PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies
items: The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster
items: Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase
items: First palaeoneurological study of a sauropod dinosaur from France and its phylogenetic significance
items: Bibliographic revision of Mesacanthion Filipjev, 1927 (Nematoda: Thoracostomopsidae) with description of a new species from Jeju Island, South Korea
items: Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies
items: A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis
items: Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion
items: Angiogenic signaling in the lungs of a metabolically suppressed hibernating mammal (Ictidomys tridecemlineatus)
items: Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato

Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies
type: item
type: AcademicArticle
description: Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens.
format: application/pdf
format: text/html
creator: Tapakorn Chamchoy
creator: Deneice R. Williams
creator: John M. Adaska
creator: Randall J. Anderson
creator: Sharif S. Aly
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.8081
publisher: PeerJ Inc.
rights: © 2019 Chamchoy et al.
abstract: Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens.
bibliographic citation: Chamchoy et al. (2019) Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies. PeerJ 7:e8081 https://doi.org/10.7717/peerj.8081
date submitted: 2019-06-10
date accepted: 2019-10-21
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chamchoy
  given name: Tapakorn
author list: Agent
  family name: Williams
  given name: Deneice R.
author list: Agent
  family name: Adaska
  given name: John M.
author list: Agent
  family name: Anderson
  given name: Randall J.
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.8081
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Chamchoy et al.
attribution name: Chamchoy et al.

The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster
type: item
type: AcademicArticle
description: Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster…
format: application/pdf
format: text/html
creator: Gabrielle M. Solomon
creator: Hiruni Dodangoda
creator: Tylea McCarthy-Walker
creator: Rita Ntim-Gyakari
creator: Peter D. Newell
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.8097
publisher: PeerJ Inc.
rights: © 2019 Solomon et al.
abstract: Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster…
bibliographic citation: Solomon et al. (2019) The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster. PeerJ 7:e8097 https://doi.org/10.7717/peerj.8097
date submitted: 2019-08-13
date accepted: 2019-10-24
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solomon
  given name: Gabrielle M.
author list: Agent
  family name: Dodangoda
  given name: Hiruni
author list: Agent
  family name: McCarthy-Walker
  given name: Tylea
author list: Agent
  family name: Ntim-Gyakari
  given name: Rita
author list: Agent
  family name: Newell
  given name: Peter D.
doi: 10.7717/peerj.8097
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: ©2019 Solomon et al.
attribution name: Solomon et al.

Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase
type: item
type: AcademicArticle
description: Background Increased daily cumulative hip moment in the frontal plane (i.e., the product of hip moment impulse in the frontal plane during the stance phase and mean steps per day) is a risk factor for progression of hip osteoarthritis. Although hip osteoarthritis generally causes a decrease in the walking speed, its effect on hip moment impulse in the frontal plane is unclear. The purpose of this study was to examine the relationship between decrease in walking speed and hip moment impulse in the frontal plane. Methods We used a public dataset of treadmill walking in 17 older adults (mean (SD) age: 63.2 (8.0) years). The subjects walked on the treadmill for 30 s under five conditions: (1) 40% of comfortable non-dimensional speed (CNDS), (2) 55% CNDS, (3) 70% CNDS, (4) 85% CNDS, and (5) 100% CNDS. The hip moment impulse in the frontal plane non-normalized (or normalized) to step length (Nm s/kg [or Nm s/(kg m)]) for each condition was calculated. Furthermore, the relationship between walking speed and hip moment impulse in the frontal plane non-normalized (or normalized) to step length was examined using regression analysis based on a previous study. Results A decrease in non-dimensional speed (i.e., walking speed) significantly increased the non-normalized (or normalized) hip moment impulse in the frontal plane during the stance phase. The relationship between walking speed and non-normalized (or normalized) hip moment impulse in the frontal plane was fitted by a second-order polynomial. Discussion This study revealed that a decrease in walking speed increased the non-normalized (or normalized) hip moment impulse in the frontal plane in healthy older adults. This finding is useful for understanding the relationship between walking speed and hip moment impulse in the frontal plane and suggests that a decrease in walking speed may actually increase the daily cumulative hip moment in the frontal plane of patients with hip osteoarthritis.
