PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Different visual manipulations have similar effects on quasi-static and dynamic balance responses of young and older people
items: Experimental indications of gardeners’ anecdotes that snails interfere with invasive slugs
items: Limb myology and muscle architecture of the Indian rhinoceros Rhinoceros unicornis and the white rhinoceros Ceratotherium simum (Mammalia: Rhinocerotidae)
items: Identification of robust diagnostic and prognostic gene signatures in different grades of gliomas: a retrospective study
items: Artificial light source selection in seaweed production: growth of seaweed and biosynthesis of photosynthetic pigments and soluble protein
items: Durnonovariaodus maiseyi gen. et sp. nov., a new hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of England
items: Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations
items: Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements
items: Mapping open knowledge institutions: an exploratory analysis of Australian universities
items: Shiftwork, functional bowel symptoms, and the microbiome

Different visual manipulations have similar effects on quasi-static and dynamic balance responses of young and older people
type: item
type: AcademicArticle
description: Background Studies demonstrated that the older adults can be more susceptible to balance instability after acute visual manipulation. There are different manipulation approaches used to investigate the importance of visual inputs on balance, e.g., eyes closed and blackout glasses. However, there is evidence that eyes open versus eyes closed results in a different organization of human brain functional networks. It is, however, unclear how different visual manipulations affect balance, and whether such effects differ between young and elderly persons. Therefore, this study aimed to determine whether different visual manipulation approaches affect quasi-static and dynamic balance responses differently, and to investigate whether balance responses of young and older adults are affected differently by these various visual conditions. Methods Thirty-six healthy participants (20 young and 16 older adults) performed balance tests (quasi-static and unexpected perturbations) under four visual conditions: Eyes Open, Eyes Closed, Blackout Glasses, and Dark Room. Center of pressure (CoP) and muscle activation (EMG) were quantified. Results As expected, visual deprivation resulted in larger CoP excursions and higher muscle activations during balance tests for all participants. Surprisingly, the visual manipulation approach did not influence balance control in either group. Furthermore, quasi-static and dynamic balance control did not differ between young or older adults. The visual system plays an important role in balance control, however, similarly for both young and older adults. Different visual deprivation approaches did not influence balance results, meaning our results are comparable between participants of different ages. Further studies should investigate whether a critical illumination level may elicit different postural responses between young and older adults.
format: application/pdf
format: text/html
creator: Daniel Schmidt
creator: Felipe P. Carpes
creator: Thomas L. Milani
creator: Andresa M.C. Germano
subject: Neuroscience
subject: Geriatrics
subject: Kinesiology
subject: Neurology
subject: Pediatrics
description: doi:10.7717/peerj.11221
publisher: PeerJ Inc.
rights: © 2021 Schmidt et al.
abstract: Background Studies demonstrated that the older adults can be more susceptible to balance instability after acute visual manipulation. There are different manipulation approaches used to investigate the importance of visual inputs on balance, e.g., eyes closed and blackout glasses. However, there is evidence that eyes open versus eyes closed results in a different organization of human brain functional networks. It is, however, unclear how different visual manipulations affect balance, and whether such effects differ between young and elderly persons. Therefore, this study aimed to determine whether different visual manipulation approaches affect quasi-static and dynamic balance responses differently, and to investigate whether balance responses of young and older adults are affected differently by these various visual conditions. Methods Thirty-six healthy participants (20 young and 16 older adults) performed balance tests (quasi-static and unexpected perturbations) under four visual conditions: Eyes Open, Eyes Closed, Blackout Glasses, and Dark Room. Center of pressure (CoP) and muscle activation (EMG) were quantified. Results As expected, visual deprivation resulted in larger CoP excursions and higher muscle activations during balance tests for all participants. Surprisingly, the visual manipulation approach did not influence balance control in either group. Furthermore, quasi-static and dynamic balance control did not differ between young or older adults. The visual system plays an important role in balance control, however, similarly for both young and older adults. Different visual deprivation approaches did not influence balance results, meaning our results are comparable between participants of different ages. Further studies should investigate whether a critical illumination level may elicit different postural responses between young and older adults.
bibliographic citation: Schmidt et al. (2021) Different visual manipulations have similar effects on quasi-static and dynamic balance responses of young and older people. PeerJ 9:e11221 https://doi.org/10.7717/peerj.11221
date submitted: 2020-09-18
date accepted: 2021-03-15
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmidt
  given name: Daniel
author list: Agent
  family name: Carpes
  given name: Felipe P.
author list: Agent
  family name: Milani
  given name: Thomas L.
author list: Agent
  family name: Germano
  given name: Andresa M.C.
doi: 10.7717/peerj.11221
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: ©2021 Schmidt et al.
attribution name: Schmidt et al.

