PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016
items: The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity?
items: Seasonal migrations, body temperature fluctuations, and infection dynamics in adult amphibians
items: Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing
items: Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts
items: Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution
items: Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico
items: Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth
items: Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis
items: A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing

Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016
type: item
type: AcademicArticle
description: Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant.
format: application/pdf
format: text/html
creator: Supansa Tuanthap
creator: Cherdpong Phupolphan
creator: Supol Luengyosluechakul
creator: Ausanee Duang-in
creator: Apiradee Theamboonlers
creator: Suphot Wattanaphansak
creator: Sompong Vongpunsawad
creator: Alongkorn Amonsin
creator: Yong Poovorawan
subject: Molecular Biology
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.4724
publisher: PeerJ Inc.
rights: © 2018 Tuanthap et al.
abstract: Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant.
bibliographic citation: Tuanthap et al. (2018) Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016. PeerJ 6:e4724 https://doi.org/10.7717/peerj.4724
date submitted: 2018-01-08
date accepted: 2018-04-17
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tuanthap
  given name: Supansa
author list: Agent
  family name: Phupolphan
  given name: Cherdpong
author list: Agent
  family name: Luengyosluechakul
  given name: Supol
author list: Agent
  family name: Duang-in
  given name: Ausanee
author list: Agent
  family name: Theamboonlers
  given name: Apiradee
author list: Agent
  family name: Wattanaphansak
  given name: Suphot
author list: Agent
  family name: Vongpunsawad
  given name: Sompong
author list: Agent
  family name: Amonsin
  given name: Alongkorn
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.4724
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: © 2018 Tuanthap et al.
attribution name: Tuanthap et al.

The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity?
type: item
type: AcademicArticle
description: Animal signalling structures are amongst the most variable characteristics, as they are subjected to a diversity of selection pressures. A well-known example of a diverse signalling system in the animal kingdom is the dewlap of Anolis lizards. Dewlap characteristics can vary remarkably among and within species, and also between sexes. Although a considerable amount of studies have attempted to disentangle the functional significance of the staggering dewlap diversity in Anolis, the underlying evolutionary processes remain elusive. In this study, we focus on the contribution of biotic selective pressures in shaping geographic variation in dewlap design (size, colour, and pattern) and dewlap display behaviour at the intraspecific level. Notably, we have tried to replicate and extend previously reported results hereof in both sexes of the brown anole lizard (Anolis sagrei). To do this, we assembled a dataset consisting of 17 A. sagrei heterogeneous island populations from the Caribbean and specifically tested whether predation pressure, sexual selection, or species recognition could explain interpopulational variation in an array of dewlap characteristics. Our findings show that in neither males nor females estimates of predation pressure (island size, tail break frequency, model attack rate, presence of predatory Leiocephalus lizards) or sexual selection (sexual size dimorphism) could explain variation in dewlap design. We did find that A. sagrei males from larger islands showed higher dewlap display intensities than males from smaller islands, but the direct connection with predation pressure remains ambiguous and demands further investigation. Last, we could show indirect support for species recognition only in males, as they are more likely to have a ‘spotted’ dewlap pattern when co-occurring with a higher number of syntopic Anolis species. In conclusion, we found overall limited support for the idea that the extensive interpopulational variability in dewlap design…
format: application/pdf
format: text/html
creator: Simon Baeckens
creator: Tess Driessens
creator: Raoul Van Damme
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.4722
publisher: PeerJ Inc.
rights: © 2018 Baeckens et al.
abstract: Animal signalling structures are amongst the most variable characteristics, as they are subjected to a diversity of selection pressures. A well-known example of a diverse signalling system in the animal kingdom is the dewlap of Anolis lizards. Dewlap characteristics can vary remarkably among and within species, and also between sexes. Although a considerable amount of studies have attempted to disentangle the functional significance of the staggering dewlap diversity in Anolis, the underlying evolutionary processes remain elusive. In this study, we focus on the contribution of biotic selective pressures in shaping geographic variation in dewlap design (size, colour, and pattern) and dewlap display behaviour at the intraspecific level. Notably, we have tried to replicate and extend previously reported results hereof in both sexes of the brown anole lizard (Anolis sagrei). To do this, we assembled a dataset consisting of 17 A. sagrei heterogeneous island populations from the Caribbean and specifically tested whether predation pressure, sexual selection, or species recognition could explain interpopulational variation in an array of dewlap characteristics. Our findings show that in neither males nor females estimates of predation pressure (island size, tail break frequency, model attack rate, presence of predatory Leiocephalus lizards) or sexual selection (sexual size dimorphism) could explain variation in dewlap design. We did find that A. sagrei males from larger islands showed higher dewlap display intensities than males from smaller islands, but the direct connection with predation pressure remains ambiguous and demands further investigation. Last, we could show indirect support for species recognition only in males, as they are more likely to have a ‘spotted’ dewlap pattern when co-occurring with a higher number of syntopic Anolis species. In conclusion, we found overall limited support for the idea that the extensive interpopulational variability in dewlap design…
bibliographic citation: Baeckens et al. (2018) The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity?. PeerJ 6:e4722 https://doi.org/10.7717/peerj.4722
date submitted: 2018-03-13
date accepted: 2018-04-16
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baeckens
  given name: Simon
author list: Agent
  family name: Driessens
  given name: Tess
author list: Agent
  family name: Van Damme
  given name: Raoul
doi: 10.7717/peerj.4722
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: © 2018 Baeckens et al.
attribution name: Baeckens et al.

