PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Gazing left, gazing right: exploring a spatial bias in social attention
items: Oil and natural gas rents and CO2 emissions nexus in MENA: spatial analysis
items: Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest
items: Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon
items: Nutritional values of wild edible freshwater macrophytes
items: The quality of the fossil record across higher taxa: compositional fidelity of phyla and classes in benthic marine associations
items: Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover
items: Antibiotic resistance profile of Helicobacter pylori to 14 antibiotics: a multicenter study in Fujian, China
items: A novel immunogenic cell death signature for the prediction of prognosis and therapies in glioma
items: Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population

Gazing left, gazing right: exploring a spatial bias in social attention
type: item
type: AcademicArticle
description: Faces oriented rightwards are sometimes perceived as more dominant than faces oriented leftwards. In this study, we explored whether faces oriented rightwards can also elicit increased attentional orienting. Participants completed a discrimination task in which they were asked to discriminate, by means of a keypress, a peripheral target. At the same time, a task-irrelevant face oriented leftwards or rightwards appeared at the centre of the screen. The results showed that, while for faces oriented rightwards targets appearing on the right were responded to faster as compared to targets appearing on the left, for faces oriented leftwards no differences emerged between left and right targets. Furthermore, we also found a negative correlation between the magnitude of the orienting response elicited by the faces oriented leftwards and the level of conservatism of the participants. Overall, these findings provide evidence for the existence of a spatial bias reflected in social orienting.
format: application/pdf
format: text/html
creator: Mario Dalmaso
creator: Giacomo Fedrigo
creator: Michele Vicovaro
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15694
publisher: PeerJ Inc.
rights: © 2023 Dalmaso et al.
abstract: Faces oriented rightwards are sometimes perceived as more dominant than faces oriented leftwards. In this study, we explored whether faces oriented rightwards can also elicit increased attentional orienting. Participants completed a discrimination task in which they were asked to discriminate, by means of a keypress, a peripheral target. At the same time, a task-irrelevant face oriented leftwards or rightwards appeared at the centre of the screen. The results showed that, while for faces oriented rightwards targets appearing on the right were responded to faster as compared to targets appearing on the left, for faces oriented leftwards no differences emerged between left and right targets. Furthermore, we also found a negative correlation between the magnitude of the orienting response elicited by the faces oriented leftwards and the level of conservatism of the participants. Overall, these findings provide evidence for the existence of a spatial bias reflected in social orienting.
bibliographic citation: Dalmaso et al. (2023) Gazing left, gazing right: exploring a spatial bias in social attention. PeerJ 11:e15694 https://doi.org/10.7717/peerj.15694
date submitted: 2022-12-23
date accepted: 2023-06-14
issued: 2023-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dalmaso
  given name: Mario
author list: Agent
  family name: Fedrigo
  given name: Giacomo
author list: Agent
  family name: Vicovaro
  given name: Michele
doi: 10.7717/peerj.15694
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-12
copyright: ©2023 Dalmaso et al.
attribution name: Dalmaso et al.

Oil and natural gas rents and CO2 emissions nexus in MENA: spatial analysis
type: item
type: AcademicArticle
description: Background Oil rents (OR) and natural gas rents (NGR) have significant contributions to the income of the Middle East and North Africa (MENA) economies and may increase emissions. Moreover, spatial autocorrelation is expected in carbon dioxide (CO2) emissions due to the geographically closed economies in the MENA region. Thus, we examine the impact of OR and NGR on CO2 emissions caring spatial dimensions and analyze the environmental Kuznets curve (EKC). Methods We apply the spatial Durbin model technique on the effects of OR, NGR, and economic growth on CO2 emissions in 17 MENA nations from 2000–2019, i.e., Algeria, Bahrain, Egypt, Iran, Iraq, Israel, Jordan, Kuwait, Libya, Morocco, Oman, Qatar, Saudi Arabia, Syria, Tunisia, the United Arab Emirates (UAE), and Yemen. Moreover, diagnostic tests are applied to reach the most appropriate spatial specification and to have the most robust results. Results The results disclose that CO2 emissions have spillovers and emissions of any country can damage the environment of neighboring countries. The EKC is corroborated with a turning point of 38,698 constant 2015 US dollars. Israel and Qatar are in 2nd phase of the EKC, and 15 MENA economies are in 1st stage. Thus, the economic expansion of most economies has ecological concerns. The effect of natural gas rents is found statistically insignificant. Oil rents have minute negative effects on emissions of local economies with an elasticity coefficient of −0.2117. Nevertheless, these have a positive indirect effect with an elasticity coefficient of 0.5328. Thus, the net effect of oil rents is positive. One percent increase in oil rents could accelerate 0.3211% of emissions. Thus, we suggest the MENA countries reduce reliance on oil rents in their income to avoid the negative environmental effects of the oil sector.
