PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Isolation, growth, and nitrogen fixation rates of the Hemiaulus-Richelia (diatom-cyanobacterium) symbiosis in culture
items: Overgrazing-induced legacy effects may permit Leymus chinensis to cope with herbivory
items: Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis
items: Adequacy of clinical information in X-ray referrals for traumatic ankle injury with reference to the Ottawa Ankle Rules—a retrospective clinical audit
items: Coupled exuviae of the Ordovician Ovalocephalus (Pliomeridae, Trilobita) in South China and its behavioral implications
items: A taxonomic review of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) from Japanese coastal waters
items: Lifestyle choices of Brazilian college students
items: Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
items: Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages
items: SlMYB102 expression enhances low-temperature stress resistance in tomato plants

Isolation, growth, and nitrogen fixation rates of the Hemiaulus-Richelia (diatom-cyanobacterium) symbiosis in culture
type: item
type: AcademicArticle
description: Nitrogen fixers (diazotrophs) are often an important nitrogen source to phytoplankton nutrient budgets in N-limited marine environments. Diazotrophic symbioses between cyanobacteria and diatoms can dominate nitrogen-fixation regionally, particularly in major river plumes and in open ocean mesoscale blooms. This study reports the successful isolation and growth in monocultures of multiple strains of a diatom-cyanobacteria symbiosis from the Gulf of Mexico using a modified artificial seawater medium. We document the influence of light and nutrients on nitrogen fixation and growth rates of the host diatom Hemiaulus hauckii Grunow together with its diazotrophic endosymbiont Richelia intracellularis Schmidt, as well as less complete results on the Hemiaulus membranaceus-R. intracellularis symbiosis. The symbioses rates reported here are for the joint diatom-cyanobacteria unit. Symbiont diazotrophy was sufficient to support both the host diatom and cyanobacteria symbionts, and the entire symbiosis replicated and grew without added nitrogen. Maximum growth rates of multiple strains of H. hauckii symbioses in N-free medium with N2 as the sole N source were 0.74–0.93 div d−1. Growth rates followed light saturation kinetics in H. hauckii symbioses with a growth compensation light intensity (EC) of 7–16 µmol m−2s−1and saturation light level (EK) of 84–110 µmol m−2s−1. Nitrogen fixation rates by the symbiont while within the host followed a diel pattern where rates increased from near-zero in the scotophase to a maximum 4–6 h into the photophase. At the onset of the scotophase, nitrogen-fixation rates declined over several hours to near-zero values. Nitrogen fixation also exhibited light saturation kinetics. Maximum N2 fixation rates (84 fmol N2 heterocyst−1h−1) in low light adapted cultures (50 µmol m−2s−1) were approximately 40–50% of rates (144–154 fmol N2 heterocyst−1h−1) in high light (150 and 200 µmol m−2s−1) adapted cultures. Maximum laboratory N2 fixation rates were ~6 …
format: application/pdf
format: text/html
creator: Amy E. Pyle
creator: Allison M. Johnson
creator: Tracy A. Villareal
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.10115
publisher: PeerJ Inc.
rights: © 2020 Pyle et al.
abstract: Nitrogen fixers (diazotrophs) are often an important nitrogen source to phytoplankton nutrient budgets in N-limited marine environments. Diazotrophic symbioses between cyanobacteria and diatoms can dominate nitrogen-fixation regionally, particularly in major river plumes and in open ocean mesoscale blooms. This study reports the successful isolation and growth in monocultures of multiple strains of a diatom-cyanobacteria symbiosis from the Gulf of Mexico using a modified artificial seawater medium. We document the influence of light and nutrients on nitrogen fixation and growth rates of the host diatom Hemiaulus hauckii Grunow together with its diazotrophic endosymbiont Richelia intracellularis Schmidt, as well as less complete results on the Hemiaulus membranaceus-R. intracellularis symbiosis. The symbioses rates reported here are for the joint diatom-cyanobacteria unit. Symbiont diazotrophy was sufficient to support both the host diatom and cyanobacteria symbionts, and the entire symbiosis replicated and grew without added nitrogen. Maximum growth rates of multiple strains of H. hauckii symbioses in N-free medium with N2 as the sole N source were 0.74–0.93 div d−1. Growth rates followed light saturation kinetics in H. hauckii symbioses with a growth compensation light intensity (EC) of 7–16 µmol m−2s−1and saturation light level (EK) of 84–110 µmol m−2s−1. Nitrogen fixation rates by the symbiont while within the host followed a diel pattern where rates increased from near-zero in the scotophase to a maximum 4–6 h into the photophase. At the onset of the scotophase, nitrogen-fixation rates declined over several hours to near-zero values. Nitrogen fixation also exhibited light saturation kinetics. Maximum N2 fixation rates (84 fmol N2 heterocyst−1h−1) in low light adapted cultures (50 µmol m−2s−1) were approximately 40–50% of rates (144–154 fmol N2 heterocyst−1h−1) in high light (150 and 200 µmol m−2s−1) adapted cultures. Maximum laboratory N2 fixation rates were ~6 …
bibliographic citation: Pyle et al. (2020) Isolation, growth, and nitrogen fixation rates of the Hemiaulus-Richelia (diatom-cyanobacterium) symbiosis in culture. PeerJ 8:e10115 https://doi.org/10.7717/peerj.10115
date submitted: 2020-04-28
date accepted: 2020-09-16
issued: 2020-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pyle
  given name: Amy E.