Experimental indications of gardeners’ anecdotes that snails interfere with invasive slugs
type: item
type: AcademicArticle
description: The invasive Spanish slug (Arion vulgaris) is an important pest species in agriculture and horticulture in Europe. In the last decades it has spread across the continent where it outcompetes native slug and snail species, thus posing a threat for biodiversity. A popular anecdote suggests to promote Roman snails (Helix pomatia) in gardens because they are able to control A. vulgaris. We examined a potential interrelationship between these two species using a mesocosm experiment with lettuce plants. 13C-15N stable isotope labelling of lettuce allowed us to investigate interactions between Helix and Arion on weight gain/loss and herbivory. Additionally, we wanted to know whether different watering regimes (daily vs. every 3rd day watering of weekly amount) and earthworms alter these interactions. Egg predation of Helix on Arion eggs was further tested in a food-choice experiment. Arion showed a five times higher herbivory per body mass than Helix in a single-species setting. However, in mesocosms containing both species percentage of herbivory per body mass was significantly lower than in Arion-only mesocosms, especially when watered every three days. Overall isotope uptake via eaten lettuce was unaffected by the presence of the other species. Only very little predation (three out of 200 eggs) of Helix on Arion eggs was observed. Our results provide no evidence for a clear dismissal or confirmation of the popular gardener’s anecdote that Helix snails have a negative effect on Arion abundance or herbivory.
format: application/pdf
format: text/html
creator: Daniel Dörler
creator: Verena Dorn
creator: Theresia Widhalm
creator: Micha Horacek
creator: Florian Heigl
creator: Pia Euteneuer
creator: Friedrich Leisch
creator: Thomas Frank
creator: Johann G. Zaller
subject: Agricultural Science
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11309
publisher: PeerJ Inc.
rights: © 2021 Dörler et al.
abstract: The invasive Spanish slug (Arion vulgaris) is an important pest species in agriculture and horticulture in Europe. In the last decades it has spread across the continent where it outcompetes native slug and snail species, thus posing a threat for biodiversity. A popular anecdote suggests to promote Roman snails (Helix pomatia) in gardens because they are able to control A. vulgaris. We examined a potential interrelationship between these two species using a mesocosm experiment with lettuce plants. 13C-15N stable isotope labelling of lettuce allowed us to investigate interactions between Helix and Arion on weight gain/loss and herbivory. Additionally, we wanted to know whether different watering regimes (daily vs. every 3rd day watering of weekly amount) and earthworms alter these interactions. Egg predation of Helix on Arion eggs was further tested in a food-choice experiment. Arion showed a five times higher herbivory per body mass than Helix in a single-species setting. However, in mesocosms containing both species percentage of herbivory per body mass was significantly lower than in Arion-only mesocosms, especially when watered every three days. Overall isotope uptake via eaten lettuce was unaffected by the presence of the other species. Only very little predation (three out of 200 eggs) of Helix on Arion eggs was observed. Our results provide no evidence for a clear dismissal or confirmation of the popular gardener’s anecdote that Helix snails have a negative effect on Arion abundance or herbivory.
bibliographic citation: Dörler et al. (2021) Experimental indications of gardeners’ anecdotes that snails interfere with invasive slugs. PeerJ 9:e11309 https://doi.org/10.7717/peerj.11309
date submitted: 2020-11-26
date accepted: 2021-03-29
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dörler
  given name: Daniel
author list: Agent
  family name: Dorn
  given name: Verena
author list: Agent
  family name: Widhalm
  given name: Theresia
author list: Agent
  family name: Horacek
  given name: Micha
author list: Agent
  family name: Heigl
  given name: Florian
author list: Agent
  family name: Euteneuer
  given name: Pia
author list: Agent
  family name: Leisch
  given name: Friedrich
author list: Agent
  family name: Frank
  given name: Thomas
author list: Agent
  family name: Zaller
  given name: Johann G.
doi: 10.7717/peerj.11309
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: © 2021 Dörler et al.
attribution name: Dörler et al.

Limb myology and muscle architecture of the Indian rhinoceros Rhinoceros unicornis and the white rhinoceros Ceratotherium simum (Mammalia: Rhinocerotidae)
type: item
type: AcademicArticle
description: Land mammals support and move their body using their musculoskeletal system. Their musculature usually presents varying adaptations with body mass or mode of locomotion. Rhinocerotidae is an interesting clade in this regard, as they are heavy animals potentially reaching three tons but are still capable of adopting a galloping gait. However, their musculature has been poorly studied. Here we report the dissection of both forelimb and hindlimb of one neonate and one adult each for two species of rhinoceroses, the Indian rhinoceros (Rhinoceros unicornis) and the white rhinoceros (Ceratotherium simum). We show that their muscular organisation is similar to that of their relatives, equids and tapirs, and that few evolutionary convergences with other heavy mammals (e.g. elephants and hippopotamuses) are present. Nevertheless, they show clear adaptations to their large body mass, such as more distal insertions for the protractor and adductor muscles of the limbs, giving them longer lever arms. The quantitative architecture of rhino muscles is again reminiscent of that of horses and tapirs, although contrary to horses, the forelimb is much stronger than the hindlimb, which is likely due to its great role in body mass support. Muscles involved mainly in counteracting gravity (e.g. serratus ventralis thoracis, infraspinatus, gastrocnemius, flexores digitorum) are usually highly pennate with short fascicles facilitating strong joint extension. Muscles involved in propulsion (e.g. gluteal muscles, gluteobiceps, quadriceps femoris) seem to represent a compromise between a high maximal isometric force and long fascicles, allowing a reasonably fast and wide working range. Neonates present higher normalized maximal isometric force than the adults for almost every muscle, except sometimes for the extensor and propulsor muscles, which presumably acquire their great force-generating capacity during the growth of the animal. Our study clarifies the way the muscles of animals of cursor…
format: application/pdf
format: text/html
creator: Cyril Etienne
creator: Alexandra Houssaye
creator: John R. Hutchinson
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.11314
publisher: PeerJ Inc.