format: application/pdf
format: text/html
creator: Haider Mahmood
creator: Najia Saqib
creator: Anass Hamadelneel Adow
creator: Muzaffar Abbas
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.15708
publisher: PeerJ Inc.
rights: © 2023 Mahmood et al.
abstract: Background Oil rents (OR) and natural gas rents (NGR) have significant contributions to the income of the Middle East and North Africa (MENA) economies and may increase emissions. Moreover, spatial autocorrelation is expected in carbon dioxide (CO2) emissions due to the geographically closed economies in the MENA region. Thus, we examine the impact of OR and NGR on CO2 emissions caring spatial dimensions and analyze the environmental Kuznets curve (EKC). Methods We apply the spatial Durbin model technique on the effects of OR, NGR, and economic growth on CO2 emissions in 17 MENA nations from 2000–2019, i.e., Algeria, Bahrain, Egypt, Iran, Iraq, Israel, Jordan, Kuwait, Libya, Morocco, Oman, Qatar, Saudi Arabia, Syria, Tunisia, the United Arab Emirates (UAE), and Yemen. Moreover, diagnostic tests are applied to reach the most appropriate spatial specification and to have the most robust results. Results The results disclose that CO2 emissions have spillovers and emissions of any country can damage the environment of neighboring countries. The EKC is corroborated with a turning point of 38,698 constant 2015 US dollars. Israel and Qatar are in 2nd phase of the EKC, and 15 MENA economies are in 1st stage. Thus, the economic expansion of most economies has ecological concerns. The effect of natural gas rents is found statistically insignificant. Oil rents have minute negative effects on emissions of local economies with an elasticity coefficient of −0.2117. Nevertheless, these have a positive indirect effect with an elasticity coefficient of 0.5328. Thus, the net effect of oil rents is positive. One percent increase in oil rents could accelerate 0.3211% of emissions. Thus, we suggest the MENA countries reduce reliance on oil rents in their income to avoid the negative environmental effects of the oil sector.
bibliographic citation: Mahmood et al. (2023) Oil and natural gas rents and CO2 emissions nexus in MENA: spatial analysis. PeerJ 11:e15708 https://doi.org/10.7717/peerj.15708
date submitted: 2023-04-14
date accepted: 2023-06-15
issued: 2023-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mahmood
  given name: Haider
author list: Agent
  family name: Saqib
  given name: Najia
author list: Agent
  family name: Adow
  given name: Anass Hamadelneel
author list: Agent
  family name: Abbas
  given name: Muzaffar
doi: 10.7717/peerj.15708
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-12
copyright: © 2023 Mahmood et al.
attribution name: Mahmood et al.

Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest
type: item
type: AcademicArticle
description: Coleopterans are the most diverse animal group on Earth and constitute good indicators of environmental change. However, little information is available about Coleopteran communities’ responses to disturbance and land-use change. Tropical dry forests have undergone especially extensive anthropogenic impacts in the past decades. This has led to mosaic landscapes consisting of areas of primary forest surrounded by pastures, agricultural fields and secondary forests, which negatively impacts many taxonomic groups. However, such impacts have not been assessed for most arthropod groups. In this work, we compared the abundance, richness and diversity of Coleopteran morphospecies in four different successional stages in a tropical dry forest in western Mexico, to answer the question: How do Coleopteran assemblages associate with vegetation change over the course of forest succession? In addition, we assessed the family composition and trophic guilds for the four successional stages. We found 971 Coleopterans belonging to 107 morphospecies distributed in 28 families. Coleopteran abundance and richness were greatest for pastures than for latter successional stages, and the most abundant family was Chrysomelidae, with 29% of the individuals. Herbivores were the most abundant guild, accounting for 57% of the individuals, followed by predators (22%) and saprophages (21%) beetles. Given the high diversity and richness found throughout the successional chronosequence of the studied tropical dry forest, in order to have the maximum number of species associated with tropical dry forests, large tracts of forest should be preserved so that successional dynamics are able to occur naturally.
format: application/pdf
format: text/html
creator: Edison A. Díaz-Álvarez
creator: Cesar Manrique
creator: Karina Boege
creator: Ek del-Val
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.15712
publisher: PeerJ Inc.
rights: © 2023 Díaz-Álvarez et al.