format: application/pdf
format: text/html
creator: Takuma Inai
creator: Tomoya Takabayashi
creator: Mutsuaki Edama
creator: Masayoshi Kubo
subject: Kinesiology
subject: Rheumatology
description: doi:10.7717/peerj.8110
publisher: PeerJ Inc.
rights: © 2019 Inai et al.
abstract: Background Increased daily cumulative hip moment in the frontal plane (i.e., the product of hip moment impulse in the frontal plane during the stance phase and mean steps per day) is a risk factor for progression of hip osteoarthritis. Although hip osteoarthritis generally causes a decrease in the walking speed, its effect on hip moment impulse in the frontal plane is unclear. The purpose of this study was to examine the relationship between decrease in walking speed and hip moment impulse in the frontal plane. Methods We used a public dataset of treadmill walking in 17 older adults (mean (SD) age: 63.2 (8.0) years). The subjects walked on the treadmill for 30 s under five conditions: (1) 40% of comfortable non-dimensional speed (CNDS), (2) 55% CNDS, (3) 70% CNDS, (4) 85% CNDS, and (5) 100% CNDS. The hip moment impulse in the frontal plane non-normalized (or normalized) to step length (Nm s/kg [or Nm s/(kg m)]) for each condition was calculated. Furthermore, the relationship between walking speed and hip moment impulse in the frontal plane non-normalized (or normalized) to step length was examined using regression analysis based on a previous study. Results A decrease in non-dimensional speed (i.e., walking speed) significantly increased the non-normalized (or normalized) hip moment impulse in the frontal plane during the stance phase. The relationship between walking speed and non-normalized (or normalized) hip moment impulse in the frontal plane was fitted by a second-order polynomial. Discussion This study revealed that a decrease in walking speed increased the non-normalized (or normalized) hip moment impulse in the frontal plane in healthy older adults. This finding is useful for understanding the relationship between walking speed and hip moment impulse in the frontal plane and suggests that a decrease in walking speed may actually increase the daily cumulative hip moment in the frontal plane of patients with hip osteoarthritis.
bibliographic citation: Inai et al. (2019) Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase. PeerJ 7:e8110 https://doi.org/10.7717/peerj.8110
date submitted: 2019-07-09
date accepted: 2019-10-28
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Inai
  given name: Takuma
author list: Agent
  family name: Takabayashi
  given name: Tomoya
author list: Agent
  family name: Edama
  given name: Mutsuaki
author list: Agent
  family name: Kubo
  given name: Masayoshi
doi: 10.7717/peerj.8110
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: ©2019 Inai et al.
attribution name: Inai et al.

First palaeoneurological study of a sauropod dinosaur from France and its phylogenetic significance
type: item
type: AcademicArticle
description: Despite continuous improvements, our knowledge of the palaeoneurology of sauropod dinosaurs is still deficient. This holds true even for Titanosauria, which is a particularly speciose clade of sauropods with representatives known from numerous Cretaceous sites in many countries on all continents. The data currently available regarding the palaeoneurology of titanosaurs is strongly biased towards Gondwanan forms (Argentina above all, but also India, Malawi and Australia). In contrast, the palaeoneurology of Laurasian titanosaurs is known only from a few taxa from Spain and Uzbekistan, despite the discovery in other countries of Laurasia of a number of neurocranial remains that would lend themselves well to investigations of this kind. To fill in this gap in our knowledge, we subjected a titanosaurian braincase from the uppermost Upper Cretaceous of southern France to X-ray computed tomographic scanning, allowing the generation of 3D renderings of the endocranial cavity enclosing the brain, cranial nerves and blood vessels, as well as the labyrinth of the inner ear. These reconstructions are used to clarify the phylogenetic position of the specimen from the Fox-Amphoux-Métisson site. A combination of characters, including the presence of two hypoglossal rami on the endocast, the average degree of development of the dorsal-head/caudal-middle-cerebral vein system and the relatively short and subequal lengths of the ipsilateral semicircular canals of the labyrinth, are particularly revealing in this respect. They suggest that, compared with the few other Laurasian titanosaurs for which in-depth palaeoneurological data are available, the French taxon is more derived than the distinctly more ancient, possibly non-lithostrotian titanosaur from the Uzbek site of Dzharakuduk but more basal than derived saltasaurids, such as the coeval or slightly more recent forms from the Spanish locality of Lo Hueco.
