PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation
items: First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna
items: Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park
items: Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries
items: Search for morphological indicators that predict implantation by principal component analysis using images of blastocyst
items: Malformations in Late Devonian brachiopods from the western Junggar, NW China and their potential causes
items: Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.)
items: Anatomical indicators of Eucalyptus spp. resistance to Glycaspis brimblecombei (Hemiptera: Aphalaridae)
items: Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.
items: Prevalence of hyperglycemia in masters athletes

The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation
type: item
type: AcademicArticle
description: Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern …
format: application/pdf
format: text/html
creator: Jinpeng Zhang
creator: Andrzej Witkowski
creator: Michał Tomczak
creator: Chao Li
creator: Kevin McCartney
creator: Zhen Xia
subject: Ecology
subject: Marine Biology
subject: Mathematical Biology
subject: Paleontology
description: doi:10.7717/peerj.13115
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern …
bibliographic citation: Zhang et al. (2022) The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation. PeerJ 10:e13115 https://doi.org/10.7717/peerj.13115
date submitted: 2021-05-17
date accepted: 2022-02-23
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jinpeng
author list: Agent
  family name: Witkowski
  given name: Andrzej
author list: Agent
  family name: Tomczak
  given name: Michał
author list: Agent
  family name: Li
  given name: Chao
author list: Agent
  family name: McCartney
  given name: Kevin
author list: Agent
  family name: Xia
  given name: Zhen
doi: 10.7717/peerj.13115
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna
type: item
type: AcademicArticle
description: The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins) OMM assemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale.
format: application/pdf
format: text/html
creator: Gabriel Aguirre-Fernández
creator: Jürg Jost
creator: Sarah Hilfiker
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13251
publisher: PeerJ Inc.
rights: © 2022 Aguirre-Fernández et al.
abstract: The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins) OMM assemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale.
bibliographic citation: Aguirre-Fernández et al. (2022) First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna. PeerJ 10:e13251 https://doi.org/10.7717/peerj.13251
date submitted: 2021-10-01
date accepted: 2022-03-21
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguirre-Fernández
  given name: Gabriel
author list: Agent
  family name: Jost
  given name: Jürg
author list: Agent
  family name: Hilfiker
  given name: Sarah
doi: 10.7717/peerj.13251
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: ©2022 Aguirre-Fernández et al.
attribution name: Aguirre-Fernández et al.

Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park
type: item
type: AcademicArticle
description: Background The reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia’s Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies. Methods This study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models. Results A total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Co…
format: application/pdf
format: text/html
creator: Elitza S. Germanov
creator: Simon J. Pierce
creator: Andrea D. Marshall
creator: I. Gede Hendrawan
creator: Ande Kefi
creator: Lars Bejder
creator: Neil Loneragan
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.13302
publisher: PeerJ Inc.
rights: © 2022 Germanov et al.
abstract: Background The reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia’s Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies. Methods This study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models. Results A total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Co…
bibliographic citation: Germanov et al. (2022) Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park. PeerJ 10:e13302 https://doi.org/10.7717/peerj.13302
date submitted: 2021-10-04
date accepted: 2022-03-29
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Germanov
  given name: Elitza S.
author list: Agent
  family name: Pierce
  given name: Simon J.
author list: Agent
  family name: Marshall
  given name: Andrea D.
author list: Agent
  family name: Hendrawan
  given name: I. Gede
author list: Agent
  family name: Kefi
  given name: Ande
author list: Agent
  family name: Bejder
  given name: Lars
author list: Agent
  family name: Loneragan
  given name: Neil
doi: 10.7717/peerj.13302
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: © 2022 Germanov et al.
attribution name: Germanov et al.

Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries
type: item
type: AcademicArticle
description: Introduction The consumption of dairy products contributes to health, nutrition, and livelihoods globally. However, dairy products do not come without microbiological food safety risks for consumers. Despite this risk, common hygiene measures in high-income countries, particularly pasteurisation, ensures that milk is safe, and is indeed frequently mandated by law. Nevertheless, over the past two decades, there has been a global increase in the number of consumers in high-income developed countries actively seeking out unpasteurised milk in liquid and product forms for perceived nutritional and health benefits, and improved taste. The often-anecdotal claims upon which consumers make such choices are not all supported by scientific evidence; however, some recent research studies have investigated (and in some cases demonstrated) the positive impact of unpasteurised milk consumption on the prevalence of asthma, atopy, rectal cancer and respiratory illness. Methods To investigate the significance of unpasteurised milk and milk product consumption for human health in high-income countries, outbreak data between the years 2000 and 2018 were obtained for the United States of America, Canada, the European Union, the United Kingdom, Japan, New Zealand and Australia, which were then categorized into three World Health Organisation subregions: AMR A, EUR A and WPR A. Outbreak dynamic variables such as pathogens, the place of consumption, numbers of outbreaks and deaths per million capita, the average number of cases per outbreak and regulations were described and analysed using R Studio. To provide an overview of unpasteurised milk-related disease outbreaks, a rapid evidence review was also undertaken to establish an overview of what is known in the current literature about hazards and drivers of consumption. Results Foodborne outbreaks associated with unpasteurised dairy consumption have risen in high-income countries over the period 2000 to 2018, with Campylobacter spp. bein…
format: application/pdf
format: text/html
creator: Joanna N. de Klerk
creator: Philip A. Robinson
subject: Food Science and Technology
subject: Global Health
subject: Infectious Diseases
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.13426
publisher: PeerJ Inc.
rights: © 2022 de Klerk and Robinson
abstract: Introduction The consumption of dairy products contributes to health, nutrition, and livelihoods globally. However, dairy products do not come without microbiological food safety risks for consumers. Despite this risk, common hygiene measures in high-income countries, particularly pasteurisation, ensures that milk is safe, and is indeed frequently mandated by law. Nevertheless, over the past two decades, there has been a global increase in the number of consumers in high-income developed countries actively seeking out unpasteurised milk in liquid and product forms for perceived nutritional and health benefits, and improved taste. The often-anecdotal claims upon which consumers make such choices are not all supported by scientific evidence; however, some recent research studies have investigated (and in some cases demonstrated) the positive impact of unpasteurised milk consumption on the prevalence of asthma, atopy, rectal cancer and respiratory illness. Methods To investigate the significance of unpasteurised milk and milk product consumption for human health in high-income countries, outbreak data between the years 2000 and 2018 were obtained for the United States of America, Canada, the European Union, the United Kingdom, Japan, New Zealand and Australia, which were then categorized into three World Health Organisation subregions: AMR A, EUR A and WPR A. Outbreak dynamic variables such as pathogens, the place of consumption, numbers of outbreaks and deaths per million capita, the average number of cases per outbreak and regulations were described and analysed using R Studio. To provide an overview of unpasteurised milk-related disease outbreaks, a rapid evidence review was also undertaken to establish an overview of what is known in the current literature about hazards and drivers of consumption. Results Foodborne outbreaks associated with unpasteurised dairy consumption have risen in high-income countries over the period 2000 to 2018, with Campylobacter spp. bein…
bibliographic citation: de Klerk et al. (2022) Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries. PeerJ 10:e13426 https://doi.org/10.7717/peerj.13426
date submitted: 2021-10-25
date accepted: 2022-04-21
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Klerk
  given name: Joanna N.
author list: Agent
  family name: Robinson
  given name: Philip A.