abstract: Coleopterans are the most diverse animal group on Earth and constitute good indicators of environmental change. However, little information is available about Coleopteran communities’ responses to disturbance and land-use change. Tropical dry forests have undergone especially extensive anthropogenic impacts in the past decades. This has led to mosaic landscapes consisting of areas of primary forest surrounded by pastures, agricultural fields and secondary forests, which negatively impacts many taxonomic groups. However, such impacts have not been assessed for most arthropod groups. In this work, we compared the abundance, richness and diversity of Coleopteran morphospecies in four different successional stages in a tropical dry forest in western Mexico, to answer the question: How do Coleopteran assemblages associate with vegetation change over the course of forest succession? In addition, we assessed the family composition and trophic guilds for the four successional stages. We found 971 Coleopterans belonging to 107 morphospecies distributed in 28 families. Coleopteran abundance and richness were greatest for pastures than for latter successional stages, and the most abundant family was Chrysomelidae, with 29% of the individuals. Herbivores were the most abundant guild, accounting for 57% of the individuals, followed by predators (22%) and saprophages (21%) beetles. Given the high diversity and richness found throughout the successional chronosequence of the studied tropical dry forest, in order to have the maximum number of species associated with tropical dry forests, large tracts of forest should be preserved so that successional dynamics are able to occur naturally.
bibliographic citation: Díaz-Álvarez et al. (2023) Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest. PeerJ 11:e15712 https://doi.org/10.7717/peerj.15712
date submitted: 2023-02-22
date accepted: 2023-06-15
issued: 2023-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Díaz-Álvarez
  given name: Edison A.
author list: Agent
  family name: Manrique
  given name: Cesar
author list: Agent
  family name: Boege
  given name: Karina
author list: Agent
  family name: del-Val
  given name: Ek
doi: 10.7717/peerj.15712
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-12
copyright: © 2023 Díaz-Álvarez et al.
attribution name: Díaz-Álvarez et al.

Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon
type: item
type: AcademicArticle
description: Background The development of anthropogenic activities has generated a decline in aquatic fauna populations, and amphibians have been the most affected. The decline of batrachofauna is concerning, as 41% of all species worldwide are endangered. For this reason, rapid, efficient, and non-invasive biodiversity monitoring techniques are needed, and environmental DNA (eDNA) is one such tool that has been sparsely applied in Ecuador. This technique has allowed scientists generates information on species diversity and amphibian community composition from a water sample. This study applied eDNA-based biomonitoring analyses and visual encounter surveys (VES) as inventory techniques to identify the diversity of aquatic amphibians in the Tena River micro-basin (TRMB). Methods The experimental design was divided into three components: (1) fieldwork: all amphibians were recorded by the VES technique and water samples were collected; (2) laboratory work: DNA isolation from amphibian tissue samples and eDNA-containing filters, amplification, electrophoresis, and sequencing were performed; (3) Data analysis: a local DNA reference database was constructed, and eDNA sequence data were processed for classification, taxonomic assignment, and ecological interpretation. Results Using both eDNA and VES, we detected 33 amphibian species (13 with eDNA only, five with VES only, and 15 with both methods). These species belonged to six amphibian families: Hylidae being the richest with 14 species (three eDNA, one VES, and 10 with both methods), followed by Strabomantidae with nine species (six eDNA, one VES, and two with both methods). All families were detected with both methods, except for the Aromobatidae, having one single record (Allobates aff. insperatus) by VES. Individually, eDNA detected 28 species and had a detection probability (DP) of 0.42 CI [0.40–0.45], while VES recorded 20 species with a DP of 0.17 CI [0.14–0.20]. Similarly, using VES, Cochranella resplendens was detected for …
format: application/pdf
format: text/html
creator: Walter Quilumbaquin
creator: Andrea Carrera-Gonzalez
creator: Christine Van der heyden
creator: H. Mauricio Ortega-Andrade
subject: Biodiversity
subject: Bioinformatics
subject: Molecular Biology
subject: Zoology
subject: Biomechanics
description: doi:10.7717/peerj.15455
publisher: PeerJ Inc.
rights: © 2023 Quilumbaquin et al.