format: application/pdf
format: text/html
creator: Fabien Knoll
creator: Stephan Lautenschlager
creator: Xavier Valentin
creator: Verónica Díez Díaz
creator: Xabier Pereda Suberbiola
creator: Géraldine Garcia
subject: Evolutionary Studies
subject: Neuroscience
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7991
publisher: PeerJ Inc.
rights: © 2019 Knoll et al.
abstract: Despite continuous improvements, our knowledge of the palaeoneurology of sauropod dinosaurs is still deficient. This holds true even for Titanosauria, which is a particularly speciose clade of sauropods with representatives known from numerous Cretaceous sites in many countries on all continents. The data currently available regarding the palaeoneurology of titanosaurs is strongly biased towards Gondwanan forms (Argentina above all, but also India, Malawi and Australia). In contrast, the palaeoneurology of Laurasian titanosaurs is known only from a few taxa from Spain and Uzbekistan, despite the discovery in other countries of Laurasia of a number of neurocranial remains that would lend themselves well to investigations of this kind. To fill in this gap in our knowledge, we subjected a titanosaurian braincase from the uppermost Upper Cretaceous of southern France to X-ray computed tomographic scanning, allowing the generation of 3D renderings of the endocranial cavity enclosing the brain, cranial nerves and blood vessels, as well as the labyrinth of the inner ear. These reconstructions are used to clarify the phylogenetic position of the specimen from the Fox-Amphoux-Métisson site. A combination of characters, including the presence of two hypoglossal rami on the endocast, the average degree of development of the dorsal-head/caudal-middle-cerebral vein system and the relatively short and subequal lengths of the ipsilateral semicircular canals of the labyrinth, are particularly revealing in this respect. They suggest that, compared with the few other Laurasian titanosaurs for which in-depth palaeoneurological data are available, the French taxon is more derived than the distinctly more ancient, possibly non-lithostrotian titanosaur from the Uzbek site of Dzharakuduk but more basal than derived saltasaurids, such as the coeval or slightly more recent forms from the Spanish locality of Lo Hueco.
bibliographic citation: Knoll et al. (2019) First palaeoneurological study of a sauropod dinosaur from France and its phylogenetic significance. PeerJ 7:e7991 https://doi.org/10.7717/peerj.7991
date submitted: 2019-04-11
date accepted: 2019-10-04
issued: 2019-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Knoll
  given name: Fabien
author list: Agent
  family name: Lautenschlager
  given name: Stephan
author list: Agent
  family name: Valentin
  given name: Xavier
author list: Agent
  family name: Díez Díaz
  given name: Verónica
author list: Agent
  family name: Pereda Suberbiola
  given name: Xabier
author list: Agent
  family name: Garcia
  given name: Géraldine
doi: 10.7717/peerj.7991
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-18
copyright: © 2019 Knoll et al.
attribution name: Knoll et al.

Bibliographic revision of Mesacanthion Filipjev, 1927 (Nematoda: Thoracostomopsidae) with description of a new species from Jeju Island, South Korea
type: item
type: AcademicArticle
description: A new species of the genus Mesacanthion Filipjev, 1927 was discovered during a survey of natural beaches of Jeju Island in South Korea. The new species Mesacanthion jejuensis sp. nov. shares general morphology of the genus such as the outer labial and cephalic setae being situated at the middle of cephalic capsule, well-developed mandibles with two columns united by a curved bar, and three equally sized and shaped teeth shorter than the mandibles. The new species belongs to a group of Mesacanthion species in which spicules are shorter than two anal body diameters. The new species is most closely related to M. pannosum, first discovered in Puget Sound, Washington, in terms of having enlarged cervical setae flap at the end of cephalic capsule, spicules which are shorter than 2 anal body diameter, both supplementary organ and gubernaculum. It can be distinguished from M. pannosum by its stronger inner labial setae, longer outer labial setae, and difference in the index value of b and c’. Along with the description of Mesacanthion jejuensis sp. nov., the genus Mesacanthion Filipjev, 1927 is bibliographically reviewed and revised. Including the new species, a total of 48 species are described within the genus; 39 which are valid; eight which are considered to be species inquirenda due to misplacement of genus and poor description; one which is considered nomen nudum. An updated diagnosis of the genus is provided along with a compiled tabular key comparing different diagnostic morphological characters of all valid species, as well as a pictorial key consisting of 21 species with spicules shorter than two anal body diameters.