rights: © 2021 Etienne et al.
abstract: Land mammals support and move their body using their musculoskeletal system. Their musculature usually presents varying adaptations with body mass or mode of locomotion. Rhinocerotidae is an interesting clade in this regard, as they are heavy animals potentially reaching three tons but are still capable of adopting a galloping gait. However, their musculature has been poorly studied. Here we report the dissection of both forelimb and hindlimb of one neonate and one adult each for two species of rhinoceroses, the Indian rhinoceros (Rhinoceros unicornis) and the white rhinoceros (Ceratotherium simum). We show that their muscular organisation is similar to that of their relatives, equids and tapirs, and that few evolutionary convergences with other heavy mammals (e.g. elephants and hippopotamuses) are present. Nevertheless, they show clear adaptations to their large body mass, such as more distal insertions for the protractor and adductor muscles of the limbs, giving them longer lever arms. The quantitative architecture of rhino muscles is again reminiscent of that of horses and tapirs, although contrary to horses, the forelimb is much stronger than the hindlimb, which is likely due to its great role in body mass support. Muscles involved mainly in counteracting gravity (e.g. serratus ventralis thoracis, infraspinatus, gastrocnemius, flexores digitorum) are usually highly pennate with short fascicles facilitating strong joint extension. Muscles involved in propulsion (e.g. gluteal muscles, gluteobiceps, quadriceps femoris) seem to represent a compromise between a high maximal isometric force and long fascicles, allowing a reasonably fast and wide working range. Neonates present higher normalized maximal isometric force than the adults for almost every muscle, except sometimes for the extensor and propulsor muscles, which presumably acquire their great force-generating capacity during the growth of the animal. Our study clarifies the way the muscles of animals of cursor…
bibliographic citation: Etienne et al. (2021) Limb myology and muscle architecture of the Indian rhinoceros Rhinoceros unicornis and the white rhinoceros Ceratotherium simum (Mammalia: Rhinocerotidae). PeerJ 9:e11314 https://doi.org/10.7717/peerj.11314
date submitted: 2021-01-13
date accepted: 2021-03-30
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Etienne
  given name: Cyril
author list: Agent
  family name: Houssaye
  given name: Alexandra
author list: Agent
  family name: Hutchinson
  given name: John R.
doi: 10.7717/peerj.11314
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: © 2021 Etienne et al.
attribution name: Etienne et al.

Identification of robust diagnostic and prognostic gene signatures in different grades of gliomas: a retrospective study
type: item
type: AcademicArticle
description: Background Gliomas are the most common primary tumors of the central nervous system. The complexity and heterogeneity of the tumor makes it difficult to obtain good biomarkers for drug development. In this study, through The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA), we analyze the common diagnostic and prognostic moleculer markers in Caucasian and Asian populations, which can be used as drug targets in the future. Methods The RNA-seq data from Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) were analyzed to identify signatures. Based on the signatures, the prognosis index (PI) of every patient was constructed to predict the prognostic risk. Also, gene ontology (GO) functional enrichment analysis and KEGG analysis were conducted to investigate the biological functions of these mRNAs. Glioma patients’ data in the CGGA database were introduced to validate the effectiveness of the signatures among Chinese populations. Excluding the previously reported prognostic markers of gliomas from this study, the expression of HSPA5 and MTPN were examined by qRT-PCR and immunohistochemical assay. Results In total, 20 mRNAs were finally selected to build PI for patients from TCGA, including 16 high-risk genes and four low-risk genes. For Chinese patients, the log-rank test p values of PI were both less than 0.0001 in two independent datasets. And the AUCs were 0.831 and 0.907 for 3 years of two datasets, respectively. Moreover, among these 20 mRNAs, 10 and 15 mRNAs also had a significant predictive effect via univariate COX analysis in CGGA_693 and CGGA_325, respectively. qRT-PCR and Immunohistochemistry assay indicated that HSPA5 and MTPN over-expressed in Glioma samples compared to normal samples. Conclusion The 20-gene signature can forecast the risk of Glioma in TCGA effectively, moreover it can also predict the risks of Chinese patients through validation in the CGGA database. HSPA5 and MTPN are possible biomarkers of gliomas suitab…
