PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica
items: Analysis of the RNA virome of basal hexapods
items: Temporal dynamics of the hummingbird-plant interaction network of a dry forest in Chamela, Mexico: a 30-year follow-up after two hurricanes
items: A multiomics comparison between endometrial cancer and serous ovarian cancer
items: Age-related alterations in inhibitory control investigated using the minimally delayed oculomotor response task
items: Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study
items: Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics
items: DNA methylation profiling in recurrent miscarriage
items: Soil aggregate size influences the impact of inorganic nitrogen deposition on soil nitrification in an alpine meadow of the Qinghai–Tibet Plateau
items: A pilot study on searching for peri-nuclear NeuN-positive cells

New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica
type: item
type: AcademicArticle
description: The middle–late Eocene of Antarctica was characterized by dramatic change as the continent became isolated from the other southern landmasses and the Antarctic Circumpolar Current formed. These events were crucial to the formation of the permanent Antarctic ice cap, affecting both regional and global climate change. Our best insight into how life in the high latitudes responded to this climatic shift is provided by the fossil record from Seymour Island, near the eastern coast of the Antarctic Peninsula. While extensive collections have been made from the La Meseta and Submeseta formations of this island, few avian taxa other than penguins have been described and mammalian postcranial remains have been scarce. Here, we report new fossils from Seymour Island collected by the Antarctic Peninsula Paleontology Project. These include a mammalian metapodial referred to Xenarthra and avian material including a partial tarsometatarsus referred to Gruiformes (cranes, rails, and allies). Penguin fossils (Sphenisciformes) continue to be most abundant in new collections from these deposits. We report several penguin remains including a large spear-like mandible preserving the symphysis, a nearly complete tarsometatarsus with similarities to the large penguin clade Palaeeudyptes but possibly representing a new species, and two small partial tarsometatarsi belonging to the genus Delphinornis. These findings expand our view of Eocene vertebrate faunas on Antarctica. Specifically, the new remains referred to Gruiformes and Xenarthra provide support for previously proposed, but contentious, earliest occurrence records of these clades on the continent.
format: application/pdf
format: text/html
creator: Sarah N. Davis
creator: Christopher R. Torres
creator: Grace M. Musser
creator: James V. Proffitt
creator: Nicholas M.A. Crouch
creator: Ernest L. Lundelius
creator: Matthew C. Lamanna
creator: Julia A. Clarke
subject: Biogeography
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.8268
publisher: PeerJ Inc.
rights: © 2020 Davis et al.
abstract: The middle–late Eocene of Antarctica was characterized by dramatic change as the continent became isolated from the other southern landmasses and the Antarctic Circumpolar Current formed. These events were crucial to the formation of the permanent Antarctic ice cap, affecting both regional and global climate change. Our best insight into how life in the high latitudes responded to this climatic shift is provided by the fossil record from Seymour Island, near the eastern coast of the Antarctic Peninsula. While extensive collections have been made from the La Meseta and Submeseta formations of this island, few avian taxa other than penguins have been described and mammalian postcranial remains have been scarce. Here, we report new fossils from Seymour Island collected by the Antarctic Peninsula Paleontology Project. These include a mammalian metapodial referred to Xenarthra and avian material including a partial tarsometatarsus referred to Gruiformes (cranes, rails, and allies). Penguin fossils (Sphenisciformes) continue to be most abundant in new collections from these deposits. We report several penguin remains including a large spear-like mandible preserving the symphysis, a nearly complete tarsometatarsus with similarities to the large penguin clade Palaeeudyptes but possibly representing a new species, and two small partial tarsometatarsi belonging to the genus Delphinornis. These findings expand our view of Eocene vertebrate faunas on Antarctica. Specifically, the new remains referred to Gruiformes and Xenarthra provide support for previously proposed, but contentious, earliest occurrence records of these clades on the continent.
bibliographic citation: Davis et al. (2020) New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica. PeerJ 8:e8268 https://doi.org/10.7717/peerj.8268
date submitted: 2019-07-15
date accepted: 2019-11-22
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davis
  given name: Sarah N.
author list: Agent
  family name: Torres
  given name: Christopher R.
author list: Agent
  family name: Musser
  given name: Grace M.
author list: Agent
  family name: Proffitt
  given name: James V.
author list: Agent
  family name: Crouch
  given name: Nicholas M.A.
author list: Agent
  family name: Lundelius
  given name: Ernest L.
author list: Agent
  family name: Lamanna
  given name: Matthew C.
author list: Agent
  family name: Clarke
  given name: Julia A.
doi: 10.7717/peerj.8268
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Davis et al.
attribution name: Davis et al.