format: application/pdf
format: text/html
creator: Raehyuk Jeong
creator: Alexei V. Tchesunov
creator: Wonchoel Lee
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8023
publisher: PeerJ Inc.
rights: © 2019 Jeong et al.
abstract: A new species of the genus Mesacanthion Filipjev, 1927 was discovered during a survey of natural beaches of Jeju Island in South Korea. The new species Mesacanthion jejuensis sp. nov. shares general morphology of the genus such as the outer labial and cephalic setae being situated at the middle of cephalic capsule, well-developed mandibles with two columns united by a curved bar, and three equally sized and shaped teeth shorter than the mandibles. The new species belongs to a group of Mesacanthion species in which spicules are shorter than two anal body diameters. The new species is most closely related to M. pannosum, first discovered in Puget Sound, Washington, in terms of having enlarged cervical setae flap at the end of cephalic capsule, spicules which are shorter than 2 anal body diameter, both supplementary organ and gubernaculum. It can be distinguished from M. pannosum by its stronger inner labial setae, longer outer labial setae, and difference in the index value of b and c’. Along with the description of Mesacanthion jejuensis sp. nov., the genus Mesacanthion Filipjev, 1927 is bibliographically reviewed and revised. Including the new species, a total of 48 species are described within the genus; 39 which are valid; eight which are considered to be species inquirenda due to misplacement of genus and poor description; one which is considered nomen nudum. An updated diagnosis of the genus is provided along with a compiled tabular key comparing different diagnostic morphological characters of all valid species, as well as a pictorial key consisting of 21 species with spicules shorter than two anal body diameters.
bibliographic citation: Jeong et al. (2019) Bibliographic revision of Mesacanthion Filipjev, 1927 (Nematoda: Thoracostomopsidae) with description of a new species from Jeju Island, South Korea. PeerJ 7:e8023 https://doi.org/10.7717/peerj.8023
date submitted: 2019-06-20
date accepted: 2019-10-10
issued: 2019-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jeong
  given name: Raehyuk
author list: Agent
  family name: Tchesunov
  given name: Alexei V.
author list: Agent
  family name: Lee
  given name: Wonchoel
doi: 10.7717/peerj.8023
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-18
copyright: ©2019 Jeong et al.
attribution name: Jeong et al.

Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies
type: item
type: AcademicArticle
description: Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies–considered to be generalist predators–consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.
format: application/pdf
format: text/html
creator: Rittik Deb
creator: Ashwin Nair
creator: Deepa Agashe
subject: Ecology
subject: Entomology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.8058
publisher: PeerJ Inc.
rights: © 2019 Deb et al.
abstract: Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies–considered to be generalist predators–consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.
bibliographic citation: Deb et al. (2019) Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies. PeerJ 7:e8058 https://doi.org/10.7717/peerj.8058
date submitted: 2019-04-30
date accepted: 2019-10-18
issued: 2019-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deb
  given name: Rittik
author list: Agent
  family name: Nair
  given name: Ashwin
author list: Agent
  family name: Agashe
  given name: Deepa
doi: 10.7717/peerj.8058
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-18
copyright: ©2019 Deb et al.
attribution name: Deb et al.

A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis
type: item
type: AcademicArticle
description: Phytophthora hibernalis, the causal agent of brown rot of citrus fruit, is an important worldwide pathogen and a quarantine pest in China. Current diagnosis of the disease relies on disease symptoms, pathogen isolation and identification by DNA sequencing. However, symptoms caused by P. hibernalis can be confused with those by other Phytophthora and fungal species. Moreover, pathogen isolation, PCR amplification and sequencing are time-consuming. In this study, a rapid assay including 20-min recombinase polymerase amplification targeting the Ypt1 gene and 5-min visualization using lateral flow dipsticks was developed for detecting P. hibernalis. This assay was able to detect 0.2 ng of P. hibernalis genomic DNA in a 50-µL reaction system. It was specific to P. hibernalis without detection of other tested species including P. citrophthora, P. nicotianae, P. palmivora and P. syringae, four other important citrus pathogens. Using this assay, P. hibernalis was also detected from artificially inoculated orange fruits. Results in this study indicated that this assay has the potential application to detect P. hibernalis at diagnostic laboratories and plant quarantine departments of customs, especially under time- and resource-limited conditions.