author list: Agent
  family name: Johnson
  given name: Allison M.
author list: Agent
  family name: Villareal
  given name: Tracy A.
doi: 10.7717/peerj.10115
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-08
copyright: © 2020 Pyle et al.
attribution name: Pyle et al.

Overgrazing-induced legacy effects may permit Leymus chinensis to cope with herbivory
type: item
type: AcademicArticle
description: There is growing evidence that herbivory-induced legacy effects permit plants to cope with herbivory. However, herbivory-induced defense strategies in plants against grazing mammals have received little attention. To further understand the grazing-induced legacy effects on plants, we conducted a greenhouse experiment with Leymus chinensis experiencing different grazing histories. We focused on grazing-induced legacy effects on above-ground spatial avoidance and below-ground biomass allocation. Our results showed that L. chinensis collected from the continuous overgrazing plot (OG) exhibited higher performance under simulated grazing in terms of growth, cloning and colonizing ability than those collected from the 35-year no-grazing plot (NG). The enhanced adaptability of OG was attributed to increased above-ground spatial avoidance, which was mediated by larger leaf angle and shorter height (reduced vertical height and increased leaf angle contributed to the above-ground spatial avoidance at a lower herbivory stubble height, while reduced tiller natural height contributed to above-ground spatial avoidance at a higher herbivory stubble height). Contrary to our prediction, OG pre-allocated less biomass to the rhizome, which does not benefit the herbivory tolerance and avoidance of L. chinensis; however, this also may reflect a tolerance strategy where reduced allocation to rhizomes is associated with increased production of ramets.
format: application/pdf
format: text/html
creator: Fenghui Guo
creator: Xiliang Li
creator: Saheed Olaide Jimoh
creator: Yong Ding
creator: Yong Zhang
creator: Shangli Shi
creator: Xiangyang Hou
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.10116
publisher: PeerJ Inc.
rights: © 2020 Guo et al.
abstract: There is growing evidence that herbivory-induced legacy effects permit plants to cope with herbivory. However, herbivory-induced defense strategies in plants against grazing mammals have received little attention. To further understand the grazing-induced legacy effects on plants, we conducted a greenhouse experiment with Leymus chinensis experiencing different grazing histories. We focused on grazing-induced legacy effects on above-ground spatial avoidance and below-ground biomass allocation. Our results showed that L. chinensis collected from the continuous overgrazing plot (OG) exhibited higher performance under simulated grazing in terms of growth, cloning and colonizing ability than those collected from the 35-year no-grazing plot (NG). The enhanced adaptability of OG was attributed to increased above-ground spatial avoidance, which was mediated by larger leaf angle and shorter height (reduced vertical height and increased leaf angle contributed to the above-ground spatial avoidance at a lower herbivory stubble height, while reduced tiller natural height contributed to above-ground spatial avoidance at a higher herbivory stubble height). Contrary to our prediction, OG pre-allocated less biomass to the rhizome, which does not benefit the herbivory tolerance and avoidance of L. chinensis; however, this also may reflect a tolerance strategy where reduced allocation to rhizomes is associated with increased production of ramets.
bibliographic citation: Guo et al. (2020) Overgrazing-induced legacy effects may permit Leymus chinensis to cope with herbivory. PeerJ 8:e10116 https://doi.org/10.7717/peerj.10116
date submitted: 2020-06-04
date accepted: 2020-09-16
issued: 2020-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Fenghui
author list: Agent
  family name: Li
  given name: Xiliang
author list: Agent
  family name: Jimoh
  given name: Saheed Olaide
author list: Agent
  family name: Ding
  given name: Yong
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Shi
  given name: Shangli
author list: Agent
  family name: Hou
  given name: Xiangyang
doi: 10.7717/peerj.10116
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-08
copyright: ©2020 Guo et al.
attribution name: Guo et al.

Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis
type: item
type: AcademicArticle
description: Background Flower and fruit development are vital stages of the angiosperm lifecycle. We previously investigated the multi-silique trait in the rapeseed (Brassica napus) line zws-ms on a genomic and transcriptomic level, leading to the identification of two genomic regions and several candidate genes associated with this trait. However, some events on the transcriptome level, like alternative splicing, were poorly understood. Methods Plants from zws-ms and its near-isogenic line (NIL) zws-217 were both grown in Xindu with normal conditions and a colder area Ma’erkang. Buds from the two lines were sampled and RNA was isolated to perform the transcriptomic sequencing. The numbers and types of alternative splicing (AS) events from the two lines were counted and classified. Genes with AS events and expressed differentially between the two lines, as well as genes with AS events which occurred in only one line were emphasized. Their annotations were further studied. Results From the plants in Xindu District, an average of 205,496 AS events, which could be sorted into five AS types, were identified. zws-ms and zws-217 shared highly similar ratios of each AS type: The alternative 5′ and 3′ splice site types were the most common, while the exon skipping type was observed least often. Eleven differentially expressed AS genes were identified, of which four were upregulated and seven were downregulated in zws-ms. Their annotations implied that five of these genes were directly associated with the multi-silique trait. While samples from colder area Ma’erkang generated generally reduced number of each type of AS events except for Intron Retention; but the number of differentially expressed AS genes increased significantly. Further analysis found that among the 11 differentially expressed AS genes from Xindu, three of them maintained the same expression models, while the other eight genes did not show significant difference between the two lines in expression level. Additionally, …
format: application/pdf
format: text/html
creator: Liang Chai
creator: Jinfang Zhang
creator: Haojie Li
creator: Benchuan Zheng
creator: Jun Jiang
creator: Cheng Cui
creator: Liangcai Jiang
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10135
publisher: PeerJ Inc.
rights: © 2020 Chai et al.
abstract: Background Flower and fruit development are vital stages of the angiosperm lifecycle. We previously investigated the multi-silique trait in the rapeseed (Brassica napus) line zws-ms on a genomic and transcriptomic level, leading to the identification of two genomic regions and several candidate genes associated with this trait. However, some events on the transcriptome level, like alternative splicing, were poorly understood. Methods Plants from zws-ms and its near-isogenic line (NIL) zws-217 were both grown in Xindu with normal conditions and a colder area Ma’erkang. Buds from the two lines were sampled and RNA was isolated to perform the transcriptomic sequencing. The numbers and types of alternative splicing (AS) events from the two lines were counted and classified. Genes with AS events and expressed differentially between the two lines, as well as genes with AS events which occurred in only one line were emphasized. Their annotations were further studied. Results From the plants in Xindu District, an average of 205,496 AS events, which could be sorted into five AS types, were identified. zws-ms and zws-217 shared highly similar ratios of each AS type: The alternative 5′ and 3′ splice site types were the most common, while the exon skipping type was observed least often. Eleven differentially expressed AS genes were identified, of which four were upregulated and seven were downregulated in zws-ms. Their annotations implied that five of these genes were directly associated with the multi-silique trait. While samples from colder area Ma’erkang generated generally reduced number of each type of AS events except for Intron Retention; but the number of differentially expressed AS genes increased significantly. Further analysis found that among the 11 differentially expressed AS genes from Xindu, three of them maintained the same expression models, while the other eight genes did not show significant difference between the two lines in expression level. Additionally, …
bibliographic citation: Chai et al. (2020) Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis. PeerJ 8:e10135 https://doi.org/10.7717/peerj.10135
date submitted: 2019-12-30
date accepted: 2020-09-18
issued: 2020-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chai
  given name: Liang
author list: Agent
  family name: Zhang
  given name: Jinfang
author list: Agent
  family name: Li
  given name: Haojie
author list: Agent
  family name: Zheng
  given name: Benchuan
author list: Agent
  family name: Jiang
  given name: Jun
author list: Agent
  family name: Cui
  given name: Cheng
author list: Agent
  family name: Jiang
  given name: Liangcai
doi: 10.7717/peerj.10135
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-08
copyright: ©2020 Chai et al.
attribution name: Chai et al.