abstract: Background The development of anthropogenic activities has generated a decline in aquatic fauna populations, and amphibians have been the most affected. The decline of batrachofauna is concerning, as 41% of all species worldwide are endangered. For this reason, rapid, efficient, and non-invasive biodiversity monitoring techniques are needed, and environmental DNA (eDNA) is one such tool that has been sparsely applied in Ecuador. This technique has allowed scientists generates information on species diversity and amphibian community composition from a water sample. This study applied eDNA-based biomonitoring analyses and visual encounter surveys (VES) as inventory techniques to identify the diversity of aquatic amphibians in the Tena River micro-basin (TRMB). Methods The experimental design was divided into three components: (1) fieldwork: all amphibians were recorded by the VES technique and water samples were collected; (2) laboratory work: DNA isolation from amphibian tissue samples and eDNA-containing filters, amplification, electrophoresis, and sequencing were performed; (3) Data analysis: a local DNA reference database was constructed, and eDNA sequence data were processed for classification, taxonomic assignment, and ecological interpretation. Results Using both eDNA and VES, we detected 33 amphibian species (13 with eDNA only, five with VES only, and 15 with both methods). These species belonged to six amphibian families: Hylidae being the richest with 14 species (three eDNA, one VES, and 10 with both methods), followed by Strabomantidae with nine species (six eDNA, one VES, and two with both methods). All families were detected with both methods, except for the Aromobatidae, having one single record (Allobates aff. insperatus) by VES. Individually, eDNA detected 28 species and had a detection probability (DP) of 0.42 CI [0.40–0.45], while VES recorded 20 species with a DP of 0.17 CI [0.14–0.20]. Similarly, using VES, Cochranella resplendens was detected for …
bibliographic citation: Quilumbaquin et al. (2023) Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon. PeerJ 11:e15455 https://doi.org/10.7717/peerj.15455
date submitted: 2022-07-04
date accepted: 2023-05-03
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quilumbaquin
  given name: Walter
author list: Agent
  family name: Carrera-Gonzalez
  given name: Andrea
author list: Agent
  family name: Van der heyden
  given name: Christine
author list: Agent
  family name: Ortega-Andrade
  given name: H. Mauricio
doi: 10.7717/peerj.15455
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Quilumbaquin et al.
attribution name: Quilumbaquin et al.

Nutritional values of wild edible freshwater macrophytes
type: item
type: AcademicArticle
description: Background The social acceptability of wild freshwater macrophytes as locally consumed vegetables is widespread. Freshwater macrophytes have several uses; for example, they can be used as food for humans. This study determined the proximate composition and mineral content of three freshwater macrophyte species, i.e., Eichhornia crassipes, Limnocharis flava, and Neptunia oleracea. Methods Young shoots of E. crassipes, L. flava, and N. oleracea were collected from shallow channels of Puchong (3°00′11.89″N, 101°42′43.12″E), Ladang 10, Universiti Putra Malaysia (2°58′44.41″N, 101°42′44.45″E), and Kampung Alur Selibong, Langgar (06°5′50.9″N, 100°26′49.8″E), Kedah, Peninsular Malaysia. The nutritional values of these macrophytes were analysed by using a standard protocol from the Association of Official Analytical Chemists. Eight replicates of E. crassipes and L. flava and four replicates of N. oleracea were used for the subsequent analyses. Results In the proximate analysis, N. oleracea possessed the highest percentage of crude protein (29.61%) and energy content (4,269.65 cal g−1), whereas L. flava had the highest percentage of crude fat (5.75%) and ash (18.31%). The proximate composition trend for each species was different; specifically, all of the species possessed more carbohydrates and fewer crude lipids. All of the species demonstrated a similar mineral trend, with high nitrogen and potassium and lower copper contents. Nitrogen and potassium levels ranged from 12,380–40,380 mg kg−1 and from 11,212-33,276 mg kg−1, respectively, and copper levels ranged from 16–27 mg kg−1. The results showed that all three plant species, i.e., E. crassipes, N. oleracea, and L. flava are plant-based sources of macro- and micronutrient beneficial supplements for human consumption.
format: application/pdf
format: text/html
creator: Muta Harah Zakaria
creator: Shiamala Devi Ramaiya
creator: Nordiah Bidin
creator: Nurul Nur Farahin Syed
creator: Japar Sidik Bujang
subject: Food Science and Technology
subject: Plant Science
subject: Freshwater Biology
description: doi:10.7717/peerj.15496
publisher: PeerJ Inc.
rights: © 2023 Zakaria et al.
abstract: Background The social acceptability of wild freshwater macrophytes as locally consumed vegetables is widespread. Freshwater macrophytes have several uses; for example, they can be used as food for humans. This study determined the proximate composition and mineral content of three freshwater macrophyte species, i.e., Eichhornia crassipes, Limnocharis flava, and Neptunia oleracea. Methods Young shoots of E. crassipes, L. flava, and N. oleracea were collected from shallow channels of Puchong (3°00′11.89″N, 101°42′43.12″E), Ladang 10, Universiti Putra Malaysia (2°58′44.41″N, 101°42′44.45″E), and Kampung Alur Selibong, Langgar (06°5′50.9″N, 100°26′49.8″E), Kedah, Peninsular Malaysia. The nutritional values of these macrophytes were analysed by using a standard protocol from the Association of Official Analytical Chemists. Eight replicates of E. crassipes and L. flava and four replicates of N. oleracea were used for the subsequent analyses. Results In the proximate analysis, N. oleracea possessed the highest percentage of crude protein (29.61%) and energy content (4,269.65 cal g−1), whereas L. flava had the highest percentage of crude fat (5.75%) and ash (18.31%). The proximate composition trend for each species was different; specifically, all of the species possessed more carbohydrates and fewer crude lipids. All of the species demonstrated a similar mineral trend, with high nitrogen and potassium and lower copper contents. Nitrogen and potassium levels ranged from 12,380–40,380 mg kg−1 and from 11,212-33,276 mg kg−1, respectively, and copper levels ranged from 16–27 mg kg−1. The results showed that all three plant species, i.e., E. crassipes, N. oleracea, and L. flava are plant-based sources of macro- and micronutrient beneficial supplements for human consumption.