format: application/pdf
format: text/html
creator: Tingting Dai
creator: Tao Hu
creator: Xiao Yang
creator: Danyu Shen
creator: Binbin Jiao
creator: Wen Tian
creator: Yue Xu
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.8083
publisher: PeerJ Inc.
rights: © 2019 Dai et al.
abstract: Phytophthora hibernalis, the causal agent of brown rot of citrus fruit, is an important worldwide pathogen and a quarantine pest in China. Current diagnosis of the disease relies on disease symptoms, pathogen isolation and identification by DNA sequencing. However, symptoms caused by P. hibernalis can be confused with those by other Phytophthora and fungal species. Moreover, pathogen isolation, PCR amplification and sequencing are time-consuming. In this study, a rapid assay including 20-min recombinase polymerase amplification targeting the Ypt1 gene and 5-min visualization using lateral flow dipsticks was developed for detecting P. hibernalis. This assay was able to detect 0.2 ng of P. hibernalis genomic DNA in a 50-µL reaction system. It was specific to P. hibernalis without detection of other tested species including P. citrophthora, P. nicotianae, P. palmivora and P. syringae, four other important citrus pathogens. Using this assay, P. hibernalis was also detected from artificially inoculated orange fruits. Results in this study indicated that this assay has the potential application to detect P. hibernalis at diagnostic laboratories and plant quarantine departments of customs, especially under time- and resource-limited conditions.
bibliographic citation: Dai et al. (2019) A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis. PeerJ 7:e8083 https://doi.org/10.7717/peerj.8083
date submitted: 2019-07-24
date accepted: 2019-10-22
issued: 2019-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dai
  given name: Tingting
author list: Agent
  family name: Hu
  given name: Tao
author list: Agent
  family name: Yang
  given name: Xiao
author list: Agent
  family name: Shen
  given name: Danyu
author list: Agent
  family name: Jiao
  given name: Binbin
author list: Agent
  family name: Tian
  given name: Wen
author list: Agent
  family name: Xu
  given name: Yue
doi: 10.7717/peerj.8083
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-18
copyright: © 2019 Dai et al.
attribution name: Dai et al.

Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion
type: item
type: AcademicArticle
description: Microbial symbionts can play critical roles when their host attempts to colonize a new habitat. The lack of symbiont adaptation can in fact hinder the invasion process of their host. This scenario could change if the exotic species are able to acquire microorganisms from the invaded environment. Understanding the ecological factors that influence the take-up of new microorganisms is thus essential to clarify the mechanisms behind biological invasions. In this study, we tested whether different forest habitats influence the structure of the fungal communities associated with ambrosia beetles. We collected individuals of the most widespread exotic (Xylosandrus germanus) and native (Xyleborinus saxesenii) ambrosia beetle species in Europe in several old-growth and restored forests. We characterized the fungal communities associated with both species via metabarcoding. We showed that forest habitat shaped the community of fungi associated with both species, but the effect was stronger for the exotic X. germanus. Our results support the hypothesis that the direct contact with the mycobiome of the invaded environment might lead an exotic species to acquire native fungi. This process is likely favored by the occurrence of a bottleneck effect at the mycobiome level and/or the disruption of the mechanisms sustaining co-evolved insect-fungi symbiosis. Our study contributes to the understanding of the factors affecting insect-microbes interactions, helping to clarify the mechanisms behind biological invasions.
format: application/pdf
format: text/html
creator: Davide Rassati
creator: Lorenzo Marini
creator: Antonino Malacrinò
subject: Ecology
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.8103
publisher: PeerJ Inc.
rights: © 2019 Rassati et al.
abstract: Microbial symbionts can play critical roles when their host attempts to colonize a new habitat. The lack of symbiont adaptation can in fact hinder the invasion process of their host. This scenario could change if the exotic species are able to acquire microorganisms from the invaded environment. Understanding the ecological factors that influence the take-up of new microorganisms is thus essential to clarify the mechanisms behind biological invasions. In this study, we tested whether different forest habitats influence the structure of the fungal communities associated with ambrosia beetles. We collected individuals of the most widespread exotic (Xylosandrus germanus) and native (Xyleborinus saxesenii) ambrosia beetle species in Europe in several old-growth and restored forests. We characterized the fungal communities associated with both species via metabarcoding. We showed that forest habitat shaped the community of fungi associated with both species, but the effect was stronger for the exotic X. germanus. Our results support the hypothesis that the direct contact with the mycobiome of the invaded environment might lead an exotic species to acquire native fungi. This process is likely favored by the occurrence of a bottleneck effect at the mycobiome level and/or the disruption of the mechanisms sustaining co-evolved insect-fungi symbiosis. Our study contributes to the understanding of the factors affecting insect-microbes interactions, helping to clarify the mechanisms behind biological invasions.
