PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The needs of cancer patients during the COVID-19 pandemic—psychosocial, ethical and spiritual aspects—systematic review
items: The effect of age and sexual maturation on thermal preferences of honey bee drones
items: Genetic diversity analysis for wild and cultivated accessions of Cymbopogon citratus (D.C.) Stapf using phytochemical and molecular markers
items: A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest
items: Fungal diversity in shade-coffee plantations in Soconusco, Mexico
items: Nest characteristics and composition of the colonial nesting Azure-winged magpie Cyanopica cyanus in South Korea
items: Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia
items: Agricultural big data and methods and models for food security analysis—a mini-review
items: Public awareness of seafood mislabeling
items: G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice

The needs of cancer patients during the COVID-19 pandemic—psychosocial, ethical and spiritual aspects—systematic review
type: item
type: AcademicArticle
description: The COVID-19 pandemic resulted in unprecedented changes in the functioning of the health care system, which were connected with the occurrence of new challenges for both the health care system’s employees and for the patients. The purpose of the present article is to analyze the needs of persons with oncological diseases. Taking into account the multiple aspects of the term health, psychological, social, and existential needs of the patients were analyzed. This article is directed mainly at persons who remain in a direct therapeutic relation with a patient. It is to facilitate recognizing the needs of ill people and to increase sensitivity to the issue of maintaining or improving the well-being of patients which requires paying special attention to their psychological, social, and existential needs during the period of hindered access to the health care system. This systematic review takes advantage of quantitative and qualitative methods of text analysis with phenomenological analysis factored in. The COVID-19 pandemic resulted in the appearance of new problems in the population of oncological patients or it made the existing problems more severe. As a consequence, it made it significantly more difficult to meet their needs on various levels and sometimes it even made it impossible. It seems necessary to determine and introduce strategies to ensure that patients with oncological diseases have access to psychological and spiritual support in the period of the pandemic.
format: application/pdf
format: text/html
creator: Joanna Zapała
creator: Monika Matecka
creator: Agnieszka Zok
creator: Ewa Baum
subject: Oncology
subject: Psychiatry and Psychology
subject: Mental Health
subject: COVID-19
subject: Healthcare Services
description: doi:10.7717/peerj.13480
publisher: PeerJ Inc.
rights: © 2022 Zapała et al.
abstract: The COVID-19 pandemic resulted in unprecedented changes in the functioning of the health care system, which were connected with the occurrence of new challenges for both the health care system’s employees and for the patients. The purpose of the present article is to analyze the needs of persons with oncological diseases. Taking into account the multiple aspects of the term health, psychological, social, and existential needs of the patients were analyzed. This article is directed mainly at persons who remain in a direct therapeutic relation with a patient. It is to facilitate recognizing the needs of ill people and to increase sensitivity to the issue of maintaining or improving the well-being of patients which requires paying special attention to their psychological, social, and existential needs during the period of hindered access to the health care system. This systematic review takes advantage of quantitative and qualitative methods of text analysis with phenomenological analysis factored in. The COVID-19 pandemic resulted in the appearance of new problems in the population of oncological patients or it made the existing problems more severe. As a consequence, it made it significantly more difficult to meet their needs on various levels and sometimes it even made it impossible. It seems necessary to determine and introduce strategies to ensure that patients with oncological diseases have access to psychological and spiritual support in the period of the pandemic.
bibliographic citation: Zapała et al. (2022) The needs of cancer patients during the COVID-19 pandemic—psychosocial, ethical and spiritual aspects—systematic review. PeerJ 10:e13480 https://doi.org/10.7717/peerj.13480
date submitted: 2021-11-29
date accepted: 2022-05-01
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zapała
  given name: Joanna
author list: Agent
  family name: Matecka
  given name: Monika
author list: Agent
  family name: Zok
  given name: Agnieszka
author list: Agent
  family name: Baum
  given name: Ewa
doi: 10.7717/peerj.13480
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: ©2022 Zapała et al.
attribution name: Zapała et al.