bibliographic citation: Zakaria et al. (2023) Nutritional values of wild edible freshwater macrophytes. PeerJ 11:e15496 https://doi.org/10.7717/peerj.15496
date submitted: 2022-12-20
date accepted: 2023-05-11
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zakaria
  given name: Muta Harah
author list: Agent
  family name: Ramaiya
  given name: Shiamala Devi
author list: Agent
  family name: Bidin
  given name: Nordiah
author list: Agent
  family name: Syed
  given name: Nurul Nur Farahin
author list: Agent
  family name: Bujang
  given name: Japar Sidik
doi: 10.7717/peerj.15496
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: ©2023 Zakaria et al.
attribution name: Zakaria et al.

The quality of the fossil record across higher taxa: compositional fidelity of phyla and classes in benthic marine associations
type: item
type: AcademicArticle
description: Although the fossil record preserves a wealth of historical data about past ecosystems, the current paradigm, which postulates that fossils provide faithful archives of ecological information, stems from research primarily focused on a single group of organisms known for their high fossilization potential: molluscs. Here, we quantify the fidelity of higher taxa (six phyla and 11 classes) by comparing live communities and sympatric dead remains (death assemblages) using comprehensive surveys of benthic marine invertebrates from coastal habitats in North Carolina (U.S.A). We found that although community composition differed between the two assemblages across phyla and classes, these differences were predictable with an overabundance of robust and more preservable groups. In addition, dead molluscs appear to be an excellent proxy for all taxa when tracking spatio-temporal patterns and shifts in community structure using a variety of ecological metrics, including measures of α, γ, and β diversity/evenness. This suggests that despite filters imposed by differential preservation of taxa and time-averaging, the fossil record is likely to be reliable with respect to relative comparisons of composition and diversity in shallow benthic marine paleocommunities. This is consistent with previous work indicating that shallow marine death assemblages can yield robust ecological estimates adequate for assessing the variability of ecosystems that existed under natural, pre-anthropogenic conditions.
format: application/pdf
format: text/html
creator: Carrie Tyler
creator: Michał Kowalewski
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.15574
publisher: PeerJ Inc.
rights: © 2023 Tyler and Kowalewski
abstract: Although the fossil record preserves a wealth of historical data about past ecosystems, the current paradigm, which postulates that fossils provide faithful archives of ecological information, stems from research primarily focused on a single group of organisms known for their high fossilization potential: molluscs. Here, we quantify the fidelity of higher taxa (six phyla and 11 classes) by comparing live communities and sympatric dead remains (death assemblages) using comprehensive surveys of benthic marine invertebrates from coastal habitats in North Carolina (U.S.A). We found that although community composition differed between the two assemblages across phyla and classes, these differences were predictable with an overabundance of robust and more preservable groups. In addition, dead molluscs appear to be an excellent proxy for all taxa when tracking spatio-temporal patterns and shifts in community structure using a variety of ecological metrics, including measures of α, γ, and β diversity/evenness. This suggests that despite filters imposed by differential preservation of taxa and time-averaging, the fossil record is likely to be reliable with respect to relative comparisons of composition and diversity in shallow benthic marine paleocommunities. This is consistent with previous work indicating that shallow marine death assemblages can yield robust ecological estimates adequate for assessing the variability of ecosystems that existed under natural, pre-anthropogenic conditions.