format: application/pdf
format: text/html
creator: Jieting Liu
creator: Hongrui Zhang
creator: Jingyun Zhang
creator: Zhitong Bing
creator: Yingbin Wang
creator: Qiao Li
creator: Kehu Yang
subject: Bioinformatics
subject: Molecular Biology
subject: Neurology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11350
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Gliomas are the most common primary tumors of the central nervous system. The complexity and heterogeneity of the tumor makes it difficult to obtain good biomarkers for drug development. In this study, through The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA), we analyze the common diagnostic and prognostic moleculer markers in Caucasian and Asian populations, which can be used as drug targets in the future. Methods The RNA-seq data from Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) were analyzed to identify signatures. Based on the signatures, the prognosis index (PI) of every patient was constructed to predict the prognostic risk. Also, gene ontology (GO) functional enrichment analysis and KEGG analysis were conducted to investigate the biological functions of these mRNAs. Glioma patients’ data in the CGGA database were introduced to validate the effectiveness of the signatures among Chinese populations. Excluding the previously reported prognostic markers of gliomas from this study, the expression of HSPA5 and MTPN were examined by qRT-PCR and immunohistochemical assay. Results In total, 20 mRNAs were finally selected to build PI for patients from TCGA, including 16 high-risk genes and four low-risk genes. For Chinese patients, the log-rank test p values of PI were both less than 0.0001 in two independent datasets. And the AUCs were 0.831 and 0.907 for 3 years of two datasets, respectively. Moreover, among these 20 mRNAs, 10 and 15 mRNAs also had a significant predictive effect via univariate COX analysis in CGGA_693 and CGGA_325, respectively. qRT-PCR and Immunohistochemistry assay indicated that HSPA5 and MTPN over-expressed in Glioma samples compared to normal samples. Conclusion The 20-gene signature can forecast the risk of Glioma in TCGA effectively, moreover it can also predict the risks of Chinese patients through validation in the CGGA database. HSPA5 and MTPN are possible biomarkers of gliomas suitab…
bibliographic citation: Liu et al. (2021) Identification of robust diagnostic and prognostic gene signatures in different grades of gliomas: a retrospective study. PeerJ 9:e11350 https://doi.org/10.7717/peerj.11350
date submitted: 2020-10-20
date accepted: 2021-04-05
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Jieting
author list: Agent
  family name: Zhang
  given name: Hongrui
author list: Agent
  family name: Zhang
  given name: Jingyun
author list: Agent
  family name: Bing
  given name: Zhitong
author list: Agent
  family name: Wang
  given name: Yingbin
author list: Agent
  family name: Li
  given name: Qiao
author list: Agent
  family name: Yang
  given name: Kehu
doi: 10.7717/peerj.11350
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Artificial light source selection in seaweed production: growth of seaweed and biosynthesis of photosynthetic pigments and soluble protein
type: item
type: AcademicArticle
description: Seaweed growth is often limited by light. Artificial light supply has been well studied in terrestrial agriculture, however, much less is known about its effect in seaweed aquaculture. In this study, the effects of four artificial light sources (white, red, green, and blue LEDs light) on a brown alga Sargassum fusiforme and a green alga Ulva pertusa were investigated. Seaweed growth, accumulation of photosynthetic pigments (chlorophyll a and carotenoid), and soluble protein were evaluated. White LED light was the optimal supplementary light when cultivating Ulva pertusa and Sargassum fusiforme, because it promoted seaweed growth while maintaining protein production. Meanwhile, red LED was unfavored in the cultivation of S. fusiforme, as it affected the seaweed growth and has a lower residual energy ratio underneath the water. LEDs would be a promising supplementary light source for seaweed cultivation.
format: application/pdf
format: text/html
creator: Shitao Huang
creator: Ke Li
creator: Yaoru Pan
creator: Yan Yu
creator: Thomas Wernberg
creator: Thibaut de Bettignies
creator: Jiaping Wu
creator: Chaosheng Zhou
creator: Zhixing Huang
creator: Xi Xiao
subject: Bioengineering
subject: Ecology
subject: Microbiology
subject: Plant Science
subject: Biological Oceanography
description: doi:10.7717/peerj.11351
publisher: PeerJ Inc.
rights: © 2021 Huang et al.