The effect of age and sexual maturation on thermal preferences of honey bee drones
type: item
type: AcademicArticle
description: The thermal preferences of Apis mellifera carnica drones (male individuals) are poorly understood, though their reproductive quality affects the quality of the inseminated queen and the whole honey bee colony. Therefore, the aim of this study was to determine the thermal preferences of individual drones according to their age and sexual maturity. Drones at the ages of 1, 5, 10, 15, 20 and 25 days were tested. The drones were placed on a platform in a temperature gradient in the range 20 °C and 46 °C. The thermal preferences of the drones were measured with the use of a thermal-imaging camera. Drones significantly differed with their choice of a preferred temperature. The one-day-old and the 25-day-old drones preferred the lowest temperatures. A slightly higher temperature was preferred by the 5-day-old drones, and the highest temperature was chosen by the drones at the ages of 10, 15, and 20 days. The changes in the thermal preferences of drones correspond to physiological changes occurring with age and connected with the rate of sexual maturation.
format: application/pdf
format: text/html
creator: Krystyna Czekońska
creator: Sylwia Łopuch
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.13494
publisher: PeerJ Inc.
rights: © 2022 Czekońska and Łopuch
abstract: The thermal preferences of Apis mellifera carnica drones (male individuals) are poorly understood, though their reproductive quality affects the quality of the inseminated queen and the whole honey bee colony. Therefore, the aim of this study was to determine the thermal preferences of individual drones according to their age and sexual maturity. Drones at the ages of 1, 5, 10, 15, 20 and 25 days were tested. The drones were placed on a platform in a temperature gradient in the range 20 °C and 46 °C. The thermal preferences of the drones were measured with the use of a thermal-imaging camera. Drones significantly differed with their choice of a preferred temperature. The one-day-old and the 25-day-old drones preferred the lowest temperatures. A slightly higher temperature was preferred by the 5-day-old drones, and the highest temperature was chosen by the drones at the ages of 10, 15, and 20 days. The changes in the thermal preferences of drones correspond to physiological changes occurring with age and connected with the rate of sexual maturation.
bibliographic citation: Czekońska et al. (2022) The effect of age and sexual maturation on thermal preferences of honey bee drones. PeerJ 10:e13494 https://doi.org/10.7717/peerj.13494
date submitted: 2021-12-14
date accepted: 2022-05-04
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Czekońska
  given name: Krystyna
author list: Agent
  family name: Łopuch
  given name: Sylwia
doi: 10.7717/peerj.13494
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: ©2022 Czekońska and Łopuch
attribution name: Czekońska and Łopuch

Genetic diversity analysis for wild and cultivated accessions of Cymbopogon citratus (D.C.) Stapf using phytochemical and molecular markers
type: item
type: AcademicArticle
description: Background Genetic diversity is being lost because of increasing urbanization and decreasing cultivation land, which leads to the abrupt use of wild resources of medicinally aromatic plants (MAPs). Cymbopogon citratus is a morphologically diverse MAP that is largely exploited in the food, cosmetics, and pharmaceutical industries. However, the intraspecific phytochemical and molecular diversity of C. citratus has yet to be explored. Methodology The germplasm was obtained from four different countries representing Pakistan, India, Bangladesh, and the United States. Oil extraction was performed by hydro distillation, and metabolic profiles of different accessions were generated by GC–MS. Seventeen functional molecular markers based on three genes encoding cytochrome P450, uridyl diphosphate glycosyltransferase and the 5S rRNA gene family were used to explore genetic diversity. Principal component analysis (PCA) and heatmaps were constructed using R software with the help of the gg-plot R package v1.0.5 for data validation. Results Among the 208 identified metabolites, citral was maximal, with a phytochemical contribution (1.92–27.73%), α-pinene (0.82–15.57%), verbenol (0.24–22.84%), neral (0.23–21.31%) and geranial acetate (0.43–15.65%). In the majority of accessions, citral was the dominant component. The highest concentration of citral was detected in 384541 (27.74%), 384527 (27.52%) belonging to Pakistan and one USA-based accession 38456 (27.71%). Region-specific grouping revealed a relationship between genetic diversity and geographical location. Pakistani accessions 384518, 38452, and 384544 genetically and 384535, 384518, and 384510 were phytochemically diverse. Conclusion The genetic diversity was more pronounced in cultivated accessions than in wild accessions. Moreover, it was observed that phytochemical diversity correlated with the altitude and temperature of the region.
format: application/pdf
format: text/html
creator: Bushra Shamsheer
creator: Nadia Riaz
creator: Zubaida Yousaf
creator: Sajjad Hyder
creator: Arusa Aftab
creator: Rashid Iqbal
creator: Muhammad Habib ur Rahman
creator: Ibrahim Al-Ashkar
creator: Khalid F. Almutairi
creator: Ayman El Sabagh
subject: Agricultural Science
subject: Biochemistry
subject: Biodiversity
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.13505
publisher: PeerJ Inc.