doi: 10.7717/peerj.13426
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: ©2022 de Klerk and Robinson
attribution name: de Klerk and Robinson

Search for morphological indicators that predict implantation by principal component analysis using images of blastocyst
type: item
type: AcademicArticle
description: Background Although the current evaluation of human blastocysts is based on the Gardner criteria, there may be other notable parameters. The purpose of our study was to clarify whether the morphology of blastocysts has notable indicators other than the Gardner criteria. Methods To find such indicators, we compared blastocysts that showed elevated human chorionic gonadotropin (hCG) levels after transplantation (hCG-positive group; n = 129) and those that did not (hCG-negative group; n = 105) using principal component analysis of pixel brightness of the images. Results The comparison revealed that the hCG-positive group had grainy morphology and the hCG-negative group had non-grainy morphology. Classification of the blastocysts by this indicator did not make a difference in Gardner score. Interestingly, all embryos with ≥20% fragmentation were non-grainy. The visual classification based on this analysis was significantly more accurate than the prediction of implantation using the Gardner score ≥3BB. As graininess can be used in combination with the Gardner score, this indicator will enhance current reproductive technologies.
format: application/pdf
format: text/html
creator: Daisuke Mashiko
creator: Mikiko Tokoro
creator: Masae Kojima
creator: Noritaka Fukunaga
creator: Yoshimasa Asada
creator: Kazuo Yamagata
subject: Developmental Biology
subject: Anatomy and Physiology
subject: Data Science
description: doi:10.7717/peerj.13441
publisher: PeerJ Inc.
rights: © 2022 Mashiko et al.
abstract: Background Although the current evaluation of human blastocysts is based on the Gardner criteria, there may be other notable parameters. The purpose of our study was to clarify whether the morphology of blastocysts has notable indicators other than the Gardner criteria. Methods To find such indicators, we compared blastocysts that showed elevated human chorionic gonadotropin (hCG) levels after transplantation (hCG-positive group; n = 129) and those that did not (hCG-negative group; n = 105) using principal component analysis of pixel brightness of the images. Results The comparison revealed that the hCG-positive group had grainy morphology and the hCG-negative group had non-grainy morphology. Classification of the blastocysts by this indicator did not make a difference in Gardner score. Interestingly, all embryos with ≥20% fragmentation were non-grainy. The visual classification based on this analysis was significantly more accurate than the prediction of implantation using the Gardner score ≥3BB. As graininess can be used in combination with the Gardner score, this indicator will enhance current reproductive technologies.
bibliographic citation: Mashiko et al. (2022) Search for morphological indicators that predict implantation by principal component analysis using images of blastocyst. PeerJ 10:e13441 https://doi.org/10.7717/peerj.13441
date submitted: 2022-02-23
date accepted: 2022-04-25
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mashiko
  given name: Daisuke
author list: Agent
  family name: Tokoro
  given name: Mikiko
author list: Agent
  family name: Kojima
  given name: Masae
author list: Agent
  family name: Fukunaga
  given name: Noritaka
author list: Agent
  family name: Asada
  given name: Yoshimasa
author list: Agent
  family name: Yamagata
  given name: Kazuo
doi: 10.7717/peerj.13441
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: © 2022 Mashiko et al.
attribution name: Mashiko et al.

Malformations in Late Devonian brachiopods from the western Junggar, NW China and their potential causes
type: item
type: AcademicArticle
description: Although malformations are found in both extant organisms and the fossil record, they are more rarely reported in the fossil record than in living organisms, and the environmental factors causing the malformations are much more difficult to identify for the fossil record. Two athyrid brachiopod taxa from the Upper Devonian Hongguleleng Formation in western Junggar (Xinjiang, NW China) show distinctive shell malformation. Of 198 Cleiothyridina and 405 Crinisarina specimens, 18 and 39 individuals were malformed, respectively; an abnormality ratio of nearly 10%. Considering the preservation status and buried environment of the abnormal specimens, and analysis of trace elements and rare earth elements from whole-rock and brachiopod shells, we conclude that the appearance of malformed athyrids is likely related to epi/endoparasites, or less likely the slightly higher content of heavy metal in the sea.
format: application/pdf
format: text/html
creator: Ruiwen Zong
creator: Yiming Gong
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.13447
publisher: PeerJ Inc.