bibliographic citation: Tyler et al. (2023) The quality of the fossil record across higher taxa: compositional fidelity of phyla and classes in benthic marine associations. PeerJ 11:e15574 https://doi.org/10.7717/peerj.15574
date submitted: 2023-02-02
date accepted: 2023-05-25
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tyler
  given name: Carrie
author list: Agent
  family name: Kowalewski
  given name: Michał
doi: 10.7717/peerj.15574
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: ©2023 Tyler and Kowalewski
attribution name: Tyler and Kowalewski

Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover
type: item
type: AcademicArticle
description: Background White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold s…
format: application/pdf
format: text/html
creator: Manman Li
creator: Xueqi Zhang
creator: Tianxiang Zhang
creator: Yan Bai
creator: Chao Chen
creator: Donglin Guo
creator: Changhong Guo
creator: Yongjun Shu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15610
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold s…
bibliographic citation: Li et al. (2023) Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover. PeerJ 11:e15610 https://doi.org/10.7717/peerj.15610
date submitted: 2023-03-13
date accepted: 2023-05-31
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Manman
author list: Agent
  family name: Zhang
  given name: Xueqi
author list: Agent
  family name: Zhang
  given name: Tianxiang
author list: Agent
  family name: Bai
  given name: Yan
author list: Agent
  family name: Chen
  given name: Chao
author list: Agent
  family name: Guo
  given name: Donglin
author list: Agent
  family name: Guo
  given name: Changhong
author list: Agent
  family name: Shu
  given name: Yongjun
doi: 10.7717/peerj.15610
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Li et al.
attribution name: Li et al.

Antibiotic resistance profile of Helicobacter pylori to 14 antibiotics: a multicenter study in Fujian, China
type: item
type: AcademicArticle
description: Background and aim Efficacy of Helicobacter pylori (H. pylori) eradication is related to the local antimicrobial resistance epidemiology. We aimed to investigate the antibiotic resistance of H. pylori in Fujian, China. Methods H. pylori-infected patients in four centers were enrolled in the study from Oct 2019 to Jan 2022. The bacteria were isolated, cultured and identified from the biopsy of patients’ gastric mucosa samples. Antimicrobial susceptibility testing was performed by a modified broth microdilution method for H. pylori to seven guideline-recommended antibiotics and seven potential choices for H. pylori eradication. Results A total of 205 H. pylori strains were isolated. The resistance rates of amoxicillin (AMX), amoxicillin and clavulanate potassium (AMC), cefixime (CFM), gentamicin (GEN), tetracycline (TET), doxycycline (DOX), azithromycin (AZM), clarithromycin (CLR), levofloxacin (LVFX), sparfloxacin (SPFX), metronidazole (MTZ), tinidazole (TID), rifampicin (RFP) and furazolidone (FZD) were 11.22%, 12.20%, 7.32%, 12.20%, 4.88%, 4.39%, 44.39%, 43.90%, 30.24%, 21.46%, 40.98%, 45.85%, 5.37% and 10.24%, respectively. The rates of pan-sensitivity, single, double, triple and multiple resistance for seven guideline-recommended antibiotics were 32.68%, 30.24%, 13.17%, 7.76%, and 14.15%, respectively. The main double-resistance patterns were CLR+MTZ (10/205, 5%) and CLR+LVFX (9/205, 4%). The main triple-resistance pattern was CLR+MTZ+ LVFX (15/205, 7%). Conclusions In Fujian, the prevalence of H. pylori resistance to AZM, CLR, LVFX, SPFX, MTZ, and TID was high, whereas that to AMX, AMC, GEN, CFM, TET, DOX, RFP and FZD was relatively low. CFM and DOX are promising new choices for H. pylori eradication.
format: application/pdf
format: text/html
creator: Xueping Huang
creator: Baihe Wu
creator: Qiuzhao Chen
creator: Yushan Chen
creator: Xinhua Ji
creator: Xiang Zhou
creator: Biao Suo
creator: Zhihui Lin
creator: Xiaoling Zheng
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.15611
publisher: PeerJ Inc.
rights: © 2023 Huang et al.
abstract: Background and aim Efficacy of Helicobacter pylori (H. pylori) eradication is related to the local antimicrobial resistance epidemiology. We aimed to investigate the antibiotic resistance of H. pylori in Fujian, China. Methods H. pylori-infected patients in four centers were enrolled in the study from Oct 2019 to Jan 2022. The bacteria were isolated, cultured and identified from the biopsy of patients’ gastric mucosa samples. Antimicrobial susceptibility testing was performed by a modified broth microdilution method for H. pylori to seven guideline-recommended antibiotics and seven potential choices for H. pylori eradication. Results A total of 205 H. pylori strains were isolated. The resistance rates of amoxicillin (AMX), amoxicillin and clavulanate potassium (AMC), cefixime (CFM), gentamicin (GEN), tetracycline (TET), doxycycline (DOX), azithromycin (AZM), clarithromycin (CLR), levofloxacin (LVFX), sparfloxacin (SPFX), metronidazole (MTZ), tinidazole (TID), rifampicin (RFP) and furazolidone (FZD) were 11.22%, 12.20%, 7.32%, 12.20%, 4.88%, 4.39%, 44.39%, 43.90%, 30.24%, 21.46%, 40.98%, 45.85%, 5.37% and 10.24%, respectively. The rates of pan-sensitivity, single, double, triple and multiple resistance for seven guideline-recommended antibiotics were 32.68%, 30.24%, 13.17%, 7.76%, and 14.15%, respectively. The main double-resistance patterns were CLR+MTZ (10/205, 5%) and CLR+LVFX (9/205, 4%). The main triple-resistance pattern was CLR+MTZ+ LVFX (15/205, 7%). Conclusions In Fujian, the prevalence of H. pylori resistance to AZM, CLR, LVFX, SPFX, MTZ, and TID was high, whereas that to AMX, AMC, GEN, CFM, TET, DOX, RFP and FZD was relatively low. CFM and DOX are promising new choices for H. pylori eradication.