rights: © 2022 Shamsheer et al.
abstract: Background Genetic diversity is being lost because of increasing urbanization and decreasing cultivation land, which leads to the abrupt use of wild resources of medicinally aromatic plants (MAPs). Cymbopogon citratus is a morphologically diverse MAP that is largely exploited in the food, cosmetics, and pharmaceutical industries. However, the intraspecific phytochemical and molecular diversity of C. citratus has yet to be explored. Methodology The germplasm was obtained from four different countries representing Pakistan, India, Bangladesh, and the United States. Oil extraction was performed by hydro distillation, and metabolic profiles of different accessions were generated by GC–MS. Seventeen functional molecular markers based on three genes encoding cytochrome P450, uridyl diphosphate glycosyltransferase and the 5S rRNA gene family were used to explore genetic diversity. Principal component analysis (PCA) and heatmaps were constructed using R software with the help of the gg-plot R package v1.0.5 for data validation. Results Among the 208 identified metabolites, citral was maximal, with a phytochemical contribution (1.92–27.73%), α-pinene (0.82–15.57%), verbenol (0.24–22.84%), neral (0.23–21.31%) and geranial acetate (0.43–15.65%). In the majority of accessions, citral was the dominant component. The highest concentration of citral was detected in 384541 (27.74%), 384527 (27.52%) belonging to Pakistan and one USA-based accession 38456 (27.71%). Region-specific grouping revealed a relationship between genetic diversity and geographical location. Pakistani accessions 384518, 38452, and 384544 genetically and 384535, 384518, and 384510 were phytochemically diverse. Conclusion The genetic diversity was more pronounced in cultivated accessions than in wild accessions. Moreover, it was observed that phytochemical diversity correlated with the altitude and temperature of the region.
bibliographic citation: Shamsheer et al. (2022) Genetic diversity analysis for wild and cultivated accessions of Cymbopogon citratus (D.C.) Stapf using phytochemical and molecular markers. PeerJ 10:e13505 https://doi.org/10.7717/peerj.13505
date submitted: 2021-12-21
date accepted: 2022-05-06
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shamsheer
  given name: Bushra
author list: Agent
  family name: Riaz
  given name: Nadia
author list: Agent
  family name: Yousaf
  given name: Zubaida
author list: Agent
  family name: Hyder
  given name: Sajjad
author list: Agent
  family name: Aftab
  given name: Arusa
author list: Agent
  family name: Iqbal
  given name: Rashid
author list: Agent
  family name: Rahman
  given name: Muhammad Habib ur
author list: Agent
  family name: Al-Ashkar
  given name: Ibrahim
author list: Agent
  family name: F. Almutairi
  given name: Khalid
author list: Agent
  family name: El Sabagh
  given name: Ayman
doi: 10.7717/peerj.13505
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: © 2022 Shamsheer et al.
attribution name: Shamsheer et al.

A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest
type: item
type: AcademicArticle
description: Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that this framework has the potential to accurately predict trends of biodiversity change for both taxonomic and phylogenetic diversity. The framework identifies areas of potential diversity loss more accurately than areas of species gain, and performs best when applied to broadly distributed groups of animals and plants.
format: application/pdf
format: text/html
creator: Andrea Paz
creator: Thiago S. Silva
creator: Ana C. Carnaval
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Climate Change Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13534
publisher: PeerJ Inc.
rights: © 2022 Paz et al.
abstract: Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that this framework has the potential to accurately predict trends of biodiversity change for both taxonomic and phylogenetic diversity. The framework identifies areas of potential diversity loss more accurately than areas of species gain, and performs best when applied to broadly distributed groups of animals and plants.
bibliographic citation: Paz et al. (2022) A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest. PeerJ 10:e13534 https://doi.org/10.7717/peerj.13534
date submitted: 2022-02-17
date accepted: 2022-05-12
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paz
  given name: Andrea
author list: Agent
  family name: Silva
  given name: Thiago S.
author list: Agent
  family name: Carnaval
  given name: Ana C.
doi: 10.7717/peerj.13534
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: ©2022 Paz et al.
attribution name: Paz et al.