Analysis of the RNA virome of basal hexapods
type: item
type: AcademicArticle
description: The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered 40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades.
format: application/pdf
format: text/html
creator: Sabina Ott Rutar
creator: Dusan Kordis
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.8336
publisher: PeerJ Inc.
rights: © 2020 Ott Rutar and Kordis
abstract: The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered 40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades.
bibliographic citation: Ott Rutar et al. (2020) Analysis of the RNA virome of basal hexapods. PeerJ 8:e8336 https://doi.org/10.7717/peerj.8336
date submitted: 2019-10-07
date accepted: 2019-12-03
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ott Rutar
  given name: Sabina
author list: Agent
  family name: Kordis
  given name: Dusan
doi: 10.7717/peerj.8336
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Ott Rutar and Kordis
attribution name: Ott Rutar and Kordis

Temporal dynamics of the hummingbird-plant interaction network of a dry forest in Chamela, Mexico: a 30-year follow-up after two hurricanes
type: item
type: AcademicArticle
description: Background Interactions among species are a driving force of community structure. The species composition of animal-plant interaction networks can be highly dynamic on a temporal scale, even though the general network structure is usually not altered. However, few studies have examined how interaction networks change over long periods of time, particularly after extreme natural events. We analyzed herein the structure of the hummingbird-plant interaction network in a dry forest of Chamela, Mexico, comparing the structure in 1985–1986 with that in 2016–2017 following the passage of two hurricanes (category 2 Jova in 2011 and category 4 Patricia in 2015). Methods The fieldwork was carried out in the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. In the last 30 years, three severe drought events and two hurricanes have affected this region. Previously, from 1985–1986, hummingbird-plant interactions were recorded monthly for one year in the study area. Then, from 2016–2017, we replicated the sampling in the same localities. We compared the network parameters describing the plant-hummingbird interactions of each period using adjacency matrices. Results We found differences in the number and identity of interacting species, especially plants. The plant species missing in 2016–2017 were either the least connected in the original network (1985–1986) or belonged to groups such as cacti, epiphytes, or trees. The new plant species incorporated in the 2016–2017 network were herbs, vines, and shrubs, or other species barely connected. These changes in the composition are consistent with reports on vegetation damage after strong hurricanes at other study sites. Conversely, all hummingbird species remained in the network, with the exception of Heliomaster constantii, which was primarily connected to a plant species absent in the 2016–2017 network. Migratory and habitat generalist species (i.e., Archilochus spp.) showed higher abundances following the disturbance events. Co…
format: application/pdf
format: text/html
creator: Sergio Díaz Infante
creator: Carlos Lara
creator: Maria del Coro Arizmendi
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.8338
publisher: PeerJ Inc.
rights: © 2020 Díaz Infante et al.
abstract: Background Interactions among species are a driving force of community structure. The species composition of animal-plant interaction networks can be highly dynamic on a temporal scale, even though the general network structure is usually not altered. However, few studies have examined how interaction networks change over long periods of time, particularly after extreme natural events. We analyzed herein the structure of the hummingbird-plant interaction network in a dry forest of Chamela, Mexico, comparing the structure in 1985–1986 with that in 2016–2017 following the passage of two hurricanes (category 2 Jova in 2011 and category 4 Patricia in 2015). Methods The fieldwork was carried out in the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. In the last 30 years, three severe drought events and two hurricanes have affected this region. Previously, from 1985–1986, hummingbird-plant interactions were recorded monthly for one year in the study area. Then, from 2016–2017, we replicated the sampling in the same localities. We compared the network parameters describing the plant-hummingbird interactions of each period using adjacency matrices. Results We found differences in the number and identity of interacting species, especially plants. The plant species missing in 2016–2017 were either the least connected in the original network (1985–1986) or belonged to groups such as cacti, epiphytes, or trees. The new plant species incorporated in the 2016–2017 network were herbs, vines, and shrubs, or other species barely connected. These changes in the composition are consistent with reports on vegetation damage after strong hurricanes at other study sites. Conversely, all hummingbird species remained in the network, with the exception of Heliomaster constantii, which was primarily connected to a plant species absent in the 2016–2017 network. Migratory and habitat generalist species (i.e., Archilochus spp.) showed higher abundances following the disturbance events. Co…
bibliographic citation: Díaz Infante et al. (2020) Temporal dynamics of the hummingbird-plant interaction network of a dry forest in Chamela, Mexico: a 30-year follow-up after two hurricanes. PeerJ 8:e8338 https://doi.org/10.7717/peerj.8338
date submitted: 2019-05-28
date accepted: 2019-12-03
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Díaz Infante
  given name: Sergio
author list: Agent
  family name: Lara
  given name: Carlos
author list: Agent
  family name: Arizmendi
  given name: Maria del Coro
doi: 10.7717/peerj.8338
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Díaz Infante et al.
attribution name: Díaz Infante et al.