abstract: Seaweed growth is often limited by light. Artificial light supply has been well studied in terrestrial agriculture, however, much less is known about its effect in seaweed aquaculture. In this study, the effects of four artificial light sources (white, red, green, and blue LEDs light) on a brown alga Sargassum fusiforme and a green alga Ulva pertusa were investigated. Seaweed growth, accumulation of photosynthetic pigments (chlorophyll a and carotenoid), and soluble protein were evaluated. White LED light was the optimal supplementary light when cultivating Ulva pertusa and Sargassum fusiforme, because it promoted seaweed growth while maintaining protein production. Meanwhile, red LED was unfavored in the cultivation of S. fusiforme, as it affected the seaweed growth and has a lower residual energy ratio underneath the water. LEDs would be a promising supplementary light source for seaweed cultivation.
bibliographic citation: Huang et al. (2021) Artificial light source selection in seaweed production: growth of seaweed and biosynthesis of photosynthetic pigments and soluble protein. PeerJ 9:e11351 https://doi.org/10.7717/peerj.11351
date submitted: 2019-12-23
date accepted: 2021-04-05
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Shitao
author list: Agent
  family name: Li
  given name: Ke
author list: Agent
  family name: Pan
  given name: Yaoru
author list: Agent
  family name: Yu
  given name: Yan
author list: Agent
  family name: Wernberg
  given name: Thomas
author list: Agent
  family name: Bettignies
  given name: Thibaut de
author list: Agent
  family name: Wu
  given name: Jiaping
author list: Agent
  family name: Zhou
  given name: Chaosheng
author list: Agent
  family name: Huang
  given name: Zhixing
author list: Agent
  family name: Xiao
  given name: Xi
doi: 10.7717/peerj.11351
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: ©2021 Huang et al.
attribution name: Huang et al.

Durnonovariaodus maiseyi gen. et sp. nov., a new hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of England
type: item
type: AcademicArticle
description: A partial skeleton of a hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of Dorset, England, is described and designated as a new genus and species, Durnonovariaodus maiseyi gen. et sp. nov. The holotype and only known specimen, which is represented by disarticulated splanchnocranial elements with associated teeth, a single dorsal fin spine, the pelvic girdle, as well as unidentifiable cartilage fragments, plus countless dermal denticles, exhibits a puzzling combination of dental and skeletal features, providing important new insights into the morphological and ecological diversity of hybodontiforms. Durnonovariaodus gen. nov. displays a unique set of dental characters, showing close morphological resemblance to Secarodus from the Middle Jurassic of England, which was erected for distinctive, strongly labio-lingually compressed multicuspid cutting teeth originally described as Hybodus polyprion. Skeletally, Durnonovariaodus gen. nov. resembles Hybodus and Egertonodus in having a palatoquadrate with a palatobasal process and an ethmoidal articular surface, combined with the possession of dorsal fin spines ornamented with costae. Therefore, and given the absence of any conclusive phylogenetic framework, Durnonovariaodus maiseyi gen. et sp. nov. is here tentatively referred to Hybodontidae until more complete material becomes available in order to enable a more reliable suprageneric identification. The holotype of Durnonovariaodus maiseyi gen. et sp. nov. contains two separate pelvic half-girdles, a feature previously considered as evolutionarily primitive among hybodontiforms. However, unfused pelvic half-girdles also occur in the supposedly closely related species Hybodus hauffianus and may in fact have been more widely distributed among hybodontiforms than previously thought, thus rendering the phylogenetic utility of separated pelvic half-girdles for inferring hybodontiform interrelationships difficult and unresolved.
format: application/pdf
format: text/html
creator: Sebastian Stumpf
creator: Steve Etches
creator: Charlie J. Underwood
creator: Jürgen Kriwet
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11362
publisher: PeerJ Inc.
rights: © 2021 Stumpf et al.
abstract: A partial skeleton of a hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of Dorset, England, is described and designated as a new genus and species, Durnonovariaodus maiseyi gen. et sp. nov. The holotype and only known specimen, which is represented by disarticulated splanchnocranial elements with associated teeth, a single dorsal fin spine, the pelvic girdle, as well as unidentifiable cartilage fragments, plus countless dermal denticles, exhibits a puzzling combination of dental and skeletal features, providing important new insights into the morphological and ecological diversity of hybodontiforms. Durnonovariaodus gen. nov. displays a unique set of dental characters, showing close morphological resemblance to Secarodus from the Middle Jurassic of England, which was erected for distinctive, strongly labio-lingually compressed multicuspid cutting teeth originally described as Hybodus polyprion. Skeletally, Durnonovariaodus gen. nov. resembles Hybodus and Egertonodus in having a palatoquadrate with a palatobasal process and an ethmoidal articular surface, combined with the possession of dorsal fin spines ornamented with costae. Therefore, and given the absence of any conclusive phylogenetic framework, Durnonovariaodus maiseyi gen. et sp. nov. is here tentatively referred to Hybodontidae until more complete material becomes available in order to enable a more reliable suprageneric identification. The holotype of Durnonovariaodus maiseyi gen. et sp. nov. contains two separate pelvic half-girdles, a feature previously considered as evolutionarily primitive among hybodontiforms. However, unfused pelvic half-girdles also occur in the supposedly closely related species Hybodus hauffianus and may in fact have been more widely distributed among hybodontiforms than previously thought, thus rendering the phylogenetic utility of separated pelvic half-girdles for inferring hybodontiform interrelationships difficult and unresolved.