Fungal diversity in shade-coffee plantations in Soconusco, Mexico
type: item
type: AcademicArticle
description: Background As forested natural habitats disappear in the world, traditional, shade-coffee plantations offer an opportunity to conserve biodiversity and ecosystem services. Traditional coffee plantations maintain a diversity of tree species that provide shade for coffee bushes and, at the same time, are important repositories for plants and animals that inhabited the original cloud forest. However, there is still little information about shade-coffee plantation’s fungal diversity despite their relevance for ecosystem functioning as decomposers, symbionts and pathogens. Specifically, it is unknown if and what mycorrhizae-forming fungi can be found on the branches and trunks of coffee bushes and trees, which hold a diversity of epiphytes. Here, we evaluate fungal communities on specific plant microsites on both coffee bushes and shade trees. We investigate the ecological roles played by this diversity, with a special focus on mycorrhizae-forming fungi that may enable the establishment and development of epiphytic plants. Methods We collected 48 bark samples from coffee bushes and shade trees (coffee; tree), from four plant microsites (upper and lower trunks, branches and twigs), in two shade-coffee plantations in the Soconusco region in southern Mexico, at different altitudes. We obtained ITS amplicon sequences that served to estimate alpha and beta diversity, to assign taxonomy and to infer the potential ecological role played by the detected taxa. Results The bark of shade trees and coffee bushes supported high fungal diversity (3,783 amplicon sequence variants). There were no strong associations between community species richness and collection site, plant type or microsite. However, we detected differences in beta diversity between collection sites. All trophic modes defined by FUNGuild database were represented in both plant types. However, when looking into guilds that involve mycorrhizae formation, the CLAM test suggests that coffee bushes are more likely to hos…
format: application/pdf
format: text/html
creator: Eugenia Zarza
creator: Alejandra López-Pastrana
creator: Anne Damon
creator: Karina Guillén-Navarro
creator: Luz Verónica García-Fajardo
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.13610
publisher: PeerJ Inc.
rights: © 2022 Zarza et al.
abstract: Background As forested natural habitats disappear in the world, traditional, shade-coffee plantations offer an opportunity to conserve biodiversity and ecosystem services. Traditional coffee plantations maintain a diversity of tree species that provide shade for coffee bushes and, at the same time, are important repositories for plants and animals that inhabited the original cloud forest. However, there is still little information about shade-coffee plantation’s fungal diversity despite their relevance for ecosystem functioning as decomposers, symbionts and pathogens. Specifically, it is unknown if and what mycorrhizae-forming fungi can be found on the branches and trunks of coffee bushes and trees, which hold a diversity of epiphytes. Here, we evaluate fungal communities on specific plant microsites on both coffee bushes and shade trees. We investigate the ecological roles played by this diversity, with a special focus on mycorrhizae-forming fungi that may enable the establishment and development of epiphytic plants. Methods We collected 48 bark samples from coffee bushes and shade trees (coffee; tree), from four plant microsites (upper and lower trunks, branches and twigs), in two shade-coffee plantations in the Soconusco region in southern Mexico, at different altitudes. We obtained ITS amplicon sequences that served to estimate alpha and beta diversity, to assign taxonomy and to infer the potential ecological role played by the detected taxa. Results The bark of shade trees and coffee bushes supported high fungal diversity (3,783 amplicon sequence variants). There were no strong associations between community species richness and collection site, plant type or microsite. However, we detected differences in beta diversity between collection sites. All trophic modes defined by FUNGuild database were represented in both plant types. However, when looking into guilds that involve mycorrhizae formation, the CLAM test suggests that coffee bushes are more likely to hos…
bibliographic citation: Zarza et al. (2022) Fungal diversity in shade-coffee plantations in Soconusco, Mexico. PeerJ 10:e13610 https://doi.org/10.7717/peerj.13610
date submitted: 2021-10-04
date accepted: 2022-05-29
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zarza
  given name: Eugenia
author list: Agent
  family name: López-Pastrana
  given name: Alejandra
author list: Agent
  family name: Damon
  given name: Anne
author list: Agent
  family name: Guillén-Navarro
  given name: Karina
author list: Agent
  family name: García-Fajardo
  given name: Luz Verónica
doi: 10.7717/peerj.13610
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: ©2022 Zarza et al.
attribution name: Zarza et al.