A multiomics comparison between endometrial cancer and serous ovarian cancer
type: item
type: AcademicArticle
description: Background Endometrial carcinoma (EC) and serous ovarian carcinoma (OvCa) are both among the common cancer types in women. EC can be divided into two subtypes, endometroid EC and serous-like EC, with distinct histological characterizations and molecular phenotypes. There is an increasing awareness that serous-like EC resembles serous OvCa in genetic landscape, but a clear relationship between them is still lacking. Methods Here, we took advantage of the large-scale molecular profiling of The Cancer Genome Atlas(TCGA) to compare the two EC subtypes and serous OvCa. We used bioinformatics data analytic methods to systematically examine the somatic mutation (SM) and copy number alteration (SCNA), gene expression, pathway activities, survival gene signatures and immune infiltration. Based on these quantifiable molecular characterizations, we asked whether serous-like EC should be grouped more closely to serous OvCa, based on the context of being serous-like; or if should be grouped more closely to endometroid EC, based on the same organ origin. Results We found that although serous-like EC and serous OvCa share some common genotypes, including mutation and copy number alteration, they differ in molecular phenotypes such as gene expression and signaling pathway activity. Moreover, no shared prognostic gene signature was found, indicating that they use unique genes governing tumor progression. Finally, although the endometrioid EC and serous OvCa are both highly immune infiltrated, the immune cell composition in serous OvCa is mostly immune suppressive, whereas endometrioid EC has a higher level of cytotoxic immune cells. Overall, our genetic aberration and molecular phenotype characterizations indicated that serous-like EC and serous OvCa cannot be simply treated as a simple “serous” cancer type. In particular, additional attention should be paid to their unique gene activities and tumor microenvironments for novel targeted therapy development.
format: application/pdf
format: text/html
creator: Hui Zhong
creator: Huiyu Chen
creator: Huahong Qiu
creator: Chen Huang
creator: Zhihui Wu
subject: Bioinformatics
subject: Genomics
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.8347
publisher: PeerJ Inc.
rights: © 2020 Zhong et al.
abstract: Background Endometrial carcinoma (EC) and serous ovarian carcinoma (OvCa) are both among the common cancer types in women. EC can be divided into two subtypes, endometroid EC and serous-like EC, with distinct histological characterizations and molecular phenotypes. There is an increasing awareness that serous-like EC resembles serous OvCa in genetic landscape, but a clear relationship between them is still lacking. Methods Here, we took advantage of the large-scale molecular profiling of The Cancer Genome Atlas(TCGA) to compare the two EC subtypes and serous OvCa. We used bioinformatics data analytic methods to systematically examine the somatic mutation (SM) and copy number alteration (SCNA), gene expression, pathway activities, survival gene signatures and immune infiltration. Based on these quantifiable molecular characterizations, we asked whether serous-like EC should be grouped more closely to serous OvCa, based on the context of being serous-like; or if should be grouped more closely to endometroid EC, based on the same organ origin. Results We found that although serous-like EC and serous OvCa share some common genotypes, including mutation and copy number alteration, they differ in molecular phenotypes such as gene expression and signaling pathway activity. Moreover, no shared prognostic gene signature was found, indicating that they use unique genes governing tumor progression. Finally, although the endometrioid EC and serous OvCa are both highly immune infiltrated, the immune cell composition in serous OvCa is mostly immune suppressive, whereas endometrioid EC has a higher level of cytotoxic immune cells. Overall, our genetic aberration and molecular phenotype characterizations indicated that serous-like EC and serous OvCa cannot be simply treated as a simple “serous” cancer type. In particular, additional attention should be paid to their unique gene activities and tumor microenvironments for novel targeted therapy development.
bibliographic citation: Zhong et al. (2020) A multiomics comparison between endometrial cancer and serous ovarian cancer. PeerJ 8:e8347 https://doi.org/10.7717/peerj.8347
date submitted: 2019-08-02
date accepted: 2019-12-04
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Hui
author list: Agent
  family name: Chen
  given name: Huiyu
author list: Agent
  family name: Qiu
  given name: Huahong
author list: Agent
  family name: Huang
  given name: Chen
author list: Agent
  family name: Wu
  given name: Zhihui
doi: 10.7717/peerj.8347
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Zhong et al.
attribution name: Zhong et al.

Age-related alterations in inhibitory control investigated using the minimally delayed oculomotor response task
type: item
type: AcademicArticle
description: Healthy, older adults are widely reported to experience cognitive decline, including impairments in inhibitory control. However, this general proposition has recently come under scrutiny because ageing effects are highly variable between individuals, are task dependent, and are sometimes not distinguished from general age-related slowing. We recently developed the minimally delayed oculomotor response (MDOR) task in which participants are presented with a simple visual target step, and instructed to saccade not to the target when it appears (a prosaccade response), but when it disappears (i.e. on target offset). Varying the target display duration (TDD) prevents offset timing being predictable from the time of target onset, and saccades prior to the offset are counted as errors. A comparison of MDOR task performance in a group of 22 older adults (mean age 62 years, range 50–72 years) with that in a group of 39 younger adults (22 years, range 19–27 years) demonstrated that MDOR latency was significantly increased in the older group by 34–68 ms depending on TDD. However, when MDOR latencies were corrected by subtracting the latency observed in a standard prosaccade task, the latency difference between groups was abolished. There was a larger latency modulation with TDD in the older group which was observed even when their generally longer latencies were taken into account. Error rates were significantly increased in the older group. An analysis of the timing distribution of errors demonstrated that most errors were failures to inhibit responses to target onsets. When error distributions were used to isolate clear inhibition failures from other types of error, the older group still exhibited significantly higher error rates as well as a higher residual error rate. Although MDOR latency in older participants may largely reflect a general slowing in the oculomotor system with age, both the latency modulation and error rate results are consistent with an age-related inhib…
format: application/pdf
format: text/html
creator: Paul C. Knox
creator: Nikitha Pasunuru
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8401
publisher: PeerJ Inc.