bibliographic citation: Stumpf et al. (2021) Durnonovariaodus maiseyi gen. et sp. nov., a new hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of England. PeerJ 9:e11362 https://doi.org/10.7717/peerj.11362
date submitted: 2021-02-24
date accepted: 2021-04-06
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stumpf
  given name: Sebastian
author list: Agent
  family name: Etches
  given name: Steve
author list: Agent
  family name: Underwood
  given name: Charlie J.
author list: Agent
  family name: Kriwet
  given name: Jürgen
doi: 10.7717/peerj.11362
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: © 2021 Stumpf et al.
attribution name: Stumpf et al.

Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations
type: item
type: AcademicArticle
description: Background Carex buxbaumii and C. hartmaniorum are sister species of the clade Papilliferae within the monophyletic section Racemosae. An unambiguous identification of these species is relatively difficult due to the interspecific continuum of some morphological characters as well as the intraspecific variability. The study was aimed at determining the range of variability, both morphological and genetic, within and between these two closely related and similar species. Methods The sedges were collected during botanical expeditions to Armenia, Estonia, the Netherlands, and Poland. The morphological separation of the two species and their populations was tested using the Discriminant Function Analysis (DFA). The genetic variability of the 19 Carex populations was assessed in the presence of eight Inter Simple Sequence Repeat (ISSR) primers. Results Results of the study indicate a considerable genetic affinity between the two sedge species (mean Si = 0.619). However, the populations of C. hartmaniorum are, morphologically and genetically, more homogenous than the populations of C. buxbaumii. Compared to C. hartmaniorum, C. buxbaumii usually has wider leaf blades, a shorter inflorescence, a lower number of spikes which are shorter, but wider, and longer bracts and utricles. The AMOVA showed a larger variation between the populations of C. buxbaumii, representing 25.65% of the total variation in the taxon. Two populations of C. buxbaumii (from Poland and Estonia) are separated from the remaining populations, both genetically and morphologically; their individuals show shorter utricles and glumes, compared to the typical specimens of C. buxbaumii, and correspond with the morphology of putative infraspecific taxa described by Cajander (var. brevisquamosa and var. confusa). Conclusions The taxonomic status of the putative infraspecific taxa within C. buxbaumii requires further studies throughout the distribution range of C. buxbaumii, addressing habitats, morphology and ge…
format: application/pdf
format: text/html
creator: Helena Więcław
creator: Magdalena Szenejko
creator: Thea Kull
creator: Zofia Sotek
creator: Ewa Rębacz-Maron
creator: Jacob Koopman
subject: Genetics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.11372
publisher: PeerJ Inc.
rights: © 2021 Więcław et al.
abstract: Background Carex buxbaumii and C. hartmaniorum are sister species of the clade Papilliferae within the monophyletic section Racemosae. An unambiguous identification of these species is relatively difficult due to the interspecific continuum of some morphological characters as well as the intraspecific variability. The study was aimed at determining the range of variability, both morphological and genetic, within and between these two closely related and similar species. Methods The sedges were collected during botanical expeditions to Armenia, Estonia, the Netherlands, and Poland. The morphological separation of the two species and their populations was tested using the Discriminant Function Analysis (DFA). The genetic variability of the 19 Carex populations was assessed in the presence of eight Inter Simple Sequence Repeat (ISSR) primers. Results Results of the study indicate a considerable genetic affinity between the two sedge species (mean Si = 0.619). However, the populations of C. hartmaniorum are, morphologically and genetically, more homogenous than the populations of C. buxbaumii. Compared to C. hartmaniorum, C. buxbaumii usually has wider leaf blades, a shorter inflorescence, a lower number of spikes which are shorter, but wider, and longer bracts and utricles. The AMOVA showed a larger variation between the populations of C. buxbaumii, representing 25.65% of the total variation in the taxon. Two populations of C. buxbaumii (from Poland and Estonia) are separated from the remaining populations, both genetically and morphologically; their individuals show shorter utricles and glumes, compared to the typical specimens of C. buxbaumii, and correspond with the morphology of putative infraspecific taxa described by Cajander (var. brevisquamosa and var. confusa). Conclusions The taxonomic status of the putative infraspecific taxa within C. buxbaumii requires further studies throughout the distribution range of C. buxbaumii, addressing habitats, morphology and ge…
bibliographic citation: Więcław et al. (2021) Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations. PeerJ 9:e11372 https://doi.org/10.7717/peerj.11372
date submitted: 2020-09-10
date accepted: 2021-04-07
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Więcław
  given name: Helena
author list: Agent
  family name: Szenejko
  given name: Magdalena
author list: Agent
  family name: Kull
  given name: Thea
author list: Agent
  family name: Sotek
  given name: Zofia
author list: Agent
  family name: Rębacz-Maron
  given name: Ewa
author list: Agent
  family name: Koopman
  given name: Jacob
doi: 10.7717/peerj.11372
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: ©2021 Więcław et al.
attribution name: Więcław et al.

Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements
type: item
type: AcademicArticle
description: Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37–89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72–96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.
format: application/pdf
format: text/html
creator: Jose Luis Gonzalez-Pimentel
creator: Tamara Martin-Pozas
creator: Valme Jurado
creator: Ana Zelia Miller
creator: Ana Teresa Caldeira
creator: Octavio Fernandez-Lorenzo
creator: Sergio Sanchez-Moral
creator: Cesareo Saiz-Jimenez
subject: Biodiversity
subject: Microbiology
subject: Molecular Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.11386
publisher: PeerJ Inc.
rights: © 2021 Gonzalez-Pimentel et al.
abstract: Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37–89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72–96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.
bibliographic citation: Gonzalez-Pimentel et al. (2021) Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PeerJ 9:e11386 https://doi.org/10.7717/peerj.11386
date submitted: 2021-02-26
date accepted: 2021-04-10
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzalez-Pimentel
  given name: Jose Luis
author list: Agent
  family name: Martin-Pozas
  given name: Tamara
author list: Agent
  family name: Jurado
  given name: Valme
author list: Agent
  family name: Miller
  given name: Ana Zelia
author list: Agent
  family name: Caldeira
  given name: Ana Teresa
author list: Agent
  family name: Fernandez-Lorenzo
  given name: Octavio
author list: Agent
  family name: Sanchez-Moral
  given name: Sergio
author list: Agent
  family name: Saiz-Jimenez
  given name: Cesareo
doi: 10.7717/peerj.11386
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: ©2021 Gonzalez-Pimentel et al.
attribution name: Gonzalez-Pimentel et al.

Mapping open knowledge institutions: an exploratory analysis of Australian universities
type: item
type: AcademicArticle
description: While the movement for open research has gained momentum in recent years, there remain concerns about the broader commitment to openness in knowledge production and dissemination. Increasingly, universities are under pressure to transform themselves to engage with the wider community and to be more inclusive. Open knowledge institutions (OKIs) provide a framework that encourages universities to act with the principles of openness at their centre; not only should universities embrace digital open access (OA), but also lead actions in cultivating diversity, equity, transparency and positive changes in society. This leads to questions of whether we can evaluate the progress of OKIs and what are potential indicators for OKIs. As an exploratory study, this article reports on the collection and analysis of a list of potential OKI indicators. Data for these indicators are gathered for 43 Australian universities. The indicators provide high-dimensional and complex signals about university performances. They show evidence of large disparities in characteristics such as Indigenous employment and gender equity, and a preference for repository-mediated OA across Australian universities. We demonstrate use of the OKI evaluation framework to categorise these indicators into three platforms of diversity, communication and coordination. The analysis provides new insights into the Australian open knowledge landscape and ways of mapping different paths of OKIs.
format: application/pdf
format: text/html
creator: Chun-Kai (Karl) Huang
creator: Katie Wilson
creator: Cameron Neylon
creator: Alkim Ozaygen
creator: Lucy Montgomery
creator: Richard Hosking
subject: Science and Medical Education
subject: Science Policy
subject: Data Science
description: doi:10.7717/peerj.11391
publisher: PeerJ Inc.
rights: © 2021 Huang et al.
abstract: While the movement for open research has gained momentum in recent years, there remain concerns about the broader commitment to openness in knowledge production and dissemination. Increasingly, universities are under pressure to transform themselves to engage with the wider community and to be more inclusive. Open knowledge institutions (OKIs) provide a framework that encourages universities to act with the principles of openness at their centre; not only should universities embrace digital open access (OA), but also lead actions in cultivating diversity, equity, transparency and positive changes in society. This leads to questions of whether we can evaluate the progress of OKIs and what are potential indicators for OKIs. As an exploratory study, this article reports on the collection and analysis of a list of potential OKI indicators. Data for these indicators are gathered for 43 Australian universities. The indicators provide high-dimensional and complex signals about university performances. They show evidence of large disparities in characteristics such as Indigenous employment and gender equity, and a preference for repository-mediated OA across Australian universities. We demonstrate use of the OKI evaluation framework to categorise these indicators into three platforms of diversity, communication and coordination. The analysis provides new insights into the Australian open knowledge landscape and ways of mapping different paths of OKIs.
bibliographic citation: Huang et al. (2021) Mapping open knowledge institutions: an exploratory analysis of Australian universities. PeerJ 9:e11391 https://doi.org/10.7717/peerj.11391
date submitted: 2020-09-25
date accepted: 2021-04-12
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Chun-Kai (Karl)
author list: Agent
  family name: Wilson
  given name: Katie
author list: Agent
  family name: Neylon
  given name: Cameron
author list: Agent
  family name: Ozaygen
  given name: Alkim
author list: Agent
  family name: Montgomery
  given name: Lucy
author list: Agent
  family name: Hosking
  given name: Richard
doi: 10.7717/peerj.11391
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: © 2021 Huang et al.
attribution name: Huang et al.