Adequacy of clinical information in X-ray referrals for traumatic ankle injury with reference to the Ottawa Ankle Rules—a retrospective clinical audit
type: item
type: AcademicArticle
description: Study Objective To assess the adequacy of clinical information with reference to the Ottawa Ankle Rules (OAR) in X-ray referrals for adults with traumatic ankle injury in the ED of a South Australian tertiary hospital and report upon referring trends between emergency department clinicians. Methods A retrospective clinical audit of adult ankle X-ray referrals in the emergency department was conducted. Eligible referrals were screened for their adherence to the OAR, patient details, clinical history and referrer. A logistic regression was used to determine the influence of these factors on the likelihood of being referred for X-rays despite not meeting the OAR criteria. Sensitivity, specificity, positive and negative likelihood ratios and their associated confidence intervals were calculated to assess the diagnostic accuracy of the OAR for those referred. Results Out of the 262 eligible referrals, 163 were deemed to have met the criteria for the OAR. Physiotherapists showed the highest OAR compliance of 77.3% and were the most accurate in their use of the rules, with a sensitivity of 0.86. Medical officers, registrars and interns were 2.5 times more likely to still refer a patient for X-ray if they did not meet the OAR criteria, compared to physiotherapists as the baseline. Patient age, duration of injury etc. were not significantly associated with likelihood of referral (even when they did not meet OAR criteria). The overall sensitivity, specificity, positive and negative likelihood ratios of the OAR were 0.59 (95% CI [0.47–0.71]), 0.37 (95% CI [0.30–0.44]), 0.93 (95% CI [0.76–1.16]) and 1.10 (95% CI [0.82–1.48]) respectively. Conclusion The results of this audit demonstrated poor sensitivity and moderate compliance by referrers with the rule. Reasonable evidence exists for the implementation of individual and/or institutional-based change strategies to improve clinician compliance and accuracy with use of the OAR.
format: application/pdf
format: text/html
creator: Yolanda E. Gomes
creator: Minh Chau
creator: Helen A. Banwell
creator: Josephine Davies
creator: Ryan S. Causby
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Orthopedics
subject: Radiology and Medical Imaging
subject: Rheumatology
description: doi:10.7717/peerj.10152
publisher: PeerJ Inc.
rights: © 2020 Gomes et al.
abstract: Study Objective To assess the adequacy of clinical information with reference to the Ottawa Ankle Rules (OAR) in X-ray referrals for adults with traumatic ankle injury in the ED of a South Australian tertiary hospital and report upon referring trends between emergency department clinicians. Methods A retrospective clinical audit of adult ankle X-ray referrals in the emergency department was conducted. Eligible referrals were screened for their adherence to the OAR, patient details, clinical history and referrer. A logistic regression was used to determine the influence of these factors on the likelihood of being referred for X-rays despite not meeting the OAR criteria. Sensitivity, specificity, positive and negative likelihood ratios and their associated confidence intervals were calculated to assess the diagnostic accuracy of the OAR for those referred. Results Out of the 262 eligible referrals, 163 were deemed to have met the criteria for the OAR. Physiotherapists showed the highest OAR compliance of 77.3% and were the most accurate in their use of the rules, with a sensitivity of 0.86. Medical officers, registrars and interns were 2.5 times more likely to still refer a patient for X-ray if they did not meet the OAR criteria, compared to physiotherapists as the baseline. Patient age, duration of injury etc. were not significantly associated with likelihood of referral (even when they did not meet OAR criteria). The overall sensitivity, specificity, positive and negative likelihood ratios of the OAR were 0.59 (95% CI [0.47–0.71]), 0.37 (95% CI [0.30–0.44]), 0.93 (95% CI [0.76–1.16]) and 1.10 (95% CI [0.82–1.48]) respectively. Conclusion The results of this audit demonstrated poor sensitivity and moderate compliance by referrers with the rule. Reasonable evidence exists for the implementation of individual and/or institutional-based change strategies to improve clinician compliance and accuracy with use of the OAR.