rights: © 2020 Knox and Pasunuru
abstract: Healthy, older adults are widely reported to experience cognitive decline, including impairments in inhibitory control. However, this general proposition has recently come under scrutiny because ageing effects are highly variable between individuals, are task dependent, and are sometimes not distinguished from general age-related slowing. We recently developed the minimally delayed oculomotor response (MDOR) task in which participants are presented with a simple visual target step, and instructed to saccade not to the target when it appears (a prosaccade response), but when it disappears (i.e. on target offset). Varying the target display duration (TDD) prevents offset timing being predictable from the time of target onset, and saccades prior to the offset are counted as errors. A comparison of MDOR task performance in a group of 22 older adults (mean age 62 years, range 50–72 years) with that in a group of 39 younger adults (22 years, range 19–27 years) demonstrated that MDOR latency was significantly increased in the older group by 34–68 ms depending on TDD. However, when MDOR latencies were corrected by subtracting the latency observed in a standard prosaccade task, the latency difference between groups was abolished. There was a larger latency modulation with TDD in the older group which was observed even when their generally longer latencies were taken into account. Error rates were significantly increased in the older group. An analysis of the timing distribution of errors demonstrated that most errors were failures to inhibit responses to target onsets. When error distributions were used to isolate clear inhibition failures from other types of error, the older group still exhibited significantly higher error rates as well as a higher residual error rate. Although MDOR latency in older participants may largely reflect a general slowing in the oculomotor system with age, both the latency modulation and error rate results are consistent with an age-related inhib…
bibliographic citation: Knox et al. (2020) Age-related alterations in inhibitory control investigated using the minimally delayed oculomotor response task. PeerJ 8:e8401 https://doi.org/10.7717/peerj.8401
date submitted: 2019-05-23
date accepted: 2019-12-16
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Knox
  given name: Paul C.
author list: Agent
  family name: Pasunuru
  given name: Nikitha
doi: 10.7717/peerj.8401
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: © 2020 Knox and Pasunuru
attribution name: Knox and Pasunuru

Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study
type: item
type: AcademicArticle
description: Purpose The iPro Cube is a small portable point-of-care device designed to analyse salivary markers of stress in a user-friendly manner (e.g., fast, convenient). Our aim was to test the reliability and validity of the iPro Cube to measure salivary cortisol and α-amylase as compared to the common laboratory standard method (ELISA immunoassay) prior to and after moderate intensity exercise. Methods The study was a repeated measures, pre-registered design, and statistical framework that incorporated prior knowledge directly into the estimation process. Twenty-nine individuals (age = 27.4 ± 6.6 y; body-mass = 70.8 ± 11.3 kg; height = 1.74 ± 0.92 m; 18 males) completed a single PWC75%HRmax, with repeated measures of salivary cortisol and -amylase pre, immediately post, and 30 min post-exercise. Results Correlation between the iPro Cube and laboratory-based assessments of salivary cortisol was moderate-to-large (0.53 > r < 0.81) across all three testing points. In contrast, correlation between the iPro Cube and laboratory-based assessments of -amylase was small-to-moderate (0.25 > r < 0.46). We found a large correlation between duplicate samples of iPro Cube cortisol assessment (0.75 > r < 0.82), and a moderate-to-large correlation for -amylase (0.51> r < 0.77). Conclusions The iPro Cube is capable of taking measures of salivary cortisol that are moderately correlated to values obtained via ELISA immunoassay, however the unit underestimates salivary cortisol and overestimates salivary -amylase at rest and post-moderate intensity exercise. It is recommended that researchers continue using standard laboratory techniques to assess these salivary stress markers.
format: application/pdf
format: text/html
creator: Kagan J. Ducker
creator: Robin L.J. Lines
creator: Michael T. Chapman
creator: Peter Peeling
creator: Alannah K.A. McKay
creator: Daniel F. Gucciardi
subject: Anatomy and Physiology
subject: Diabetes and Endocrinology
subject: Drugs and Devices
subject: Kinesiology
description: doi:10.7717/peerj.8366
publisher: PeerJ Inc.