Seasonal migrations, body temperature fluctuations, and infection dynamics in adult amphibians
type: item
type: AcademicArticle
description: Risks of parasitism vary over time, with infection prevalence often fluctuating with seasonal changes in the annual cycle. Identifying the biological mechanisms underlying seasonality in infection can enable better prediction and prevention of future infection peaks. Obtaining longitudinal data on individual infections and traits across seasons throughout the annual cycle is perhaps the most effective means of achieving this aim, yet few studies have obtained such information for wildlife. Here, we tracked spiny common toads (Bufo spinosus) within and across annual cycles to assess seasonal variation in movement, body temperatures and infection from the fungal parasite, Batrachochytrium dendrobatidis (Bd). Across annual cycles, toads did not consistently sustain infections but instead gained and lost infections from year to year. Radio-tracking showed that infected toads lose infections during post-breeding migrations, and no toads contracted infection following migration, which may be one explanation for the inter-annual variability in Bd infections. We also found pronounced seasonal variation in toad body temperatures. Body temperatures approached 0 °C during winter hibernation but remained largely within the thermal tolerance range of Bd. These findings provide direct documentation of migratory recovery (i.e., loss of infection during migration) and escape in a wild population. The body temperature reductions that we observed during hibernation warrant further consideration into the role that this period plays in seasonal Bd dynamics.
format: application/pdf
format: text/html
creator: David R. Daversa
creator: Camino Monsalve-Carcaño
creator: Luis M. Carrascal
creator: Jaime Bosch
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.4698
publisher: PeerJ Inc.
rights: © 2018 Daversa et al.
abstract: Risks of parasitism vary over time, with infection prevalence often fluctuating with seasonal changes in the annual cycle. Identifying the biological mechanisms underlying seasonality in infection can enable better prediction and prevention of future infection peaks. Obtaining longitudinal data on individual infections and traits across seasons throughout the annual cycle is perhaps the most effective means of achieving this aim, yet few studies have obtained such information for wildlife. Here, we tracked spiny common toads (Bufo spinosus) within and across annual cycles to assess seasonal variation in movement, body temperatures and infection from the fungal parasite, Batrachochytrium dendrobatidis (Bd). Across annual cycles, toads did not consistently sustain infections but instead gained and lost infections from year to year. Radio-tracking showed that infected toads lose infections during post-breeding migrations, and no toads contracted infection following migration, which may be one explanation for the inter-annual variability in Bd infections. We also found pronounced seasonal variation in toad body temperatures. Body temperatures approached 0 °C during winter hibernation but remained largely within the thermal tolerance range of Bd. These findings provide direct documentation of migratory recovery (i.e., loss of infection during migration) and escape in a wild population. The body temperature reductions that we observed during hibernation warrant further consideration into the role that this period plays in seasonal Bd dynamics.
bibliographic citation: Daversa et al. (2018) Seasonal migrations, body temperature fluctuations, and infection dynamics in adult amphibians. PeerJ 6:e4698 https://doi.org/10.7717/peerj.4698
date submitted: 2017-12-04
date accepted: 2018-04-12
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Daversa
  given name: David R.
author list: Agent
  family name: Monsalve-Carcaño
  given name: Camino
author list: Agent
  family name: Carrascal
  given name: Luis M.
author list: Agent
  family name: Bosch
  given name: Jaime
doi: 10.7717/peerj.4698
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: ©2018 Daversa et al.
attribution name: Daversa et al.

