma glucose, insulin and HOMA-IR levels were similar between the groups. Plasma leptin and cholesterol levels were markedly higher in CAF than C and HF. Discussion We have demonstrated that there are differential effects of high fat diet and cafeteria diet upon obesity and obesity-related parameters, with CAF leading to a more pronounced adiposity in comparison to high fat diet in young male rats. Future studies should consider the varied outcomes of different diet induced obesity models and development of a standardized approach in similar research practices.
format: application/pdf
format: text/html
creator: Yucel Buyukdere
creator: Atila Gulec
creator: Asli Akyol
subject: Animal Behavior
subject: Nutrition
description: doi:10.7717/peerj.6656
publisher: PeerJ Inc.
rights: © 2019 Buyukdere et al.
abstract: Background Dietary intervention studies in animal models of obesity are crucial to elucidate the mechanistic effects of specific nutrients and diets. Although several models of diet induced obesity have been examined in rodents to assess obesity, there are few studies that have researched influence of different high fat and/or westernized diets. The aim of this study was to compare a high fat diet and a cafeteria diet on obesity related biochemical and physiological parameters in young male rats. Methods Five week old Wistar male rats were fed a control chow diet (C), butter-based high fat diet (HF) or cafeteria diet (CAF) for twelve weeks. In HF, 40% of energy came from fat and this ratio was 46% in CAF. CAF composed of highly energetic and palatable human foods along with chow diet. At the end of the feeding protocol all animals were culled using CO2 asphyxia and cervical dislocation after an overnight fasting. Results Total energy and fat intake of CAF was significantly higher than C and HF. CAF was more effective in inducing obesity, as demonstrated by increased weight gain, Lee index, fat depot weights and total body fat in comparison to C and HF. Despite increased adiposity in CAF, plasma glucose, insulin and HOMA-IR levels were similar between the groups. Plasma leptin and cholesterol levels were markedly higher in CAF than C and HF. Discussion We have demonstrated that there are differential effects of high fat diet and cafeteria diet upon obesity and obesity-related parameters, with CAF leading to a more pronounced adiposity in comparison to high fat diet in young male rats. Future studies should consider the varied outcomes of different diet induced obesity models and development of a standardized approach in similar research practices.
bibliographic citation: Buyukdere et al. (2019) Cafeteria diet increased adiposity in comparison to high fat diet in young male rats. PeerJ 7:e6656 https://doi.org/10.7717/peerj.6656
date submitted: 2018-10-30
date accepted: 2019-02-21
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buyukdere
  given name: Yucel
author list: Agent
  family name: Gulec
  given name: Atila
author list: Agent
  family name: Akyol
  given name: Asli
doi: 10.7717/peerj.6656
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Buyukdere et al.
attribution name: Buyukdere et al.

Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica
type: item
type: AcademicArticle
description: Background Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu2+ at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecula…
format: application/pdf
format: text/html
creator: Nikolay B. Pestov
creator: Daniel V. Kalinovsky
creator: Tatyana D. Larionova
creator: Alia Z. Zakirova
creator: Nikolai N. Modyanov
creator: Irina A. Okkelman
creator: Tatyana V. Korneenko
subject: Biochemistry
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6691
publisher: PeerJ Inc.
rights: © 2019 Pestov et al.
abstract: Background Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu2+ at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecula…
bibliographic citation: Pestov et al. (2019) Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica. PeerJ 7:e6691 https://doi.org/10.7717/peerj.6691
date submitted: 2018-01-02
date accepted: 2019-02-26
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pestov
  given name: Nikolay B.
author list: Agent
  family name: Kalinovsky
  given name: Daniel V.
author list: Agent
  family name: Larionova
  given name: Tatyana D.
author list: Agent
  family name: Zakirova
  given name: Alia Z.
author list: Agent
  family name: Modyanov
  given name: Nikolai N.
author list: Agent
  family name: Okkelman
  given name: Irina A.
author list: Agent
  family name: Korneenko
  given name: Tatyana V.
doi: 10.7717/peerj.6691
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Pestov et al.
attribution name: Pestov et al.

Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore
type: item
type: AcademicArticle
description: Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale’s stomach contents. Plastic debris was also found in the whale’s stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.
format: application/pdf
format: text/html
creator: Marcus A.H. Chua
creator: David J.W. Lane
creator: Seng Keat Ooi
creator: Serene H.X. Tay
creator: Tsunemi Kubodera
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.6705
publisher: PeerJ Inc.
rights: © 2019 Chua et al.
abstract: Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale’s stomach contents. Plastic debris was also found in the whale’s stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.
bibliographic citation: Chua et al. (2019) Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore. PeerJ 7:e6705 https://doi.org/10.7717/peerj.6705
date submitted: 2018-12-15
date accepted: 2019-03-03
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chua
  given name: Marcus A.H.
author list: Agent
  family name: Lane
  given name: David J.W.
author list: Agent
  family name: Ooi
  given name: Seng Keat
author list: Agent
  family name: Tay
  given name: Serene H.X.
author list: Agent
  family name: Kubodera
  given name: Tsunemi
doi: 10.7717/peerj.6705
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Chua et al.
attribution name: Chua et al.