rights: © 2020 Ducker et al.
abstract: Purpose The iPro Cube is a small portable point-of-care device designed to analyse salivary markers of stress in a user-friendly manner (e.g., fast, convenient). Our aim was to test the reliability and validity of the iPro Cube to measure salivary cortisol and α-amylase as compared to the common laboratory standard method (ELISA immunoassay) prior to and after moderate intensity exercise. Methods The study was a repeated measures, pre-registered design, and statistical framework that incorporated prior knowledge directly into the estimation process. Twenty-nine individuals (age = 27.4 ± 6.6 y; body-mass = 70.8 ± 11.3 kg; height = 1.74 ± 0.92 m; 18 males) completed a single PWC75%HRmax, with repeated measures of salivary cortisol and -amylase pre, immediately post, and 30 min post-exercise. Results Correlation between the iPro Cube and laboratory-based assessments of salivary cortisol was moderate-to-large (0.53 > r < 0.81) across all three testing points. In contrast, correlation between the iPro Cube and laboratory-based assessments of -amylase was small-to-moderate (0.25 > r < 0.46). We found a large correlation between duplicate samples of iPro Cube cortisol assessment (0.75 > r < 0.82), and a moderate-to-large correlation for -amylase (0.51> r < 0.77). Conclusions The iPro Cube is capable of taking measures of salivary cortisol that are moderately correlated to values obtained via ELISA immunoassay, however the unit underestimates salivary cortisol and overestimates salivary -amylase at rest and post-moderate intensity exercise. It is recommended that researchers continue using standard laboratory techniques to assess these salivary stress markers.
bibliographic citation: Ducker et al. (2020) Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study. PeerJ 8:e8366 https://doi.org/10.7717/peerj.8366
date submitted: 2019-08-09
date accepted: 2019-12-06
issued: 2020-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ducker
  given name: Kagan J.
author list: Agent
  family name: Lines
  given name: Robin L.J.
author list: Agent
  family name: Chapman
  given name: Michael T.
author list: Agent
  family name: Peeling
  given name: Peter
author list: Agent
  family name: McKay
  given name: Alannah K.A.
author list: Agent
  family name: Gucciardi
  given name: Daniel F.
doi: 10.7717/peerj.8366
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-08
copyright: ©2020 Ducker et al.
attribution name: Ducker et al.

Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics
type: item
type: AcademicArticle
description: The use of zebrafish larvae has aroused wide interest in the medical field for its potential role in the development of new therapies. The larvae grow extremely quickly and the embryos are nearly transparent which allows easy examination of its internal structures using fluorescent imaging techniques. Medical treatment of zebrafish larvae can directly influence its swimming behaviours. These behaviour changes are related to functional changes of central nervous system and transformations of the zebrafish body such as muscle mechanical power and force variation, which cannot be measured directly by pure experiment observation. To quantify the influence of drugs on zebrafish larvae swimming behaviours and energetics, we have developed a novel methodology to exploit intravital changes based on observed zebrafish locomotion. Specifically, by using an in-house MATLAB code to process the recorded live zebrafish swimming video, the kinematic locomotion equation of a 3D zebrafish larvae was obtained, and a customised Computational Fluid Dynamics tool was used to solve the fluid flow around the fish model which was geometrically the same as experimentally tested zebrafish. The developed methodology was firstly verified against experiment, and further applied to quantify the fish internal body force, torque and power consumption associated with a group of normal zebrafish larvae vs. those immersed in acetic acid and two neuroactive drugs. As indicated by our results, zebrafish larvae immersed in 0.01% acetic acid display approximately 30% higher hydrodynamic power and 10% higher cost of transport than control group. In addition, 500 μM diphenylhydantoin significantly decreases the locomotion activity for approximately 50% lower hydrodynamic power, whereas 100 mg/L yohimbine has not caused any significant influences on 5 dpf zebrafish larvae locomotion. The approach has potential to evaluate the influence of drugs on the aquatic animal’s behaviour changes and thus support the …
format: application/pdf
format: text/html
creator: Zhenkai Zhao
creator: Gen Li
creator: Qing Xiao
creator: Hui-Rong Jiang
creator: Gabriel Mbuta Tchivelekete
creator: Xinhua Shu
creator: Hao Liu
subject: Animal Behavior
subject: Bioengineering
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.8374
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: The use of zebrafish larvae has aroused wide interest in the medical field for its potential role in the development of new therapies. The larvae grow extremely quickly and the embryos are nearly transparent which allows easy examination of its internal structures using fluorescent imaging techniques. Medical treatment of zebrafish larvae can directly influence its swimming behaviours. These behaviour changes are related to functional changes of central nervous system and transformations of the zebrafish body such as muscle mechanical power and force variation, which cannot be measured directly by pure experiment observation. To quantify the influence of drugs on zebrafish larvae swimming behaviours and energetics, we have developed a novel methodology to exploit intravital changes based on observed zebrafish locomotion. Specifically, by using an in-house MATLAB code to process the recorded live zebrafish swimming video, the kinematic locomotion equation