bibliographic citation: Gomes et al. (2020) Adequacy of clinical information in X-ray referrals for traumatic ankle injury with reference to the Ottawa Ankle Rules—a retrospective clinical audit. PeerJ 8:e10152 https://doi.org/10.7717/peerj.10152
date submitted: 2020-08-05
date accepted: 2020-09-21
issued: 2020-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gomes
  given name: Yolanda E.
author list: Agent
  family name: Chau
  given name: Minh
author list: Agent
  family name: Banwell
  given name: Helen A.
author list: Agent
  family name: Davies
  given name: Josephine
author list: Agent
  family name: Causby
  given name: Ryan S.
doi: 10.7717/peerj.10152
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-08
copyright: ©2020 Gomes et al.
attribution name: Gomes et al.

Coupled exuviae of the Ordovician Ovalocephalus (Pliomeridae, Trilobita) in South China and its behavioral implications
type: item
type: AcademicArticle
description: Ecdysis was a vital process during the lives of trilobites. In addition to preserving the morphological changes in trilobite ontogeny, the preservation of its action often captured interesting behavioral information. Abundant exuviae of Ovalocephalus tetrasulcatus are preserved in the Ordovician strata in central Hubei, China, and some of them are arranged with two or three together end to end or superimposed. The preserved patterns and burial conditions indicate that these specimens were caused by the active behavior of trilobites. It is speculated that these exuvial clusters were formed by two or three trilobites in line to molt; that is, after one trilobite finished molting, other trilobites molted in front of, behind, or overlying the previously molted shells. This ecdysis strategy is interpreted as related to the postulated herding behavior of some trilobites, representing a behavioral response of the trilobites to choose a nearby safe zone during some risky life activities.
format: application/pdf
format: text/html
creator: Ruiwen Zong
subject: Animal Behavior
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.10166
publisher: PeerJ Inc.
rights: © 2020 Zong
abstract: Ecdysis was a vital process during the lives of trilobites. In addition to preserving the morphological changes in trilobite ontogeny, the preservation of its action often captured interesting behavioral information. Abundant exuviae of Ovalocephalus tetrasulcatus are preserved in the Ordovician strata in central Hubei, China, and some of them are arranged with two or three together end to end or superimposed. The preserved patterns and burial conditions indicate that these specimens were caused by the active behavior of trilobites. It is speculated that these exuvial clusters were formed by two or three trilobites in line to molt; that is, after one trilobite finished molting, other trilobites molted in front of, behind, or overlying the previously molted shells. This ecdysis strategy is interpreted as related to the postulated herding behavior of some trilobites, representing a behavioral response of the trilobites to choose a nearby safe zone during some risky life activities.
bibliographic citation: Zong (2020) Coupled exuviae of the Ordovician Ovalocephalus (Pliomeridae, Trilobita) in South China and its behavioral implications. PeerJ 8:e10166 https://doi.org/10.7717/peerj.10166
date submitted: 2020-05-20
date accepted: 2020-09-22
issued: 2020-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zong
  given name: Ruiwen
doi: 10.7717/peerj.10166
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-08
copyright: ©2020 Zong
attribution name: Zong

A taxonomic review of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) from Japanese coastal waters
type: item
type: AcademicArticle
description: Japanese species of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) are reviewed. Astrocladus coniferus recently has two junior synonyms, A. dofleini Döderlein and A. pardalis Döderlein, however, status of these species has long been questioned. These species concepts have not been reviewed in recent years and no molecular phylogenetic analyses have been performed. Observations of the lectotype of A. coniferus, as well as the lectotype and four paralectotypes of A. dofleini and the holotype of A. pardalis have revealed that A. coniferus and A. pardalis are conspecific and morphologically distinguishable from A. dofleini. Astrocladus coniferus and A. dofleini are supported as distinct species by our molecular data. Additionally, we re-describe A. exiguus and A. annulatus, based on recently collected specimens and the holotype. We conclude that four species, A. annulatus, A. coniferus, A. dofleini, and A. exiguus are present in Japanese waters.
format: application/pdf
format: text/html
creator: Masanori Okanishi
creator: Hisanori Kohtsuka
creator: Toshihiko Fujita
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9836
publisher: PeerJ Inc.
rights: © 2020 Okanishi et al.