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing
type: item
type: AcademicArticle
description: Background Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Methods & Results Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus. However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons. Discussion Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port …
format: application/pdf
format: text/html
creator: Lauren O’Connell
creator: Song Gao
creator: Donald McCorquodale
creator: Jay Fleisher
creator: Jose V. Lopez
subject: Environmental Sciences
subject: Genomics
subject: Marine Biology
subject: Microbiology
subject: Environmental Impacts
description: doi:10.7717/peerj.4671
publisher: PeerJ Inc.
rights: © 2018 O’Connell et al.
abstract: Background Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Methods & Results Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus. However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons. Discussion Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port …
bibliographic citation: O’Connell et al. (2018) Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing. PeerJ 6:e4671 https://doi.org/10.7717/peerj.4671
date submitted: 2017-10-24
date accepted: 2018-04-05
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Connell
  given name: Lauren
author list: Agent
  family name: Gao
  given name: Song
author list: Agent
  family name: McCorquodale
  given name: Donald
author list: Agent
  family name: Fleisher
  given name: Jay
author list: Agent
  family name: Lopez
  given name: Jose V.
doi: 10.7717/peerj.4671
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: ©2018 O’Connell et al.
attribution name: O’Connell et al.

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts
type: item
type: AcademicArticle
description: The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.
format: application/pdf
format: text/html
creator: Anne Duplouy
creator: Emily A. Hornett
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.4629
publisher: PeerJ Inc.
rights: © 2018 Duplouy and Hornett
abstract: The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.
bibliographic citation: Duplouy et al. (2018) Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts. PeerJ 6:e4629 https://doi.org/10.7717/peerj.4629
date submitted: 2018-01-22
date accepted: 2018-03-27
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duplouy
  given name: Anne
author list: Agent
  family name: Hornett
  given name: Emily A.
doi: 10.7717/peerj.4629
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: © 2018 Duplouy and Hornett
attribution name: Duplouy and Hornett

Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution
type: item
type: AcademicArticle
description: Marine caves possess unique biocoenotic and ecological characteristics. Sessile benthic species such as sponges associated with cave habitats typically show a marked zonation from the cave entrance towards the end of the cave. We describe three semi-submerged karstic caves of 50 to 83 m length and 936 to 2,291 m3 volume from the poorly explored cavernicolous fauna of North-East Bulgaria. We surveyed sponge diversity and spatial variability. Eight demosponge species were identified based on morphological and molecular data, of which six are known from the adjacent open sea waters of the Black Sea. Two species, Protosuberites denhartogi van Soest & de Kluijver, 2003 and Halichondria bowerbanki Burton, 1930, are reported from the Black Sea for the first time. The spatial sponge distribution inside the caves is in general similar, but shows some differences in species composition and distribution depending on cave relief and hydrodynamics. The species composition of sponges of Bulgarian caves is found to be different from Crimean caves. An updated checklist of the Black Sea sponges is provided.
format: application/pdf
format: text/html
creator: Alexander Ereskovsky
creator: Oleg A. Kovtun
creator: Konstantin K. Pronin
creator: Apostol Apostolov
creator: Dirk Erpenbeck
creator: Viatcheslav Ivanenko
subject: Biodiversity
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.4596
publisher: PeerJ Inc.
rights: © 2018 Ereskovsky et al.
abstract: Marine caves possess unique biocoenotic and ecological characteristics. Sessile benthic species such as sponges associated with cave habitats typically show a marked zonation from the cave entrance towards the end of the cave. We describe three semi-submerged karstic caves of 50 to 83 m length and 936 to 2,291 m3 volume from the poorly explored cavernicolous fauna of North-East Bulgaria. We surveyed sponge diversity and spatial variability. Eight demosponge species were identified based on morphological and molecular data, of which six are known from the adjacent open sea waters of the Black Sea. Two species, Protosuberites denhartogi van Soest & de Kluijver, 2003 and Halichondria bowerbanki Burton, 1930, are reported from the Black Sea for the first time. The spatial sponge distribution inside the caves is in general similar, but shows some differences in species composition and distribution depending on cave relief and hydrodynamics. The species composition of sponges of Bulgarian caves is found to be different from Crimean caves. An updated checklist of the Black Sea sponges is provided.
bibliographic citation: Ereskovsky et al. (2018) Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution. PeerJ 6:e4596 https://doi.org/10.7717/peerj.4596
date submitted: 2017-12-22
date accepted: 2018-03-20
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ereskovsky
  given name: Alexander
author list: Agent
  family name: Kovtun
  given name: Oleg A.
author list: Agent
  family name: Pronin
  given name: Konstantin K.
author list: Agent
  family name: Apostolov
  given name: Apostol
author list: Agent
  family name: Erpenbeck
  given name: Dirk
author list: Agent
  family name: Ivanenko
  given name: Viatcheslav
doi: 10.7717/peerj.4596
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: ©2018 Ereskovsky et al.
attribution name: Ereskovsky et al.

Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico
type: item
type: AcademicArticle
description: Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.
format: application/pdf
format: text/html
creator: Carolina A. Martínez-Gutiérrez
creator: Hever Latisnere-Barragán
creator: José Q. García-Maldonado
creator: Alejandro López-Cortés
subject: Biotechnology
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.4780
publisher: PeerJ Inc.
rights: © 2018 Martínez-Gutiérrez et al.
abstract: Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.
bibliographic citation: Martínez-Gutiérrez et al. (2018) Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. PeerJ 6:e4780 https://doi.org/10.7717/peerj.4780
date submitted: 2018-02-28
date accepted: 2018-04-23
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Gutiérrez
  given name: Carolina A.
author list: Agent
  family name: Latisnere-Barragán
  given name: Hever
author list: Agent
  family name: García-Maldonado
  given name: José Q.
author list: Agent
  family name: López-Cortés
  given name: Alejandro
doi: 10.7717/peerj.4780
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: © 2018 Martínez-Gutiérrez et al.
attribution name: Martínez-Gutiérrez et al.

Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth
type: item
type: AcademicArticle
description: Organic agriculture is becoming increasingly important, and many natural products are now available for organic farmers to manage and improve their crops. Several ethnobotanical studies have indicated that the use of nettle slurry as fertilizer in organic farming for horticultural crops is spreading. Sometimes, however, the consequences of using these natural products have been poorly evaluated, and there is very little scientific evidence for the effects of using these slurries. In this study, we aimed to analyze the possible effect of nettle slurry on potato yields produced by organic farming. To achieve this main objective, we assessed the effect of nettle slurry on potato yields, plant size and growth parameters, chlorophyll content, and the presence of pests and diseases. Different slurry doses were assessed in 36 plots and nine variables were measured during the crop cycle. Under these field experimental conditions, nettle slurry (including one treatment with Urtica in combination with Equisetum) had no significant effects on yield, chlorophyll content, or the presence of pests and diseases in organic potato crops. The highest chlorophyll content was found in the double dose treatment, but the difference was not significant. This result, together with a small improvement in plant height with the double dose treatment, might indicate very slight crop enhancement which, under our experimental conditions, was not enough to improve yield. The Urtica and Equisetum slurry chemical analyses showed very low levels of nitrogen, phosphorus, and potassium.
format: application/pdf
format: text/html
creator: Alfonso Garmendia
creator: María Dolores Raigón
creator: Olmo Marques
creator: María Ferriol
creator: Jorge Royo
creator: Hugo Merle
subject: Agricultural Science
subject: Plant Science
subject: Natural Resource Management
subject: Green Chemistry
description: doi:10.7717/peerj.4729
publisher: PeerJ Inc.
rights: © 2018 Garmendia et al.
abstract: Organic agriculture is becoming increasingly important, and many natural products are now available for organic farmers to manage and improve their crops. Several ethnobotanical studies have indicated that the use of nettle slurry as fertilizer in organic farming for horticultural crops is spreading. Sometimes, however, the consequences of using these natural products have been poorly evaluated, and there is very little scientific evidence for the effects of using these slurries. In this study, we aimed to analyze the possible effect of nettle slurry on potato yields produced by organic farming. To achieve this main objective, we assessed the effect of nettle slurry on potato yields, plant size and growth parameters, chlorophyll content, and the presence of pests and diseases. Different slurry doses were assessed in 36 plots and nine variables were measured during the crop cycle. Under these field experimental conditions, nettle slurry (including one treatment with Urtica in combination with Equisetum) had no significant effects on yield, chlorophyll content, or the presence of pests and diseases in organic potato crops. The highest chlorophyll content was found in the double dose treatment, but the difference was not significant. This result, together with a small improvement in plant height with the double dose treatment, might indicate very slight crop enhancement which, under our experimental conditions, was not enough to improve yield. The Urtica and Equisetum slurry chemical analyses showed very low levels of nitrogen, phosphorus, and potassium.
bibliographic citation: Garmendia et al. (2018) Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth. PeerJ 6:e4729 https://doi.org/10.7717/peerj.4729
date submitted: 2018-02-19
date accepted: 2018-04-16
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garmendia
  given name: Alfonso
author list: Agent
  family name: Raigón
  given name: María Dolores
author list: Agent
  family name: Marques
  given name: Olmo
author list: Agent
  family name: Ferriol
  given name: María
author list: Agent
  family name: Royo
  given name: Jorge
author list: Agent
  family name: Merle
  given name: Hugo
doi: 10.7717/peerj.4729
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: © 2018 Garmendia et al.
attribution name: Garmendia et al.

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis
type: item
type: AcademicArticle
description: Type I polyketide synthase 13 (Pks13) is involved in the final step of the biosynthesis of mycolic acid in Mycobacterium tuberculosis. Recent articles have reported that Pks13 is an essential enzyme in the mycolic acid biosynthesis pathway, and it has been deeply studied as a drug target in Tuberculosis. We report a high-resolution structure of the acyltransferase (AT) domain of Pks13 at 2.59 Å resolution. Structural comparison with the full-length AT domain (PDB code, 3TZW, and 3TZZ) reveals a different orientation of the C-terminal helix and rearrangement of some conserved residues.
format: application/pdf
format: text/html
creator: Mingjing Yu
creator: Chao Dou
creator: Yijun Gu
creator: Wei Cheng
subject: Biochemistry
subject: Microbiology
subject: Global Health
description: doi:10.7717/peerj.4728
publisher: PeerJ Inc.
rights: © 2018 Yu et al.
abstract: Type I polyketide synthase 13 (Pks13) is involved in the final step of the biosynthesis of mycolic acid in Mycobacterium tuberculosis. Recent articles have reported that Pks13 is an essential enzyme in the mycolic acid biosynthesis pathway, and it has been deeply studied as a drug target in Tuberculosis. We report a high-resolution structure of the acyltransferase (AT) domain of Pks13 at 2.59 Å resolution. Structural comparison with the full-length AT domain (PDB code, 3TZW, and 3TZZ) reveals a different orientation of the C-terminal helix and rearrangement of some conserved residues.
bibliographic citation: Yu et al. (2018) Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis. PeerJ 6:e4728 https://doi.org/10.7717/peerj.4728
date submitted: 2017-11-09
date accepted: 2018-04-17
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Mingjing
author list: Agent
  family name: Dou
  given name: Chao
author list: Agent
  family name: Gu
  given name: Yijun
author list: Agent
  family name: Cheng
  given name: Wei
doi: 10.7717/peerj.4728
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: © 2018 Yu et al.
attribution name: Yu et al.