rights: © 2022 Zong and Gong
abstract: Although malformations are found in both extant organisms and the fossil record, they are more rarely reported in the fossil record than in living organisms, and the environmental factors causing the malformations are much more difficult to identify for the fossil record. Two athyrid brachiopod taxa from the Upper Devonian Hongguleleng Formation in western Junggar (Xinjiang, NW China) show distinctive shell malformation. Of 198 Cleiothyridina and 405 Crinisarina specimens, 18 and 39 individuals were malformed, respectively; an abnormality ratio of nearly 10%. Considering the preservation status and buried environment of the abnormal specimens, and analysis of trace elements and rare earth elements from whole-rock and brachiopod shells, we conclude that the appearance of malformed athyrids is likely related to epi/endoparasites, or less likely the slightly higher content of heavy metal in the sea.
bibliographic citation: Zong et al. (2022) Malformations in Late Devonian brachiopods from the western Junggar, NW China and their potential causes. PeerJ 10:e13447 https://doi.org/10.7717/peerj.13447
date submitted: 2021-10-04
date accepted: 2022-04-26
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zong
  given name: Ruiwen
author list: Agent
  family name: Gong
  given name: Yiming
doi: 10.7717/peerj.13447
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: © 2022 Zong and Gong
attribution name: Zong and Gong

Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.)
type: item
type: AcademicArticle
description: Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree.
format: application/pdf
format: text/html
creator: Bingbing Guo
creator: Hong Yang
creator: Longjun Dai
creator: Xizhu Zhao
creator: Li-feng Wang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13189
publisher: PeerJ Inc.
rights: © 2022 Guo et al.
abstract: Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree.
bibliographic citation: Guo et al. (2022) Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.). PeerJ 10:e13189 https://doi.org/10.7717/peerj.13189
date submitted: 2021-11-19
date accepted: 2022-03-08
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Bingbing
author list: Agent
  family name: Yang
  given name: Hong
author list: Agent
  family name: Dai
  given name: Longjun
author list: Agent
  family name: Zhao
  given name: Xizhu
author list: Agent
  family name: Wang
  given name: Li-feng
doi: 10.7717/peerj.13189
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: ©2022 Guo et al.
attribution name: Guo et al.

Anatomical indicators of Eucalyptus spp. resistance to Glycaspis brimblecombei (Hemiptera: Aphalaridae)
type: item
type: AcademicArticle
description: The total area of forest crops in Brazil is 9.55 million hectares, of which 7.5 million hectares are Eucalyptus. These crops are the most productive in the world, but may suffer losses due to exotic pests, including Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae) found in Brazil since 2003. Interactions between Eucalyptus plants and insect pests may led to the selection of resistant genotypes. Eucalyptus species are either susceptible or resistant to this pest group, but the damage they suffer needs to be evaluated. The objective was to determine possible leaf anatomy indicators of different Eucalyptus species associated with G. brimblecombei infestations, focusing on plant resistance to this pest. The study was carried out with Eucalyptus camaldulensis, Eucalyptus grandis, Eucalyptus saligna and Eucalyptus urophylla saplings infested or not by G. brimblecombei eggs and nymphs. Eighteen anatomical characteristics of the leaves of these plants were analyzed. The number of stomata on the adaxial and abaxial sides and the glandular area in the central leaf vein are associated with greater or lesser infestation by G. brimblecombei in the Eucalyptus genotypes.
format: application/pdf
format: text/html
creator: Fernando Henrique Moreno de Oliveira Del Piero
creator: Carlos Frederico Wilcken
creator: Maurício Magalhães Domingues
creator: Ana Laura Favoreto
creator: Roberto Antonio Rodella
creator: Alexandre Igor Azevedo Pereira
creator: Wiane Meloni Silva
creator: José Eduardo Serrão
creator: José Cola Zanuncio
subject: Entomology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.13346
publisher: PeerJ Inc.
rights: © 2022 Del Piero et al.