Nest characteristics and composition of the colonial nesting Azure-winged magpie Cyanopica cyanus in South Korea
type: item
type: AcademicArticle
description: Bird nests are crucial for reproductive success since they serve as structures to hold the eggs and nestlings safely. Therefore, the structural characteristics of bird nests have optimally evolved to maximize reproductive success, which are known to be affected by various factors. We gathered information on the nest characteristics such as nest structure and constituent materials in the colonial breeding Azure-winged magpie (Cyanopica cyanus) and investigated the relationship between ecologically relevant factors and the size and mass of the nests. The Azure-winged magpie nest can be deconstructed into an outer nest and an inner cup, and the type and mass of materials used for the construction of each part varies. Compared to the inner cup, the outer nest, which constitutes the overall shape of the nest, is composed of relatively harder materials, such as branches and soil. In contrast, the inner cup, which is the part where birds directly incubate eggs and raise nestlings, is composed of more flexible and softer materials, such as fiber and moss. We found that there was no relationship between nest characteristics and ecologically relevant factors. However, as the breeding season progressed, the volume of the inner cup decreased with increasing ambient temperatures. Our results show that Azure-winged magpies use differing materials for structurally distinct parts of the nests during construction. The results also indirectly suggest that the choice regarding the amount of insulating materials relative to changing temperatures during the breeding season may be one of the more significant adaptive strategies in the nest-building behaviors of Azure-winged magpies.
format: application/pdf
format: text/html
creator: Ki-Ho Kang
creator: Ki-Baek Nam
creator: Ji-Sub Kim
creator: Jeong-Chil Yoo
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13637
publisher: PeerJ Inc.
rights: © 2022 Kang et al.
abstract: Bird nests are crucial for reproductive success since they serve as structures to hold the eggs and nestlings safely. Therefore, the structural characteristics of bird nests have optimally evolved to maximize reproductive success, which are known to be affected by various factors. We gathered information on the nest characteristics such as nest structure and constituent materials in the colonial breeding Azure-winged magpie (Cyanopica cyanus) and investigated the relationship between ecologically relevant factors and the size and mass of the nests. The Azure-winged magpie nest can be deconstructed into an outer nest and an inner cup, and the type and mass of materials used for the construction of each part varies. Compared to the inner cup, the outer nest, which constitutes the overall shape of the nest, is composed of relatively harder materials, such as branches and soil. In contrast, the inner cup, which is the part where birds directly incubate eggs and raise nestlings, is composed of more flexible and softer materials, such as fiber and moss. We found that there was no relationship between nest characteristics and ecologically relevant factors. However, as the breeding season progressed, the volume of the inner cup decreased with increasing ambient temperatures. Our results show that Azure-winged magpies use differing materials for structurally distinct parts of the nests during construction. The results also indirectly suggest that the choice regarding the amount of insulating materials relative to changing temperatures during the breeding season may be one of the more significant adaptive strategies in the nest-building behaviors of Azure-winged magpies.
bibliographic citation: Kang et al. (2022) Nest characteristics and composition of the colonial nesting Azure-winged magpie Cyanopica cyanus in South Korea. PeerJ 10:e13637 https://doi.org/10.7717/peerj.13637
date submitted: 2021-12-20
date accepted: 2022-06-06
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Ki-Ho
author list: Agent
  family name: Nam
  given name: Ki-Baek
author list: Agent
  family name: Kim
  given name: Ji-Sub
author list: Agent
  family name: Yoo
  given name: Jeong-Chil
doi: 10.7717/peerj.13637
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: © 2022 Kang et al.
attribution name: Kang et al.

Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia
type: item
type: AcademicArticle
description: Background Radix Ardisia (Jab Bik Lik Jib) is a common Miao medicine and is widely distributed in the Guizhou region of southern China. The botanical origin of Radix Ardisia includes the dry root and rhizome of Ardisia Crenata Sims (ACS) or Ardisia Crispa (Thunb.) A.DC. (AC), which are closely related species morphologically. However, the secondary metabolites in their roots are different from one another, especially the flavonoids, and these differences have not been thoroughly explored at the molecular level. This project preliminarily identified regulatory molecular mechanisms in the biosynthetic pathways of the flavonoids between ACS and AC using a multi-omics association analysis. Methods In this study, we determined the total levels of saponin, flavonoid, and phenolic in Radix Ardisia from different origins. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially expressed metabolites (DEM). We also performed conjoint analyses on DEGs and DEMs to ascertain the degree pathways, and explore the regulation of flavonoid biosynthesis. Results The total flavonoid and phenolic levels in ACS were significantly higher than in AC (P < 0.05). There were 17,685 DEGs between ACS vs. AC, 8,854 were upregulated and 8,831 were downregulated. Based on this, we continued to study the gene changes in the flavonoid biosynthesis pathway, and 100 DEGs involving flavonoid biosynthesis were differentially expressed in ACS and AC. We validated the accuracy of the RNA-seq data using qRT-PCR. Metabolomic analyses showed that 11 metabolites were involved in flavonoid biosynthesis including: Naringenin, Luteolin, Catechin, and Quercetin. A conjoint analysis of the genome-wide connection network revealed the differences in the types and levels of flavonoid compounds between ACS and AC. The correlation analysis showed that Naringenin, Luteolin, Catechin, and Quercetin were more likely to be key compounds in the flav…
format: application/pdf
format: text/html
creator: Chang Liu
creator: Jie Pan
creator: Zhi-Gang Yin
creator: Tingting Feng
creator: Jiehong Zhao
creator: Xiu Dong
creator: Ying Zhou
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13670
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Background Radix Ardisia (Jab Bik Lik Jib) is a common Miao medicine and is widely distributed in the Guizhou region of southern China. The botanical origin of Radix Ardisia includes the dry root and rhizome of Ardisia Crenata Sims (ACS) or Ardisia Crispa (Thunb.) A.DC. (AC), which are closely related species morphologically. However, the secondary metabolites in their roots are different from one another, especially the flavonoids, and these differences have not been thoroughly explored at the molecular level. This project preliminarily identified regulatory molecular mechanisms in the biosynthetic pathways of the flavonoids between ACS and AC using a multi-omics association analysis. Methods In this study, we determined the total levels of saponin, flavonoid, and phenolic in Radix Ardisia from different origins. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially expressed metabolites (DEM). We also performed conjoint analyses on DEGs and DEMs to ascertain the degree pathways, and explore the regulation of flavonoid biosynthesis. Results The total flavonoid and phenolic levels in ACS were significantly higher than in AC (P < 0.05). There were 17,685 DEGs between ACS vs. AC, 8,854 were upregulated and 8,831 were downregulated. Based on this, we continued to study the gene changes in the flavonoid biosynthesis pathway, and 100 DEGs involving flavonoid biosynthesis were differentially expressed in ACS and AC. We validated the accuracy of the RNA-seq data using qRT-PCR. Metabolomic analyses showed that 11 metabolites were involved in flavonoid biosynthesis including: Naringenin, Luteolin, Catechin, and Quercetin. A conjoint analysis of the genome-wide connection network revealed the differences in the types and levels of flavonoid compounds between ACS and AC. The correlation analysis showed that Naringenin, Luteolin, Catechin, and Quercetin were more likely to be key compounds in the flav…
bibliographic citation: Liu et al. (2022) Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia. PeerJ 10:e13670 https://doi.org/10.7717/peerj.13670
date submitted: 2021-09-30
date accepted: 2022-06-10
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chang
author list: Agent
  family name: Pan
  given name: Jie
author list: Agent
  family name: Yin
  given name: Zhi-Gang
author list: Agent
  family name: Feng
  given name: Tingting
author list: Agent
  family name: Zhao
  given name: Jiehong
author list: Agent
  family name: Dong
  given name: Xiu
author list: Agent
  family name: Zhou
  given name: Ying
doi: 10.7717/peerj.13670
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Agricultural big data and methods and models for food security analysis—a mini-review
type: item
type: AcademicArticle
description: Background Big data and data analysis methods and models are important tools in food security (FS) studies for gap analysis and preparation of appropriate analytical frameworks. These innovations necessitate the development of novel methods for collecting, storing, processing, and extracting data. Methodology The primary goal of this study was to conduct a critical review of agricultural big data and methods and models used for FS studies published in peer-reviewed journals since 2010. Approximately 130 articles were selected for full content review after the pre-screening process. Results There are different sources of data collection, including but not limited to online databases, the internet, omics, Internet of Things, social media, survey rounds, remote sensing, and the Food and Agriculture Organization Corporate Statistical Database. The collected data require analysis (i.e., mining, neural networks, Bayesian networks, and other ML algorithms) before data visualization using Python, R, Circos, Gephi, Tableau, or Cytoscape. Approximately 122 models, all of which were used in FS studies worldwide, were selected from 130 articles. However, most of these models addressed only one or two dimensions of FS (i.e., availability and access) and ignored the other dimensions (i.e., stability and utilization), creating a gap in the global context. Conclusions There are certain FS gaps both worldwide and in the United Arab Emirates that need to be addressed by scientists and policymakers. Following the identification of the drivers, policies, and indicators, the findings of this review could be used to develop an appropriate analytical framework for FS and nutrition.