A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing
type: item
type: AcademicArticle
description: Background Antibiotic misuse in the community contributes to antimicrobial resistance. One way to address this may be by better utilizing community pharmacists’ skills in antibiotic prescribing. The aims of this study were to examine the level of support for “down-scheduling” selected antibiotics and to evaluate factors determining the appropriateness of community pharmacist prescribing for a limited range of infections, including their decision to refer to a doctor. Methods Self-administered questionnaires, including graded case vignette scenarios simulating real practice, were sent to Western Australian community pharmacists. In addition to descriptive statistics and chi-square testing, a General Estimating Equation (GEE) was used to identify factors associated with appropriateness of therapy and the decision to refer, for each of the seven vignettes. Results Of the 240 pharmacists surveyed, 90 (37.5%) responded, yielding 630 responses to seven different case vignettes. There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics. Overall 426/630 (67.6%) chose to treat the patient while the remaining 204/630 (32.4%) referred the patient to a doctor. Of those electing to treat, 380/426 (89.2%) opted to use oral antibiotics, with 293/380 (77.2%) treating with an appropriate selection and regimen. The GEE model indicated that pharmacists were more likely to prescribe inappropriately for conditions such as otitis media (p = 0.0060) and urinary tract infection in pregnancy (p < 0.0001) compared to more complex conditions. Over 80% of all pharmacists would refer the patient to a doctor following no improvement within 3 days, or within 24 h in the case of community acquired pneumonia. It was more common for younger pharmacists to refer the patient to a doctor (p = 0.0165). Discussion This study adds further insight into community pharmacy/pharmacist characteristics associated with appropriateness of oral antibiotic…
format: application/pdf
format: text/html
creator: Fatima Sinkala
creator: Richard Parsons
creator: Bruce Sunderland
creator: Kreshnik Hoti
creator: Petra Czarniak
subject: Health Policy
subject: Translational Medicine
description: doi:10.7717/peerj.4726
publisher: PeerJ Inc.
rights: © 2018 Sinkala et al.
abstract: Background Antibiotic misuse in the community contributes to antimicrobial resistance. One way to address this may be by better utilizing community pharmacists’ skills in antibiotic prescribing. The aims of this study were to examine the level of support for “down-scheduling” selected antibiotics and to evaluate factors determining the appropriateness of community pharmacist prescribing for a limited range of infections, including their decision to refer to a doctor. Methods Self-administered questionnaires, including graded case vignette scenarios simulating real practice, were sent to Western Australian community pharmacists. In addition to descriptive statistics and chi-square testing, a General Estimating Equation (GEE) was used to identify factors associated with appropriateness of therapy and the decision to refer, for each of the seven vignettes. Results Of the 240 pharmacists surveyed, 90 (37.5%) responded, yielding 630 responses to seven different case vignettes. There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics. Overall 426/630 (67.6%) chose to treat the patient while the remaining 204/630 (32.4%) referred the patient to a doctor. Of those electing to treat, 380/426 (89.2%) opted to use oral antibiotics, with 293/380 (77.2%) treating with an appropriate selection and regimen. The GEE model indicated that pharmacists were more likely to prescribe inappropriately for conditions such as otitis media (p = 0.0060) and urinary tract infection in pregnancy (p < 0.0001) compared to more complex conditions. Over 80% of all pharmacists would refer the patient to a doctor following no improvement within 3 days, or within 24 h in the case of community acquired pneumonia. It was more common for younger pharmacists to refer the patient to a doctor (p = 0.0165). Discussion This study adds further insight into community pharmacy/pharmacist characteristics associated with appropriateness of oral antibiotic…
bibliographic citation: Sinkala et al. (2018) A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing. PeerJ 6:e4726 https://doi.org/10.7717/peerj.4726
date submitted: 2017-11-15
date accepted: 2018-04-17
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sinkala
  given name: Fatima
author list: Agent
  family name: Parsons
  given name: Richard
author list: Agent
  family name: Sunderland
  given name: Bruce
author list: Agent
  family name: Hoti
  given name: Kreshnik
author list: Agent
  family name: Czarniak
  given name: Petra
doi: 10.7717/peerj.4726
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: ©2018 Sinkala et al.
attribution name: Sinkala et al.

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