Shiftwork, functional bowel symptoms, and the microbiome
type: item
type: AcademicArticle
description: Background There are about 15 million Americans working full-time on evening, night, or rotating shifts. Between 48% and 81.9% of those working rotating or night shifts report abdominal pain, constipation, diarrhea and other symptoms of functional bowel disorders. The basis for this high prevalence of functional bowel disorders, including irritable bowel syndrome (IBS), among shift workers is unknown. Animal studies, however, suggest that circadian disruption, similar to that in shift workers, may contribute to the development of GI complaints among shift workers by altering the composition and normal diurnal rhythmicity of the resident intestinal microbes. Therefore, the present study was designed to determine if there were differences in (1) composition and diversity of the microbiome of night shift workers compared to day shift workers; and (2) the composition and diversity of the microbiome among shift workers experiencing functional bowel symptoms compared to shift workers who did not experience functional bowel symptoms. Methods Fifty-one full time staff nurses who worked either 12-hour day or night shifts completed demographic information, and the Rome III IBS module. They also collected two samples of gut microbiota before the beginning and at the end of their last work shift on day 14, using validated field-tested methods consistent with the Human Microbiome Project. After DNA extraction, 16S rRNA sequencing and assignment to the genus level was completed, samples were then compared to determine if there were (1) differences in the diversity and profile of the microbiome by shift type; (2) if there were differences in the microbiome by time of day for collection; and (3) whether there were differences in the diversity and profile of the microbiome of nurses with IBS and those without IBS. Results There were no differences in alpha or beta diversity of gut microbiota when specimens from day and night shift nurses were compared. There were however marginal di…
format: application/pdf
format: text/html
creator: Ann E. Rogers
creator: Yi-Juan Hu
creator: Ye Yue
creator: Emily F. Wissel
creator: Robert A. Petit III
creator: Simone Jarrett
creator: Jennifer Christie
creator: Timothy D. Read
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Nursing
description: doi:10.7717/peerj.11406
publisher: PeerJ Inc.
rights: © 2021 Rogers et al.
abstract: Background There are about 15 million Americans working full-time on evening, night, or rotating shifts. Between 48% and 81.9% of those working rotating or night shifts report abdominal pain, constipation, diarrhea and other symptoms of functional bowel disorders. The basis for this high prevalence of functional bowel disorders, including irritable bowel syndrome (IBS), among shift workers is unknown. Animal studies, however, suggest that circadian disruption, similar to that in shift workers, may contribute to the development of GI complaints among shift workers by altering the composition and normal diurnal rhythmicity of the resident intestinal microbes. Therefore, the present study was designed to determine if there were differences in (1) composition and diversity of the microbiome of night shift workers compared to day shift workers; and (2) the composition and diversity of the microbiome among shift workers experiencing functional bowel symptoms compared to shift workers who did not experience functional bowel symptoms. Methods Fifty-one full time staff nurses who worked either 12-hour day or night shifts completed demographic information, and the Rome III IBS module. They also collected two samples of gut microbiota before the beginning and at the end of their last work shift on day 14, using validated field-tested methods consistent with the Human Microbiome Project. After DNA extraction, 16S rRNA sequencing and assignment to the genus level was completed, samples were then compared to determine if there were (1) differences in the diversity and profile of the microbiome by shift type; (2) if there were differences in the microbiome by time of day for collection; and (3) whether there were differences in the diversity and profile of the microbiome of nurses with IBS and those without IBS. Results There were no differences in alpha or beta diversity of gut microbiota when specimens from day and night shift nurses were compared. There were however marginal di…
bibliographic citation: Rogers et al. (2021) Shiftwork, functional bowel symptoms, and the microbiome. PeerJ 9:e11406 https://doi.org/10.7717/peerj.11406
date submitted: 2021-02-17
date accepted: 2021-04-14
issued: 2021-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rogers
  given name: Ann E.
author list: Agent
  family name: Hu
  given name: Yi-Juan
author list: Agent
  family name: Yue
  given name: Ye
author list: Agent
  family name: Wissel
  given name: Emily F.
author list: Agent
  family name: Petit III
  given name: Robert A.
author list: Agent
  family name: Jarrett
  given name: Simone
author list: Agent
  family name: Christie
  given name: Jennifer
author list: Agent
  family name: Read
  given name: Timothy D.
doi: 10.7717/peerj.11406
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-11
copyright: ©2021 Rogers et al.
attribution name: Rogers et al.

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