format: application/pdf
format: text/html
creator: Khalil A. Ammar
creator: Ahmed M.S. Kheir
creator: Ioannis Manikas
subject: Agricultural Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.13674
publisher: PeerJ Inc.
rights: © 2022 Ammar et al.
abstract: Background Big data and data analysis methods and models are important tools in food security (FS) studies for gap analysis and preparation of appropriate analytical frameworks. These innovations necessitate the development of novel methods for collecting, storing, processing, and extracting data. Methodology The primary goal of this study was to conduct a critical review of agricultural big data and methods and models used for FS studies published in peer-reviewed journals since 2010. Approximately 130 articles were selected for full content review after the pre-screening process. Results There are different sources of data collection, including but not limited to online databases, the internet, omics, Internet of Things, social media, survey rounds, remote sensing, and the Food and Agriculture Organization Corporate Statistical Database. The collected data require analysis (i.e., mining, neural networks, Bayesian networks, and other ML algorithms) before data visualization using Python, R, Circos, Gephi, Tableau, or Cytoscape. Approximately 122 models, all of which were used in FS studies worldwide, were selected from 130 articles. However, most of these models addressed only one or two dimensions of FS (i.e., availability and access) and ignored the other dimensions (i.e., stability and utilization), creating a gap in the global context. Conclusions There are certain FS gaps both worldwide and in the United Arab Emirates that need to be addressed by scientists and policymakers. Following the identification of the drivers, policies, and indicators, the findings of this review could be used to develop an appropriate analytical framework for FS and nutrition.
bibliographic citation: Ammar et al. (2022) Agricultural big data and methods and models for food security analysis—a mini-review. PeerJ 10:e13674 https://doi.org/10.7717/peerj.13674
date submitted: 2022-02-21
date accepted: 2022-06-13
issued: 2022-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ammar
  given name: Khalil A.
author list: Agent
  family name: Kheir
  given name: Ahmed M.S.
author list: Agent
  family name: Manikas
  given name: Ioannis
doi: 10.7717/peerj.13674
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-29
copyright: ©2022 Ammar et al.
attribution name: Ammar et al.

Public awareness of seafood mislabeling
type: item
type: AcademicArticle
description: A substantial portion of seafood is mislabeled, causing significant impacts to human health, the environment, the economy, and society. Despite the large scientific literature documenting seafood mislabeling the public’s awareness of seafood mislabeling is unknown. We conducted an online survey to assess the public’s awareness and perceptions of seafood mislabeling. Of the 1,216 respondents, 38% had never heard of seafood mislabeling and 49% were only ‘vaguely familiar’ with it. After being provided the definition of seafood mislabeling 95% had some degree of concern. Respondents were the most concerned about environmental impacts caused by seafood mislabeling and the least concerned about the social justice implications. Respondents who were also more concerned and familiar with seafood mislabeling stated that they would be more likely to purchase seafood from a vendor where the labeling was independently verified.
format: application/pdf
format: text/html
creator: Savannah J. Ryburn
creator: Wilker M. Ballantine
creator: Florencia M. Loncan
creator: Olivia G. Manning
creator: Meggan A. Alston
creator: Blaire Steinwand
creator: John F. Bruno
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Food Science and Technology
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.13486
publisher: PeerJ Inc.
rights: © 2022 Ryburn et al.
abstract: A substantial portion of seafood is mislabeled, causing significant impacts to human health, the environment, the economy, and society. Despite the large scientific literature documenting seafood mislabeling the public’s awareness of seafood mislabeling is unknown. We conducted an online survey to assess the public’s awareness and perceptions of seafood mislabeling. Of the 1,216 respondents, 38% had never heard of seafood mislabeling and 49% were only ‘vaguely familiar’ with it. After being provided the definition of seafood mislabeling 95% had some degree of concern. Respondents were the most concerned about environmental impacts caused by seafood mislabeling and the least concerned about the social justice implications. Respondents who were also more concerned and familiar with seafood mislabeling stated that they would be more likely to purchase seafood from a vendor where the labeling was independently verified.