bibliographic citation: Rassati et al. (2019) Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion. PeerJ 7:e8103 https://doi.org/10.7717/peerj.8103
date submitted: 2019-06-10
date accepted: 2019-10-25
issued: 2019-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rassati
  given name: Davide
author list: Agent
  family name: Marini
  given name: Lorenzo
author list: Agent
  family name: Malacrinò
  given name: Antonino
doi: 10.7717/peerj.8103
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-18
copyright: ©2019 Rassati et al.
attribution name: Rassati et al.

Angiogenic signaling in the lungs of a metabolically suppressed hibernating mammal (Ictidomys tridecemlineatus)
type: item
type: AcademicArticle
description: To conserve energy in times of limited resource availability, particularly during cold winters, hibernators suppress even the most basic of physiologic processes. Breathing rates decrease from 40 breaths/minute to less than 1 breath/min as they decrease body temperature from 37 °C to ambient. Nevertheless, after months of hibernation, these incredible mammals emerge from torpor unscathed. This study was conducted to better understand the protective and possibly anti-inflammatory adaptations that hibernator lungs may use to prevent damage associated with entering and emerging from natural torpor. We postulated that the differential protein expression of soluble protein receptors (decoy receptors that sequester soluble ligands to inhibit signal transduction) would help identify inhibited inflammatory signaling pathways in metabolically suppressed lungs. Instead, the only two soluble receptors that responded to torpor were sVEGFR1 and sVEGFR2, two receptors whose full-length forms are bound by VEGF-A to regulate endothelial cell function and angiogenesis. Decreased sVEGFR1/2 correlated with increased total VEGFR2 protein levels. Maintained or increased levels of key γ-secretase subunits suggested that decreased sVEGFR1/2 protein levels were not due to decreased levels of intramembrane cleavage complex subunits. VEGF-A protein levels did not change, suggesting that hibernators may regulate VEGFR1/2 signaling at the level of the receptor instead of increasing relative ligand abundance. A panel of angiogenic factors used to identify biomarkers of angiogenesis showed a decrease in FGF-1 and an increase in BMP-9. Torpid lungs may use VEGF and BMP-9 signaling to balance angiogenesis and vascular stability, possibly through the activation of SMAD signaling for adaptive tissue remodeling.
format: application/pdf
format: text/html
creator: Samantha M. Logan
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8116
publisher: PeerJ Inc.
rights: © 2019 Logan and Storey
abstract: To conserve energy in times of limited resource availability, particularly during cold winters, hibernators suppress even the most basic of physiologic processes. Breathing rates decrease from 40 breaths/minute to less than 1 breath/min as they decrease body temperature from 37 °C to ambient. Nevertheless, after months of hibernation, these incredible mammals emerge from torpor unscathed. This study was conducted to better understand the protective and possibly anti-inflammatory adaptations that hibernator lungs may use to prevent damage associated with entering and emerging from natural torpor. We postulated that the differential protein expression of soluble protein receptors (decoy receptors that sequester soluble ligands to inhibit signal transduction) would help identify inhibited inflammatory signaling pathways in metabolically suppressed lungs. Instead, the only two soluble receptors that responded to torpor were sVEGFR1 and sVEGFR2, two receptors whose full-length forms are bound by VEGF-A to regulate endothelial cell function and angiogenesis. Decreased sVEGFR1/2 correlated with increased total VEGFR2 protein levels. Maintained or increased levels of key γ-secretase subunits suggested that decreased sVEGFR1/2 protein levels were not due to decreased levels of intramembrane cleavage complex subunits. VEGF-A protein levels did not change, suggesting that hibernators may regulate VEGFR1/2 signaling at the level of the receptor instead of increasing relative ligand abundance. A panel of angiogenic factors used to identify biomarkers of angiogenesis showed a decrease in FGF-1 and an increase in BMP-9. Torpid lungs may use VEGF and BMP-9 signaling to balance angiogenesis and vascular stability, possibly through the activation of SMAD signaling for adaptive tissue remodeling.