abstract: The total area of forest crops in Brazil is 9.55 million hectares, of which 7.5 million hectares are Eucalyptus. These crops are the most productive in the world, but may suffer losses due to exotic pests, including Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae) found in Brazil since 2003. Interactions between Eucalyptus plants and insect pests may led to the selection of resistant genotypes. Eucalyptus species are either susceptible or resistant to this pest group, but the damage they suffer needs to be evaluated. The objective was to determine possible leaf anatomy indicators of different Eucalyptus species associated with G. brimblecombei infestations, focusing on plant resistance to this pest. The study was carried out with Eucalyptus camaldulensis, Eucalyptus grandis, Eucalyptus saligna and Eucalyptus urophylla saplings infested or not by G. brimblecombei eggs and nymphs. Eighteen anatomical characteristics of the leaves of these plants were analyzed. The number of stomata on the adaxial and abaxial sides and the glandular area in the central leaf vein are associated with greater or lesser infestation by G. brimblecombei in the Eucalyptus genotypes.
bibliographic citation: Del Piero et al. (2022) Anatomical indicators of Eucalyptus spp. resistance to Glycaspis brimblecombei (Hemiptera: Aphalaridae). PeerJ 10:e13346 https://doi.org/10.7717/peerj.13346
date submitted: 2021-12-09
date accepted: 2022-04-06
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Del Piero
  given name: Fernando Henrique Moreno de Oliveira
author list: Agent
  family name: Wilcken
  given name: Carlos Frederico
author list: Agent
  family name: Domingues
  given name: Maurício Magalhães
author list: Agent
  family name: Favoreto
  given name: Ana Laura
author list: Agent
  family name: Rodella
  given name: Roberto Antonio
author list: Agent
  family name: Pereira
  given name: Alexandre Igor Azevedo
author list: Agent
  family name: Silva
  given name: Wiane Meloni
author list: Agent
  family name: Serrão
  given name: José Eduardo
author list: Agent
  family name: Zanuncio
  given name: José Cola
doi: 10.7717/peerj.13346
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: © 2022 Del Piero et al.
attribution name: Del Piero et al.

Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.
type: item
type: AcademicArticle
description: Background Cotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development. Methods Using genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum. Results Chromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton.
format: application/pdf
format: text/html
creator: Kun Liu
creator: Nosheen Kabir
creator: Zhenzhen Wei
creator: Zhuojing Sun
creator: Jian Wang
creator: Jing Qi
creator: Miaoyang Liu
creator: Ji Liu
creator: Kehai Zhou
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13372
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Background Cotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development. Methods Using genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum. Results Chromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton.
bibliographic citation: Liu et al. (2022) Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.. PeerJ 10:e13372 https://doi.org/10.7717/peerj.13372
date submitted: 2021-11-18
date accepted: 2022-04-12
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Kun
author list: Agent
  family name: Kabir
  given name: Nosheen
author list: Agent
  family name: Wei
  given name: Zhenzhen
author list: Agent
  family name: Sun
  given name: Zhuojing
author list: Agent
  family name: Wang
  given name: Jian
author list: Agent
  family name: Qi
  given name: Jing
author list: Agent
  family name: Liu
  given name: Miaoyang
author list: Agent
  family name: Liu
  given name: Ji
author list: Agent
  family name: Zhou
  given name: Kehai
doi: 10.7717/peerj.13372
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Prevalence of hyperglycemia in masters athletes
type: item
type: AcademicArticle