HERVs, immunity, and autoimmunity: understanding the connection
type: item
type: AcademicArticle
description: Since their discovery in the 1960s, further investigation into endogenous retroviruses (ERVs) has challenged the conventional view of viral sequences as exclusively parasitic elements. Once presumed to be a group of passive genetic relics, it is becoming increasingly clear that this view of ERVs, while generally accurate, is incorrect in many specific cases. Research has identified ERV genes that appear to be co-opted by their mammalian hosts, but the biological function of ERV elements in humans remains a controversial subject. One area that has attracted some attention in this domain is the role of co-opted ERV elements in mammalian immune systems. The relationship between ERVs and human autoimmune diseases has also been investigated, but has historically been treated as a separate topic. This review will summarize the current evidence concerning the phenotypic significance of ERVs, both in the healthy immune system and in manifestations of autoimmunity. Furthermore, it will evaluate the relationship between these fields of study, and propose previously-unexplored molecular mechanisms through which human endogenous retroviruses might contribute to certain autoimmune pathologies. Investigation into these novel mechanisms could further our understanding of the molecular basis of autoimmune disease, and may one day provide new targets for treatment.
format: application/pdf
format: text/html
creator: Matthew Greenig
subject: Molecular Biology
subject: Virology
subject: Allergy and Clinical Immunology
subject: Immunology
description: doi:10.7717/peerj.6711
publisher: PeerJ Inc.
rights: © 2019 Greenig
abstract: Since their discovery in the 1960s, further investigation into endogenous retroviruses (ERVs) has challenged the conventional view of viral sequences as exclusively parasitic elements. Once presumed to be a group of passive genetic relics, it is becoming increasingly clear that this view of ERVs, while generally accurate, is incorrect in many specific cases. Research has identified ERV genes that appear to be co-opted by their mammalian hosts, but the biological function of ERV elements in humans remains a controversial subject. One area that has attracted some attention in this domain is the role of co-opted ERV elements in mammalian immune systems. The relationship between ERVs and human autoimmune diseases has also been investigated, but has historically been treated as a separate topic. This review will summarize the current evidence concerning the phenotypic significance of ERVs, both in the healthy immune system and in manifestations of autoimmunity. Furthermore, it will evaluate the relationship between these fields of study, and propose previously-unexplored molecular mechanisms through which human endogenous retroviruses might contribute to certain autoimmune pathologies. Investigation into these novel mechanisms could further our understanding of the molecular basis of autoimmune disease, and may one day provide new targets for treatment.
bibliographic citation: Greenig (2019) HERVs, immunity, and autoimmunity: understanding the connection. PeerJ 7:e6711 https://doi.org/10.7717/peerj.6711
date submitted: 2018-11-09
date accepted: 2019-02-28
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greenig
  given name: Matthew
doi: 10.7717/peerj.6711
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Greenig
attribution name: Greenig

Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells
type: item
type: AcademicArticle
description: The function of long non-coding RNA H19 (H19) on cell proliferation has been observed in various cell types, and the increased expression of H19 was also found in the lipopolysaccharide (LPS)-induced inflammatory bovine mammary epithelial cells (MAC-T). However, the roles of H19 in the inflammatory response and physiological functions of bovine mammary epithelial cell are not clear. In the present study, we found that overexpression of H19 in MAC-T cells significantly promoted cell proliferation, increased the protein and mRNA level of β-casein, and enhanced the expression of tight junction (TJ)-related proteins while inhibited staphylococcus aureus adhesion to cells. In addition, results demonstrated that overexpression of H19 affected the LPS-induced immune response of MAC-T cells by promoting expressions of inflammatory factors, including TNF-α, IL-6, CXCL2 and CCL5, and activating the NF-κB signal pathway. Our findings indicate that H19 is likely to play an important role in maintaining normal functions and regulating immune response of bovine mammary epithelial cells.
format: application/pdf
format: text/html
creator: Xuezhong Li
creator: Hao Wang
creator: Yanfen Zhang
creator: Jinjing Zhang
creator: Shaopei Qi
creator: Yong Zhang
creator: Ming-Qing Gao
subject: Cell Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6715
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: The function of long non-coding RNA H19 (H19) on cell proliferation has been observed in various cell types, and the increased expression of H19 was also found in the lipopolysaccharide (LPS)-induced inflammatory bovine mammary epithelial cells (MAC-T). However, the roles of H19 in the inflammatory response and physiological functions of bovine mammary epithelial cell are not clear. In the present study, we found that overexpression of H19 in MAC-T cells significantly promoted cell proliferation, increased the protein and mRNA level of β-casein, and enhanced the expression of tight junction (TJ)-related proteins while inhibited staphylococcus aureus adhesion to cells. In addition, results demonstrated that overexpression of H19 affected the LPS-induced immune response of MAC-T cells by promoting expressions of inflammatory factors, including TNF-α, IL-6, CXCL2 and CCL5, and activating the NF-κB signal pathway. Our findings indicate that H19 is likely to play an important role in maintaining normal functions and regulating immune response of bovine mammary epithelial cells.
bibliographic citation: Li et al. (2019) Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells. PeerJ 7:e6715 https://doi.org/10.7717/peerj.6715
date submitted: 2018-10-20
date accepted: 2019-03-05
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xuezhong
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Yanfen
author list: Agent
  family name: Zhang
  given name: Jinjing
author list: Agent
  family name: Qi
  given name: Shaopei
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Gao
  given name: Ming-Qing
doi: 10.7717/peerj.6715
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Li et al.
attribution name: Li et al.

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