of a 3D zebrafish larvae was obtained, and a customised Computational Fluid Dynamics tool was used to solve the fluid flow around the fish model which was geometrically the same as experimentally tested zebrafish. The developed methodology was firstly verified against experiment, and further applied to quantify the fish internal body force, torque and power consumption associated with a group of normal zebrafish larvae vs. those immersed in acetic acid and two neuroactive drugs. As indicated by our results, zebrafish larvae immersed in 0.01% acetic acid display approximately 30% higher hydrodynamic power and 10% higher cost of transport than control group. In addition, 500 μM diphenylhydantoin significantly decreases the locomotion activity for approximately 50% lower hydrodynamic power, whereas 100 mg/L yohimbine has not caused any significant influences on 5 dpf zebrafish larvae locomotion. The approach has potential to evaluate the influence of drugs on the aquatic animal’s behaviour changes and thus support the …
bibliographic citation: Zhao et al. (2020) Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics. PeerJ 8:e8374 https://doi.org/10.7717/peerj.8374
date submitted: 2019-09-04
date accepted: 2019-12-09
issued: 2020-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Zhenkai
author list: Agent
  family name: Li
  given name: Gen
author list: Agent
  family name: Xiao
  given name: Qing
author list: Agent
  family name: Jiang
  given name: Hui-Rong
author list: Agent
  family name: Tchivelekete
  given name: Gabriel Mbuta
author list: Agent
  family name: Shu
  given name: Xinhua
author list: Agent
  family name: Liu
  given name: Hao
doi: 10.7717/peerj.8374
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-08
copyright: © 2020 Zhao et al.
attribution name: Zhao et al.

DNA methylation profiling in recurrent miscarriage
type: item
type: AcademicArticle
description: Recurrent miscarriage (RM) is a complex clinical problem. However, specific diagnostic biomarkers and candidate regulatory targets have not yet been identified. To explore RM-related biological markers and processes, we performed a genome-wide DNA methylation analysis using the Illumina Infinium HumanMethylation450 array platform. Methylation variable positions and differentially methylated regions (DMRs) were selected using the Limma package in R language. Thereafter, gene ontology (GO) enrichment analysis and pathway enrichment analysis were performed on these DMRs. A total of 1,799 DMRs were filtered out between patients with RM and healthy pregnant women. The GO terms were mainly related to system development, plasma membrane part, and sequence-specific DNA binding, while the enriched pathways included cell adhesion molecules, type I diabetes mellitus, and ECM–receptor interactions. In addition, genes, including ABR, ALCAM, HLA-E, HLA-G, and ISG15, were obtained. These genes may be potential candidates for diagnostic biomarkers and possible regulatory targets in RM. We then detected the mRNA expression levels of the candidate genes. The mRNA expression levels of the candidate genes in the RM group were significantly higher than those in the control group. However, additional research is still required to confirm their potential roles in the occurrence of RM.
format: application/pdf
format: text/html
creator: Li Pi
creator: Zhaofeng Zhang
creator: Yan Gu
creator: Xinyue Wang
creator: Jianmei Wang
creator: Jianhua Xu
creator: Junwei Liu
creator: Xuan Zhang
creator: Jing Du
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Women’s Health
description: doi:10.7717/peerj.8196
publisher: PeerJ Inc.
rights: © 2020 Pi et al.
abstract: Recurrent miscarriage (RM) is a complex clinical problem. However, specific diagnostic biomarkers and candidate regulatory targets have not yet been identified. To explore RM-related biological markers and processes, we performed a genome-wide DNA methylation analysis using the Illumina Infinium HumanMethylation450 array platform. Methylation variable positions and differentially methylated regions (DMRs) were selected using the Limma package in R language. Thereafter, gene ontology (GO) enrichment analysis and pathway enrichment analysis were performed on these DMRs. A total of 1,799 DMRs were filtered out between patients with RM and healthy pregnant women. The GO terms were mainly related to system development, plasma membrane part, and sequence-specific DNA binding, while the enriched pathways included cell adhesion molecules, type I diabetes mellitus, and ECM–receptor interactions. In addition, genes, including ABR, ALCAM, HLA-E, HLA-G, and ISG15, were obtained. These genes may be potential candidates for diagnostic biomarkers and possible regulatory targets in RM. We then detected the mRNA expression levels of the candidate genes. The mRNA expression levels of the candidate genes in the RM group were significantly higher than those in the control group. However, additional research is still required to confirm their potential roles in the occurrence of RM.
bibliographic citation: Pi et al. (2020) DNA methylation profiling in recurrent miscarriage. PeerJ 8:e8196 https://doi.org/10.7717/peerj.8196
date submitted: 2019-06-11
date accepted: 2019-11-12
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pi
  given name: Li
author list: Agent
  family name: Zhang
  given name: Zhaofeng
author list: Agent
  family name: Gu
  given name: Yan
author list: Agent
  family name: Wang
  given name: Xinyue
author list: Agent
  family name: Wang
  given name: Jianmei
author list: Agent
  family name: Xu
  given name: Jianhua
author list: Agent
  family name: Liu
  given name: Junwei
author list: Agent
  family name: Zhang
  given name: Xuan
author list: Agent
  family name: Du
  given name: Jing
doi: 10.7717/peerj.8196
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: ©2020 Pi et al.
attribution name: Pi et al.