abstract: Japanese species of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) are reviewed. Astrocladus coniferus recently has two junior synonyms, A. dofleini Döderlein and A. pardalis Döderlein, however, status of these species has long been questioned. These species concepts have not been reviewed in recent years and no molecular phylogenetic analyses have been performed. Observations of the lectotype of A. coniferus, as well as the lectotype and four paralectotypes of A. dofleini and the holotype of A. pardalis have revealed that A. coniferus and A. pardalis are conspecific and morphologically distinguishable from A. dofleini. Astrocladus coniferus and A. dofleini are supported as distinct species by our molecular data. Additionally, we re-describe A. exiguus and A. annulatus, based on recently collected specimens and the holotype. We conclude that four species, A. annulatus, A. coniferus, A. dofleini, and A. exiguus are present in Japanese waters.
bibliographic citation: Okanishi et al. (2020) A taxonomic review of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) from Japanese coastal waters. PeerJ 8:e9836 https://doi.org/10.7717/peerj.9836
date submitted: 2020-06-03
date accepted: 2020-08-07
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Okanishi
  given name: Masanori
author list: Agent
  family name: Kohtsuka
  given name: Hisanori
author list: Agent
  family name: Fujita
  given name: Toshihiko
doi: 10.7717/peerj.9836
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Okanishi et al.
attribution name: Okanishi et al.

Lifestyle choices of Brazilian college students
type: item
type: AcademicArticle
description: Background Lifestyle choices reflect the beliefs that individuals attribute to aspects of life. This construct can be assessed with the Individual Lifestyle Profile (PEVI) questionnaire, which measures elements of Nutrition, Physical Activity, Preventive Behaviors, Social Relationships and Stress Management. Objective The objective of this study was to estimate the psychometric properties of the PEVI applied to a sample of Brazilian university students, identifying the prevalence of each lifestyle component according to participants’ age, sex, weight status, course area/field and economic stratum and to estimate the contribution of these characteristics on physical and psychological lifestyle. Methods The PEVI data was analyzed by confirmatory factor analysis, using the indexes chi-square per degrees of freedom ratio (χ2/df), Comparative Fit Index (CFI), Tucker-Lewis Index (TLI) and Root Mean Square Error of Approximation (RMSEA). First-order and second-order models (physical and psychological lifestyle) were tested. Prevalences of lifestyle components were calculated and compared by participants’ age, sex, weight status, course area/field and economic stratum. A hypothetical causal structural model was elaborated to investigate the impact of sample characteristics on physical and psychological lifestyles. This model was evaluated considering the global fit to the data (χ2/df, CFI, TLI and RMSEA) and the hypothetical causal trajectories (β) (α = 5%). Results A sample of 1,303 students was used. The mean age was 20.9 (standard deviation = 2.8) years, 66.8% of participants were females, 63.4% had weights in the normal range and 73.7% were students of the social and exact sciences. The PEVI data showed an adequate fit for both the first- (χ2/df = 2.03, CFI = 0.98; TLI = 0.97; RMSEA = 0.04) and second-order (χ2/df = 2.25; CFI = 0.97; TLI = 0.97; RMSEA = 0.04) models. There was a higher prevalence of unfavorable physical and psychological lifestyle choices among females,…
format: application/pdf
format: text/html
creator: Bianca G. Martins
creator: João Marôco
creator: Mauro V.G. Barros
creator: Juliana A.D.B. Campos
subject: Epidemiology
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.9830
publisher: PeerJ Inc.
rights: © 2020 Martins et al.