bibliographic citation: Ryburn et al. (2022) Public awareness of seafood mislabeling. PeerJ 10:e13486 https://doi.org/10.7717/peerj.13486
date submitted: 2022-01-13
date accepted: 2022-05-03
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ryburn
  given name: Savannah J.
author list: Agent
  family name: Ballantine
  given name: Wilker M.
author list: Agent
  family name: Loncan
  given name: Florencia M.
author list: Agent
  family name: Manning
  given name: Olivia G.
author list: Agent
  family name: Alston
  given name: Meggan A.
author list: Agent
  family name: Steinwand
  given name: Blaire
author list: Agent
  family name: Bruno
  given name: John F.
doi: 10.7717/peerj.13486
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: © 2022 Ryburn et al.
attribution name: Ryburn et al.

G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice
type: item
type: AcademicArticle
description: Background Spermatogenesis is a complex process that includes mitosis, meiosis, and spermiogenesis. During spermatogenesis, genetic factors play a vital role inthe formation of properly functioning sperm. GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) is known to take part in immune responses, mRNA transport, and stress-granule assembly. However, its role in male fertility is unclear. Here, we generated a G3bp2 conditional knockout (cKO) mouse model to explore the function of G3BP2 in male fertility. Methods Polymerase chain reaction (PCR) and western blotting (WB) were used to confirm testis-specific G3bp2 knockout. Hematoxylin-eosin (HE) staining to observe testicular morphology and epididymal structure. Computer-aided sperm analysis (CASA) to detect sperm concentration and motility. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) assay was used to detect apoptotic cells. Results We found that cKO male mice are fertile with the normal morphology of the testis and sperm. Additionally, CASA of the semen from cKO mice showed that they all had a similar sperm concentration and motility. In addition, sperm from these mice exhibited a similar morphology. But the tunnel assay revealed increased apoptosis in their testes relative to the level in the wild type (WT). Conclusion Together, our data demonstrate that G3BP2 is dispensable for spermatogenesis and male fertility in mice albeit with the increased germ-cell apoptosis.
format: application/pdf
format: text/html
creator: Damin Yun
creator: Liwei Zhou
creator: Jie Shi
creator: Xinyao Li
creator: Xiaolong Wu
creator: Fei Sun
subject: Cell Biology
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.13532
publisher: PeerJ Inc.
rights: © 2022 Yun et al.
abstract: Background Spermatogenesis is a complex process that includes mitosis, meiosis, and spermiogenesis. During spermatogenesis, genetic factors play a vital role inthe formation of properly functioning sperm. GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) is known to take part in immune responses, mRNA transport, and stress-granule assembly. However, its role in male fertility is unclear. Here, we generated a G3bp2 conditional knockout (cKO) mouse model to explore the function of G3BP2 in male fertility. Methods Polymerase chain reaction (PCR) and western blotting (WB) were used to confirm testis-specific G3bp2 knockout. Hematoxylin-eosin (HE) staining to observe testicular morphology and epididymal structure. Computer-aided sperm analysis (CASA) to detect sperm concentration and motility. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) assay was used to detect apoptotic cells. Results We found that cKO male mice are fertile with the normal morphology of the testis and sperm. Additionally, CASA of the semen from cKO mice showed that they all had a similar sperm concentration and motility. In addition, sperm from these mice exhibited a similar morphology. But the tunnel assay revealed increased apoptosis in their testes relative to the level in the wild type (WT). Conclusion Together, our data demonstrate that G3BP2 is dispensable for spermatogenesis and male fertility in mice albeit with the increased germ-cell apoptosis.
bibliographic citation: Yun et al. (2022) G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice. PeerJ 10:e13532 https://doi.org/10.7717/peerj.13532
date submitted: 2022-03-17
date accepted: 2022-05-12
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yun
  given name: Damin
author list: Agent
  family name: Zhou
  given name: Liwei
author list: Agent
  family name: Shi
  given name: Jie
author list: Agent
  family name: Li
  given name: Xinyao
author list: Agent
  family name: Wu
  given name: Xiaolong
author list: Agent
  family name: Sun
  given name: Fei
doi: 10.7717/peerj.13532
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: © 2022 Yun et al.
attribution name: Yun et al.

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