bibliographic citation: Huang et al. (2023) Antibiotic resistance profile of Helicobacter pylori to 14 antibiotics: a multicenter study in Fujian, China. PeerJ 11:e15611 https://doi.org/10.7717/peerj.15611
date submitted: 2023-03-03
date accepted: 2023-05-31
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xueping
author list: Agent
  family name: Wu
  given name: Baihe
author list: Agent
  family name: Chen
  given name: Qiuzhao
author list: Agent
  family name: Chen
  given name: Yushan
author list: Agent
  family name: Ji
  given name: Xinhua
author list: Agent
  family name: Zhou
  given name: Xiang
author list: Agent
  family name: Suo
  given name: Biao
author list: Agent
  family name: Lin
  given name: Zhihui
author list: Agent
  family name: Zheng
  given name: Xiaoling
doi: 10.7717/peerj.15611
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Huang et al.
attribution name: Huang et al.

A novel immunogenic cell death signature for the prediction of prognosis and therapies in glioma
type: item
type: AcademicArticle
description: Glioma is a primary cranial malignancy with high recurrence rate, poor prognosis and high mortality. However, the roles of immunogenic cell death (ICD) in glioma remain unclear. Twenty ICD genes were analyzed to be differentially expressed between glioma tissues and non-tumor tissues in 371 glioma patients from The Cancer Genome Atlas (TCGA). Patients were classified into three subgroups via unsupervised clustering. Interestingly, the features of cell-infiltrating from three clusters were matched with three immune phenotypes. An applied scoring system was built depending on the expression of hub ICD-related genes. Notably, the ICD-related score was linked with immune checkpoints and the prognosis of glioma patients. In addition, the applied risk model could be used for the prediction of the effect of chemotherapy and immunotherapy for glioma patients. Furthermore, MYD88 was identified to play key roles in the risk model for glioma patients. MYD88 was specifically expressed in malignant cells and validated to correlate with cell proliferation and invasion. Ligand–receptor pairs are determined as novel communications indicating between immunocytes and malignant cells. Therefore, our research established an ICD-related score to investigate the potential effect to chemotherapy and immunotherapy for glioma patients and indicated that MYD88 was a key role in this risk model.
format: application/pdf
format: text/html
creator: Jianhua Zhang
creator: Jin Du
creator: Zhihai Jin
creator: Jiang Qian
creator: Jinfa Xu
subject: Bioinformatics
subject: Cell Biology
subject: Neuroscience
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.15615
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Glioma is a primary cranial malignancy with high recurrence rate, poor prognosis and high mortality. However, the roles of immunogenic cell death (ICD) in glioma remain unclear. Twenty ICD genes were analyzed to be differentially expressed between glioma tissues and non-tumor tissues in 371 glioma patients from The Cancer Genome Atlas (TCGA). Patients were classified into three subgroups via unsupervised clustering. Interestingly, the features of cell-infiltrating from three clusters were matched with three immune phenotypes. An applied scoring system was built depending on the expression of hub ICD-related genes. Notably, the ICD-related score was linked with immune checkpoints and the prognosis of glioma patients. In addition, the applied risk model could be used for the prediction of the effect of chemotherapy and immunotherapy for glioma patients. Furthermore, MYD88 was identified to play key roles in the risk model for glioma patients. MYD88 was specifically expressed in malignant cells and validated to correlate with cell proliferation and invasion. Ligand–receptor pairs are determined as novel communications indicating between immunocytes and malignant cells. Therefore, our research established an ICD-related score to investigate the potential effect to chemotherapy and immunotherapy for glioma patients and indicated that MYD88 was a key role in this risk model.
bibliographic citation: Zhang et al. (2023) A novel immunogenic cell death signature for the prediction of prognosis and therapies in glioma. PeerJ 11:e15615 https://doi.org/10.7717/peerj.15615
date submitted: 2023-04-26
date accepted: 2023-06-01
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jianhua
author list: Agent
  family name: Du
  given name: Jin
author list: Agent
  family name: Jin
  given name: Zhihai
author list: Agent
  family name: Qian
  given name: Jiang
author list: Agent
  family name: Xu
  given name: Jinfa
doi: 10.7717/peerj.15615
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Zhang et al.
attribution name: Zhang et al.

Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population
type: item
type: AcademicArticle
description: Introduction There are numerous reports of a higher prevalence of metabolic disorders in patients with schizophrenia and bipolar disorder (BD), yet its connections to diet and physical activity remain not fully explained. This article aimed to evaluate diet, physical activity and selected biochemical and anthropometric parameters associated with metabolism in patients with schizophrenia and BD and to analyse the relationships between these variables in the subjects. Materials and Methods A total of 126 adults participated in the study: 47 patients with schizophrenia, 54 patients with BD and 25 patients in mental illness remission (reference group). Data were collected on the underlying illness and concomitant illnesses, and the severity of symptoms of the current episode was assessed using the following scales: PANSS, MADRS and YMRS. An assessment of the subjects’ diet (KomPAN questionnaire) and their physical activity (International Physical Activity Questionnaire) was carried out. Anthropometric and blood pressure measurements were taken and BMI and WHR were calculated. Serum concentrations of fasting glucose, TSH, total cholesterol, LDL and HDL fractions, triglycerides and leptin, ghrelin and resistin were determined. For statistical analysis, the significance level was set at 0.05. For multiple comparisons one way ANOVA or Kruskal Wallis were used with post hoc Tukey and Dunn tests, respectively. To determine correlation of variables, Pearson’s linear correlation coefficient or Spearman’s rank correlation coefficient were used. Results A total of 50.8% of the subjects had at least one metabolic disorder—most commonly excessive body weight (66.7%) and abdominal obesity (64.3%). Patients did not differ significantly in terms of physical activity, but they did differ in mean time spent sitting—with this being significantly longer for all groups than in the general population. The subjects differed in diet: patients with BD consumed less unhealthy foods than patient…
format: application/pdf
format: text/html
creator: Magdalena Głodek
creator: Maria Skibinska
creator: Aleksandra Suwalska
subject: Neurology
subject: Nutrition
subject: Psychiatry and Psychology
subject: Metabolic Sciences
subject: Obesity
description: doi:10.7717/peerj.15617
publisher: PeerJ Inc.
rights: © 2023 Głodek et al.
abstract: Introduction There are numerous reports of a higher prevalence of metabolic disorders in patients with schizophrenia and bipolar disorder (BD), yet its connections to diet and physical activity remain not fully explained. This article aimed to evaluate diet, physical activity and selected biochemical and anthropometric parameters associated with metabolism in patients with schizophrenia and BD and to analyse the relationships between these variables in the subjects. Materials and Methods A total of 126 adults participated in the study: 47 patients with schizophrenia, 54 patients with BD and 25 patients in mental illness remission (reference group). Data were collected on the underlying illness and concomitant illnesses, and the severity of symptoms of the current episode was assessed using the following scales: PANSS, MADRS and YMRS. An assessment of the subjects’ diet (KomPAN questionnaire) and their physical activity (International Physical Activity Questionnaire) was carried out. Anthropometric and blood pressure measurements were taken and BMI and WHR were calculated. Serum concentrations of fasting glucose, TSH, total cholesterol, LDL and HDL fractions, triglycerides and leptin, ghrelin and resistin were determined. For statistical analysis, the significance level was set at 0.05. For multiple comparisons one way ANOVA or Kruskal Wallis were used with post hoc Tukey and Dunn tests, respectively. To determine correlation of variables, Pearson’s linear correlation coefficient or Spearman’s rank correlation coefficient were used. Results A total of 50.8% of the subjects had at least one metabolic disorder—most commonly excessive body weight (66.7%) and abdominal obesity (64.3%). Patients did not differ significantly in terms of physical activity, but they did differ in mean time spent sitting—with this being significantly longer for all groups than in the general population. The subjects differed in diet: patients with BD consumed less unhealthy foods than patient…
bibliographic citation: Głodek et al. (2023) Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population. PeerJ 11:e15617 https://doi.org/10.7717/peerj.15617
date submitted: 2023-04-26
date accepted: 2023-06-01
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Głodek
  given name: Magdalena
author list: Agent
  family name: Skibinska
  given name: Maria
author list: Agent
  family name: Suwalska
  given name: Aleksandra
doi: 10.7717/peerj.15617
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Głodek et al.
attribution name: Głodek et al.

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