Soil aggregate size influences the impact of inorganic nitrogen deposition on soil nitrification in an alpine meadow of the Qinghai–Tibet Plateau
type: item
type: AcademicArticle
description: Background Ammonium (NH4+) and nitrate (NO3−) are two inorganic forms of nitrogen (N) that are deposited from the atmosphere into soil systems. As the substrate and product of soil nitrification, these two forms of inorganic nitrogen will affect or be affected by the soil net nitrification rate (Nr). Our knowledge regarding soil nitrification is mainly derived from studies with bulk soil. However, soil is composed of different aggregate fractions, which may have an important impact on Nr. Methods In 2017, we collected soil samples from an alpine meadow of the Qinghai–Tibet Plateau and separated them into four soil aggregates (2–4, 1–2, 0.25–1, and <0.25 mm) using the dry sieving method. The four soil aggregate sizes amended with the 2 N deposition forms (NH4+-N and NO3−-N) were then incubated at 25 °C for 28 days, and the soil aggregates for each treatment were collected on day 0, 7, 14, 21, and 28 to determine the NO3−-N concentration. The soil Nr and contribution of soil aggregates to the nitrification rate in the bulk soil were calculated. Results There were differences in the physicochemical properties of the soil aggregates. The addition of N and aggregate size had strong effects on soil Nr, which were significantly increased under high levels of NH4+ addition across all soil aggregates. The Nr during the 4 week incubation period differed among aggregate sizes. Nr in the 2–4 mm aggregates was higher than in the other aggregates, which was correlated with the maximum values of the soil porosity observed in the 2–4 mm aggregates. Furthermore, almost half of the soil was composed of aggregates of <0.25 mm, indicating that the <0.25 mm aggregates made a higher contribution to the nitrification rate in the bulk soil than the other aggregates, even though these aggregates had a lower nitrification ability. Overall, our study revealed that the soil nitrification rate was influenced by both the N addition and soil aggregates, and that the 2–4 mm aggregates had a domina…
format: application/pdf
format: text/html
creator: Jingjing Li
creator: Chao Yang
creator: Xiaoli Liu
creator: Hanzhong Ji
creator: Xinqing Shao
subject: Soil Science
subject: Climate Change Biology
description: doi:10.7717/peerj.8230
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background Ammonium (NH4+) and nitrate (NO3−) are two inorganic forms of nitrogen (N) that are deposited from the atmosphere into soil systems. As the substrate and product of soil nitrification, these two forms of inorganic nitrogen will affect or be affected by the soil net nitrification rate (Nr). Our knowledge regarding soil nitrification is mainly derived from studies with bulk soil. However, soil is composed of different aggregate fractions, which may have an important impact on Nr. Methods In 2017, we collected soil samples from an alpine meadow of the Qinghai–Tibet Plateau and separated them into four soil aggregates (2–4, 1–2, 0.25–1, and <0.25 mm) using the dry sieving method. The four soil aggregate sizes amended with the 2 N deposition forms (NH4+-N and NO3−-N) were then incubated at 25 °C for 28 days, and the soil aggregates for each treatment were collected on day 0, 7, 14, 21, and 28 to determine the NO3−-N concentration. The soil Nr and contribution of soil aggregates to the nitrification rate in the bulk soil were calculated. Results There were differences in the physicochemical properties of the soil aggregates. The addition of N and aggregate size had strong effects on soil Nr, which were significantly increased under high levels of NH4+ addition across all soil aggregates. The Nr during the 4 week incubation period differed among aggregate sizes. Nr in the 2–4 mm aggregates was higher than in the other aggregates, which was correlated with the maximum values of the soil porosity observed in the 2–4 mm aggregates. Furthermore, almost half of the soil was composed of aggregates of <0.25 mm, indicating that the <0.25 mm aggregates made a higher contribution to the nitrification rate in the bulk soil than the other aggregates, even though these aggregates had a lower nitrification ability. Overall, our study revealed that the soil nitrification rate was influenced by both the N addition and soil aggregates, and that the 2–4 mm aggregates had a domina…
bibliographic citation: Li et al. (2020) Soil aggregate size influences the impact of inorganic nitrogen deposition on soil nitrification in an alpine meadow of the Qinghai–Tibet Plateau. PeerJ 8:e8230 https://doi.org/10.7717/peerj.8230
date submitted: 2019-06-18
date accepted: 2019-11-18
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jingjing
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Ji
  given name: Hanzhong
author list: Agent
  family name: Shao
  given name: Xinqing
doi: 10.7717/peerj.8230
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: © 2020 Li et al.
attribution name: Li et al.