description: Background Ageing is associated with decreased physical activity, obesity and subsequently an increased risk of developing type 2 diabetes mellitus (T2dm). Master athletes (MA) have initiated exercise or sport later in life or pursued a physically active lifestyle for an extended period. Subsequently, MAs have been proposed as a model of successful ageing as this active lifestyle is associated with health benefits including decreased health risk of chronic diseases and a reduction in premature mortality. Given long-term physical activity/exercise has previously been shown to be protective against hyperglycemia, a risk factor for T2dm, it is plausible that MA may have protective benefit against developing hyperglycemia. Therefore, the aim of this study was to investigate the prevalence of hyperglycemia via fasting plasma glucose (FPG) in MAs competing at the World Masters Games (WMG). Methods This cross-sectional, observational survey utilized an online survey using open-source web-based software was used to investigate MAs physiological and medical-related parameters. Over 28,000 MAs competed in the WMG, of which 8,072 MAs completed the survey. Of these MAs, a total of 486 (males 277, females 209; range 27 to 91 years, mean age 55.1 ± 10.2 years) attained recent pathology results which included FPG which was subsequently analyzed for this study. FPG and other outcome variables were compared between genders and to the Australian and United States general population. Results Mean FPG for MAs was 5.03 mmol (±1.2, 95% CI [4.9–5.1] mmol) with majority (75.5%) of MAs reporting a normal (<5.5 mmol) FPG, followed by pre-diabetes (20.2%, >5.51 to <5.99 mmol) and abnormal (4.3%, >7.0 mmol). There was no significant difference (P = 0.333) in FPG between genders however, males had a slightly higher (+2.1%) FPG as compared to females (5.08 ± 1.2 mmol (95% CI [4.9–5.22] mmol) versus 4.98 ± 1.1 mmol (95% CI 4.8-5.1 mmol)). The majority of males (71.8%) and females (80.3%) were cla…
format: application/pdf
format: text/html
creator: Mike Climstein
creator: Joe Walsh
creator: Kent Adams
creator: Trish Sevene
creator: Tim Heazlewood
creator: Mark DeBeliso
subject: Diabetes and Endocrinology
subject: Hematology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.13389
publisher: PeerJ Inc.
rights: © 2022 Climstein et al.
abstract: Background Ageing is associated with decreased physical activity, obesity and subsequently an increased risk of developing type 2 diabetes mellitus (T2dm). Master athletes (MA) have initiated exercise or sport later in life or pursued a physically active lifestyle for an extended period. Subsequently, MAs have been proposed as a model of successful ageing as this active lifestyle is associated with health benefits including decreased health risk of chronic diseases and a reduction in premature mortality. Given long-term physical activity/exercise has previously been shown to be protective against hyperglycemia, a risk factor for T2dm, it is plausible that MA may have protective benefit against developing hyperglycemia. Therefore, the aim of this study was to investigate the prevalence of hyperglycemia via fasting plasma glucose (FPG) in MAs competing at the World Masters Games (WMG). Methods This cross-sectional, observational survey utilized an online survey using open-source web-based software was used to investigate MAs physiological and medical-related parameters. Over 28,000 MAs competed in the WMG, of which 8,072 MAs completed the survey. Of these MAs, a total of 486 (males 277, females 209; range 27 to 91 years, mean age 55.1 ± 10.2 years) attained recent pathology results which included FPG which was subsequently analyzed for this study. FPG and other outcome variables were compared between genders and to the Australian and United States general population. Results Mean FPG for MAs was 5.03 mmol (±1.2, 95% CI [4.9–5.1] mmol) with majority (75.5%) of MAs reporting a normal (<5.5 mmol) FPG, followed by pre-diabetes (20.2%, >5.51 to <5.99 mmol) and abnormal (4.3%, >7.0 mmol). There was no significant difference (P = 0.333) in FPG between genders however, males had a slightly higher (+2.1%) FPG as compared to females (5.08 ± 1.2 mmol (95% CI [4.9–5.22] mmol) versus 4.98 ± 1.1 mmol (95% CI 4.8-5.1 mmol)). The majority of males (71.8%) and females (80.3%) were cla…
bibliographic citation: Climstein et al. (2022) Prevalence of hyperglycemia in masters athletes. PeerJ 10:e13389 https://doi.org/10.7717/peerj.13389
date submitted: 2022-01-31
date accepted: 2022-04-15
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Climstein
  given name: Mike
author list: Agent
  family name: Walsh
  given name: Joe
author list: Agent
  family name: Adams
  given name: Kent
author list: Agent
  family name: Sevene
  given name: Trish
author list: Agent
  family name: Heazlewood
  given name: Tim
author list: Agent
  family name: DeBeliso
  given name: Mark
doi: 10.7717/peerj.13389
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: ©2022 Climstein et al.
attribution name: Climstein et al.

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