abstract: Background Lifestyle choices reflect the beliefs that individuals attribute to aspects of life. This construct can be assessed with the Individual Lifestyle Profile (PEVI) questionnaire, which measures elements of Nutrition, Physical Activity, Preventive Behaviors, Social Relationships and Stress Management. Objective The objective of this study was to estimate the psychometric properties of the PEVI applied to a sample of Brazilian university students, identifying the prevalence of each lifestyle component according to participants’ age, sex, weight status, course area/field and economic stratum and to estimate the contribution of these characteristics on physical and psychological lifestyle. Methods The PEVI data was analyzed by confirmatory factor analysis, using the indexes chi-square per degrees of freedom ratio (χ2/df), Comparative Fit Index (CFI), Tucker-Lewis Index (TLI) and Root Mean Square Error of Approximation (RMSEA). First-order and second-order models (physical and psychological lifestyle) were tested. Prevalences of lifestyle components were calculated and compared by participants’ age, sex, weight status, course area/field and economic stratum. A hypothetical causal structural model was elaborated to investigate the impact of sample characteristics on physical and psychological lifestyles. This model was evaluated considering the global fit to the data (χ2/df, CFI, TLI and RMSEA) and the hypothetical causal trajectories (β) (α = 5%). Results A sample of 1,303 students was used. The mean age was 20.9 (standard deviation = 2.8) years, 66.8% of participants were females, 63.4% had weights in the normal range and 73.7% were students of the social and exact sciences. The PEVI data showed an adequate fit for both the first- (χ2/df = 2.03, CFI = 0.98; TLI = 0.97; RMSEA = 0.04) and second-order (χ2/df = 2.25; CFI = 0.97; TLI = 0.97; RMSEA = 0.04) models. There was a higher prevalence of unfavorable physical and psychological lifestyle choices among females,…
bibliographic citation: Martins et al. (2020) Lifestyle choices of Brazilian college students. PeerJ 8:e9830 https://doi.org/10.7717/peerj.9830
date submitted: 2019-11-20
date accepted: 2020-08-06
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martins
  given name: Bianca G.
author list: Agent
  family name: Marôco
  given name: João
author list: Agent
  family name: Barros
  given name: Mauro V.G.
author list: Agent
  family name: Campos
  given name: Juliana A.D.B.
doi: 10.7717/peerj.9830
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Martins et al.
attribution name: Martins et al.

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
type: item
type: AcademicArticle
description: Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specim…
format: application/pdf
format: text/html
creator: Christian F. Kammerer
creator: Michol Deutsch
creator: Jacqueline K. Lungmus
creator: Kenneth D. Angielczyk
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.9925
publisher: PeerJ Inc.
rights: © 2020 Kammerer et al.
abstract: Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specim…
bibliographic citation: Kammerer et al. (2020) Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia). PeerJ 8:e9925 https://doi.org/10.7717/peerj.9925
date submitted: 2020-04-27
date accepted: 2020-08-21
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Deutsch
  given name: Michol
author list: Agent
  family name: Lungmus
  given name: Jacqueline K.
author list: Agent
  family name: Angielczyk
  given name: Kenneth D.
doi: 10.7717/peerj.9925
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Kammerer et al.
attribution name: Kammerer et al.

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages
type: item
type: AcademicArticle
description: Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen re…
format: application/pdf
format: text/html
creator: Aili Wang
creator: Tianle Chao
creator: Zhibin Ji
creator: Rong Xuan
creator: Shuang Liu
creator: Maosen Guo
creator: Guizhi Wang
creator: Jianmin Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.9947
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen re…
bibliographic citation: Wang et al. (2020) Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages. PeerJ 8:e9947 https://doi.org/10.7717/peerj.9947
date submitted: 2020-02-04
date accepted: 2020-08-25
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Aili
author list: Agent
  family name: Chao
  given name: Tianle
author list: Agent
  family name: Ji
  given name: Zhibin
author list: Agent
  family name: Xuan
  given name: Rong
author list: Agent
  family name: Liu
  given name: Shuang
author list: Agent
  family name: Guo
  given name: Maosen
author list: Agent
  family name: Wang
  given name: Guizhi
author list: Agent
  family name: Wang
  given name: Jianmin
doi: 10.7717/peerj.9947
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: ©2020 Wang et al.
attribution name: Wang et al.

SlMYB102 expression enhances low-temperature stress resistance in tomato plants
type: item
type: AcademicArticle
description: Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
format: application/pdf
format: text/html
creator: Meiling Wang
creator: Juan Hao
creator: Xiuhua Chen
creator: Xichun Zhang
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10059
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
bibliographic citation: Wang et al. (2020) SlMYB102 expression enhances low-temperature stress resistance in tomato plants. PeerJ 8:e10059 https://doi.org/10.7717/peerj.10059
date submitted: 2019-12-30
date accepted: 2020-09-07
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Meiling
author list: Agent
  family name: Hao
  given name: Juan
author list: Agent
  family name: Chen
  given name: Xiuhua
author list: Agent
  family name: Zhang
  given name: Xichun
doi: 10.7717/peerj.10059
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: ©2020 Wang et al.
attribution name: Wang et al.

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