A pilot study on searching for peri-nuclear NeuN-positive cells
type: item
type: AcademicArticle
description: The aim of this study was to find out neuron (-like) cells in peripheral organs by cell markers in rats. Adult male Sprague-Dawley rats were anaesthetized. Their organs including brain, heart, lung, liver, kidney, stomach, duodenum, and ileum were harvested. The mRNA and protein in these organs were extracted. RNA sequencing (RNA-Seq) was carried out, and NeuN, a “specific” marker for neuronal soma, was assayed with Western blotting. The sections of the aforementioned organs were obtained after a routine fixation (4% methanal)-dehydration (ethanol)-embedding (paraffin) process. NeuN in the sections and seven non-neuronal cell lines was analyzed by immunofluorescence (IF) or immunohistochemistry (IHC). Neuronal markers, such as Eno2, NeuN (Rbfox3), choline acetyltransferase (Chat), as well as tyrosine hydroxylase (Th), and neuronal-glial markers, e.g., glial fibrillary acidic protein (Gfap), S100b, 2′, 3′-cyclic nucleotide 3′-phosphodiesterase (Cnp), and other related markers, were positively expressed in all the organs at mRNA level. NeuN was further analyzed by Western blotting. The IF and IHC assays showed that NeuN-positive cells were distributed in all the peripheral tissues (mainly peri-nuclear NeuN-positive cells) though with different patterns from that in brain (nuclear NeuN-positive cells), and a NeuN-negative tissue could not be found. Especially, NeuN and Myl3 co-expressed in the cytoplasm of myocardial cells, suggesting that NeuN could possess other functions than neuronal differentiation. Also, the protein was positively expressed in seven non-neuronal cell lines. Our findings suggested that NeuN-positive cells exist widely, and without identification of its distribution pattern, the specificity of NeuN for neurons could be limited.
format: application/pdf
format: text/html
creator: Yun Yu
creator: Meiyu Wu
creator: Nan Zhang
creator: Hua Yin
creator: Bin Shu
creator: Weigang Duan
subject: Cell Biology
subject: Neuroscience
description: doi:10.7717/peerj.8254
publisher: PeerJ Inc.
rights: © 2020 Yu et al.
abstract: The aim of this study was to find out neuron (-like) cells in peripheral organs by cell markers in rats. Adult male Sprague-Dawley rats were anaesthetized. Their organs including brain, heart, lung, liver, kidney, stomach, duodenum, and ileum were harvested. The mRNA and protein in these organs were extracted. RNA sequencing (RNA-Seq) was carried out, and NeuN, a “specific” marker for neuronal soma, was assayed with Western blotting. The sections of the aforementioned organs were obtained after a routine fixation (4% methanal)-dehydration (ethanol)-embedding (paraffin) process. NeuN in the sections and seven non-neuronal cell lines was analyzed by immunofluorescence (IF) or immunohistochemistry (IHC). Neuronal markers, such as Eno2, NeuN (Rbfox3), choline acetyltransferase (Chat), as well as tyrosine hydroxylase (Th), and neuronal-glial markers, e.g., glial fibrillary acidic protein (Gfap), S100b, 2′, 3′-cyclic nucleotide 3′-phosphodiesterase (Cnp), and other related markers, were positively expressed in all the organs at mRNA level. NeuN was further analyzed by Western blotting. The IF and IHC assays showed that NeuN-positive cells were distributed in all the peripheral tissues (mainly peri-nuclear NeuN-positive cells) though with different patterns from that in brain (nuclear NeuN-positive cells), and a NeuN-negative tissue could not be found. Especially, NeuN and Myl3 co-expressed in the cytoplasm of myocardial cells, suggesting that NeuN could possess other functions than neuronal differentiation. Also, the protein was positively expressed in seven non-neuronal cell lines. Our findings suggested that NeuN-positive cells exist widely, and without identification of its distribution pattern, the specificity of NeuN for neurons could be limited.
bibliographic citation: Yu et al. (2020) A pilot study on searching for peri-nuclear NeuN-positive cells. PeerJ 8:e8254 https://doi.org/10.7717/peerj.8254
date submitted: 2019-03-14
date accepted: 2019-11-20
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yun
author list: Agent
  family name: Wu
  given name: Meiyu
author list: Agent
  family name: Zhang
  given name: Nan
author list: Agent
  family name: Yin
  given name: Hua
author list: Agent
  family name: Shu
  given name: Bin
author list: Agent
  family name: Duan
  given name: Weigang
doi: 10.7717/peerj.8254
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: ©2020 Yu et al.
attribution name: Yu et al.

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