bibliographic citation: Logan et al. (2019) Angiogenic signaling in the lungs of a metabolically suppressed hibernating mammal (Ictidomys tridecemlineatus). PeerJ 7:e8116 https://doi.org/10.7717/peerj.8116
date submitted: 2019-08-08
date accepted: 2019-10-29
issued: 2019-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Logan
  given name: Samantha M.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.8116
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-18
copyright: © 2019 Logan and Storey
attribution name: Logan and Storey

Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato
type: item
type: AcademicArticle
description: Background Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither a complete reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid crop are available, which in turn impedes progress in research studies in I. batatas functional genomics and molecular breeding. Methods In this study, we sequenced full-length transcriptomes in I. batatas and its diploid ancestor I. trifida by single-molecule real-time sequencing and Illumina second-generation sequencing technologies. With the generated datasets, we conducted comprehensive intraspecific and interspecific sequence analyses and experimental characterization. Results A total of 53,861/51,184 high-quality long-read transcripts were obtained, which covered about 10,439/10,452 loci in the I. batatas/I. trifida genome. These datasets enabled us to predict open reading frames successfully in 96.83%/96.82% of transcripts and identify 34,963/33,637 full-length cDNA sequences, 1,401/1,457 transcription factors, 25,315/27,090 simple sequence repeats, 1,656/1,389 long non-coding RNAs, and 5,251/8,901 alternative splicing events. Approximately, 32.34%/38.54% of transcripts and 46.22%/51.18% multi-exon transcripts underwent alternative splicing in I. batatas/I. trifida. Moreover, we validated one alternative splicing event in each of 10 genes and identified tuberous-root-specific expressed isoforms from a starch-branching enzyme, an alpha-glucan phosphorylase, a neutral invertase, and several ABC transporters. Overall, the collection and analysis of large-scale long-read transcripts generated in this study will serve as a valuable resource for the I. batatas research community, which may accelerate the progress in its structural, functional, and comparative genomics studies.
format: application/pdf
format: text/html
creator: Na Ding
creator: Huihui Cui
creator: Ying Miao
creator: Jun Tang
creator: Qinghe Cao
creator: Yonghai Luo
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7933
publisher: PeerJ Inc.
rights: © 2019 Ding et al.
abstract: Background Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither a complete reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid crop are available, which in turn impedes progress in research studies in I. batatas functional genomics and molecular breeding. Methods In this study, we sequenced full-length transcriptomes in I. batatas and its diploid ancestor I. trifida by single-molecule real-time sequencing and Illumina second-generation sequencing technologies. With the generated datasets, we conducted comprehensive intraspecific and interspecific sequence analyses and experimental characterization. Results A total of 53,861/51,184 high-quality long-read transcripts were obtained, which covered about 10,439/10,452 loci in the I. batatas/I. trifida genome. These datasets enabled us to predict open reading frames successfully in 96.83%/96.82% of transcripts and identify 34,963/33,637 full-length cDNA sequences, 1,401/1,457 transcription factors, 25,315/27,090 simple sequence repeats, 1,656/1,389 long non-coding RNAs, and 5,251/8,901 alternative splicing events. Approximately, 32.34%/38.54% of transcripts and 46.22%/51.18% multi-exon transcripts underwent alternative splicing in I. batatas/I. trifida. Moreover, we validated one alternative splicing event in each of 10 genes and identified tuberous-root-specific expressed isoforms from a starch-branching enzyme, an alpha-glucan phosphorylase, a neutral invertase, and several ABC transporters. Overall, the collection and analysis of large-scale long-read transcripts generated in this study will serve as a valuable resource for the I. batatas research community, which may accelerate the progress in its structural, functional, and comparative genomics studies.
bibliographic citation: Ding et al. (2019) Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato. PeerJ 7:e7933 https://doi.org/10.7717/peerj.7933
date submitted: 2019-05-14
date accepted: 2019-09-23
issued: 2019-11-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Na
author list: Agent
  family name: Cui
  given name: Huihui
author list: Agent
  family name: Miao
  given name: Ying
author list: Agent
  family name: Tang
  given name: Jun
author list: Agent
  family name: Cao
  given name: Qinghe
author list: Agent
  family name: Luo
  given name: Yonghai
doi: 10.7717/peerj.7933
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-15
copyright: ©2019 Ding et al.
attribution name: Ding et al.

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