PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities
items: Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney
items: Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey
items: Combining multisensor images and social network data to assess the area flooded by a hurricane event
items: The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area
items: Transcriptome differential expression analysis of defoliation of two different lemon varieties
items: Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites
items: Influence of honey bee (Apis mellifera) breeding on wing venation in Serbia and neighbouring countries
items: Genome-wide identification and analysis of ascorbate peroxidase (APX) gene family in hemp (Cannabis sativa L.) under various abiotic stresses
items: A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer

Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities
type: item
type: AcademicArticle
description: Background Oat is a dual-purpose cereal used for grain and forage. The demand of oat has been increasing as the understanding of the nutritional, ecological, and economic values of oat increased. However, the frequent lodging during the growing period severely affect the high yielding potential and the quality of the grain and forage of oat. Methods Therefore, we used the lodging-resistant variety LENA and the lodging-sensitive variety QY2 as materials, implementing four different planting densities: 2.25×106 plants/ha (D1), 4.5×106 plants/ha (D2), 6.75×106 plants/ha (D3), and 9×106 plants/ha (D4). At the appropriate growth and development stages, we assessed agronomic traits, mechanical characteristics, biochemical compositions, yield and its components. The study investigated the impact of planting density on the growth, lodging, and yield of oat, as well as their interrelationships. Additionally, we identified the optimal planting density to establish a robust crop structure. The research aims to contribute to the high-yield and high-quality cultivation of oat. Results We observed that with increasing planting density, plant height, grass and grain yields of both varieties first increased and then decreased; root fresh weight, stem diameter, stem wall thickness, stem puncture strength, breaking strength, compressive strength, lignin and crude fiber contents, and yield components decreased; whereas the lodging rate and lodging coefficient increased. Planting density affects lodging by regulating plant height, height of center of gravity, stem wall thickness, internode length, and root fresh weight of oat. Additionally, it can impact stem mechanical strength by modulating the synthesis of lignin and crude fiber, which in turn affecting lodging resistance. Plant height, height of center of gravity, stem wall thickness, internode length, root fresh weight, breaking strength, compressive strength, lignin and crude fiber content, single-plant weight, grain yield and 1,…
format: application/pdf
format: text/html
creator: Lingling Liu
creator: Guoling Liang
creator: Wenhui Liu
creator: Zeliang Ju
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17310
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Oat is a dual-purpose cereal used for grain and forage. The demand of oat has been increasing as the understanding of the nutritional, ecological, and economic values of oat increased. However, the frequent lodging during the growing period severely affect the high yielding potential and the quality of the grain and forage of oat. Methods Therefore, we used the lodging-resistant variety LENA and the lodging-sensitive variety QY2 as materials, implementing four different planting densities: 2.25×106 plants/ha (D1), 4.5×106 plants/ha (D2), 6.75×106 plants/ha (D3), and 9×106 plants/ha (D4). At the appropriate growth and development stages, we assessed agronomic traits, mechanical characteristics, biochemical compositions, yield and its components. The study investigated the impact of planting density on the growth, lodging, and yield of oat, as well as their interrelationships. Additionally, we identified the optimal planting density to establish a robust crop structure. The research aims to contribute to the high-yield and high-quality cultivation of oat. Results We observed that with increasing planting density, plant height, grass and grain yields of both varieties first increased and then decreased; root fresh weight, stem diameter, stem wall thickness, stem puncture strength, breaking strength, compressive strength, lignin and crude fiber contents, and yield components decreased; whereas the lodging rate and lodging coefficient increased. Planting density affects lodging by regulating plant height, height of center of gravity, stem wall thickness, internode length, and root fresh weight of oat. Additionally, it can impact stem mechanical strength by modulating the synthesis of lignin and crude fiber, which in turn affecting lodging resistance. Plant height, height of center of gravity, stem wall thickness, internode length, root fresh weight, breaking strength, compressive strength, lignin and crude fiber content, single-plant weight, grain yield and 1,…
bibliographic citation: Liu et al. (2024) Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities. PeerJ 12:e17310 https://doi.org/10.7717/peerj.17310
date submitted: 2023-12-28
date accepted: 2024-04-08
issued: 2024-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lingling
author list: Agent
  family name: Liang
  given name: Guoling
author list: Agent
  family name: Liu
  given name: Wenhui
author list: Agent
  family name: Ju
  given name: Zeliang
doi: 10.7717/peerj.17310
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-29
copyright: ©2024 Liu et al.
attribution name: Liu et al.

Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney
type: item
type: AcademicArticle
description: This review discusses the importance of homeostasis with a particular emphasis on the acid-base (AB) balance, a crucial aspect of pH regulation in living systems. Two primary organ systems correct deviations from the standard pH balance: the respiratory system via gas exchange and the kidneys via proton/bicarbonate secretion and reabsorption. Focusing on kidney functions, we describe the complexity of renal architecture and its challenges for experimental research. We address specific roles of different nephron segments (the proximal convoluted tubule, the loop of Henle and the distal convoluted tubule) in pH homeostasis, while explaining the physiological significance of ion exchange processes maintained by the kidneys, particularly the role of bicarbonate ions (HCO3−) as an essential buffer system of the body. The review will be of interest to researchers in the fields of physiology, biochemistry and molecular biology, which builds a strong foundation and critically evaluates existing studies. Our review helps identify the gaps of knowledge by thoroughly understanding the existing literature related to kidney acid-base homeostasis.
format: application/pdf
format: text/html
creator: Elena Gantsova
creator: Oxana Serova
creator: Polina Vishnyakova
creator: Igor Deyev
creator: Andrey Elchaninov
creator: Timur Fatkhudinov
subject: Cell Biology
subject: Molecular Biology
subject: Nephrology
subject: Metabolic Sciences
description: doi:10.7717/peerj.17316
publisher: PeerJ Inc.
rights: © 2024 Gantsova et al.
abstract: This review discusses the importance of homeostasis with a particular emphasis on the acid-base (AB) balance, a crucial aspect of pH regulation in living systems. Two primary organ systems correct deviations from the standard pH balance: the respiratory system via gas exchange and the kidneys via proton/bicarbonate secretion and reabsorption. Focusing on kidney functions, we describe the complexity of renal architecture and its challenges for experimental research. We address specific roles of different nephron segments (the proximal convoluted tubule, the loop of Henle and the distal convoluted tubule) in pH homeostasis, while explaining the physiological significance of ion exchange processes maintained by the kidneys, particularly the role of bicarbonate ions (HCO3−) as an essential buffer system of the body. The review will be of interest to researchers in the fields of physiology, biochemistry and molecular biology, which builds a strong foundation and critically evaluates existing studies. Our review helps identify the gaps of knowledge by thoroughly understanding the existing literature related to kidney acid-base homeostasis.
bibliographic citation: Gantsova et al. (2024) Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney. PeerJ 12:e17316 https://doi.org/10.7717/peerj.17316
date submitted: 2023-09-08
date accepted: 2024-04-09
issued: 2024-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gantsova
  given name: Elena
author list: Agent
  family name: Serova
  given name: Oxana
author list: Agent
  family name: Vishnyakova
  given name: Polina
author list: Agent
  family name: Deyev
  given name: Igor
author list: Agent
  family name: Elchaninov
  given name: Andrey
author list: Agent
  family name: Fatkhudinov
  given name: Timur
doi: 10.7717/peerj.17316
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-29
copyright: © 2024 Gantsova et al.
attribution name: Gantsova et al.

Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey
type: item
type: AcademicArticle
description: Background Thailand recently decriminalized (de facto legalized) cannabis use and sales. However, nationally representative data are scarce with regard to cannabis use behaviors and its association with cannabis outlet density. The objectives of this study are: (1) to describe the prevalence of cannabis use behaviors and cannabis use disorder among the general adult population of Thailand; (2) to describe the extent that the density of cannabis outlets is associated with cannabis use behaviors, cannabis use disorder, and the amount of cannabis smoked per day. Methods We conducted a community-based cross-sectional study in 11 provinces and the Bangkok Metropolitan Area. Participants were residents of sampled communities aged 20 years or older. We requested literate participants to self-administer the questionnaire and interviewed participants who could not read. We analyzed data using descriptive statistics with sampling weight adjustments and multivariate logistic regression analyses. Results The prevalence of current cannabis use was 15 percent. At a 400-m radius, participants who reported three cannabis outlets had 4.2 times higher odds of being current users than participants who reported no outlet (Adjusted OR = 4.82; 95% CI [3.04–7.63]). We found no association between outlet density and hazardous cannabis use or cannabis use disorder, nor association with the amount of cannabis use among cannabis smokers. Discussion and Conclusion The patterns of association between outlet density and cannabis use behaviors were inconsistent. Furthermore, limitations regarding outlet density measurement and lack of temporality should be considered as caveats in the interpretation of the study findings.
format: application/pdf
format: text/html
creator: Wit Wichaidit
creator: Ilham Chapakiya
creator: Aneesah Waeuseng
creator: Kemmapon Chumchuen
creator: Sawitri Assanangkornchai
subject: Epidemiology
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.17317
publisher: PeerJ Inc.
rights: © 2024 Wichaidit et al.
abstract: Background Thailand recently decriminalized (de facto legalized) cannabis use and sales. However, nationally representative data are scarce with regard to cannabis use behaviors and its association with cannabis outlet density. The objectives of this study are: (1) to describe the prevalence of cannabis use behaviors and cannabis use disorder among the general adult population of Thailand; (2) to describe the extent that the density of cannabis outlets is associated with cannabis use behaviors, cannabis use disorder, and the amount of cannabis smoked per day. Methods We conducted a community-based cross-sectional study in 11 provinces and the Bangkok Metropolitan Area. Participants were residents of sampled communities aged 20 years or older. We requested literate participants to self-administer the questionnaire and interviewed participants who could not read. We analyzed data using descriptive statistics with sampling weight adjustments and multivariate logistic regression analyses. Results The prevalence of current cannabis use was 15 percent. At a 400-m radius, participants who reported three cannabis outlets had 4.2 times higher odds of being current users than participants who reported no outlet (Adjusted OR = 4.82; 95% CI [3.04–7.63]). We found no association between outlet density and hazardous cannabis use or cannabis use disorder, nor association with the amount of cannabis use among cannabis smokers. Discussion and Conclusion The patterns of association between outlet density and cannabis use behaviors were inconsistent. Furthermore, limitations regarding outlet density measurement and lack of temporality should be considered as caveats in the interpretation of the study findings.
bibliographic citation: Wichaidit et al. (2024) Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey. PeerJ 12:e17317 https://doi.org/10.7717/peerj.17317
date submitted: 2023-09-18
date accepted: 2024-04-09
issued: 2024-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wichaidit
  given name: Wit
author list: Agent
  family name: Chapakiya
  given name: Ilham
author list: Agent
  family name: Waeuseng
  given name: Aneesah
author list: Agent
  family name: Chumchuen
  given name: Kemmapon
author list: Agent
  family name: Assanangkornchai
  given name: Sawitri
doi: 10.7717/peerj.17317
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-29
copyright: © 2024 Wichaidit et al.
attribution name: Wichaidit et al.

Combining multisensor images and social network data to assess the area flooded by a hurricane event
type: item
type: AcademicArticle
description: In this study, multisensor remote sensing datasets were used to characterize the land use and land covers (LULC) flooded by Hurricane Willa which made landfall on October 24, 2018. The landscape characterization was done using an unsupervised K-means algorithm of a cloud-free Sentinel-2 MultiSpectral Instrument (MSI) image, acquired during the dry season before Hurricane Willa. A flood map was derived using the histogram thresholding technique over a Synthetic Aperture Radar (SAR) Sentinel-1 C-band and combined with a flood map derived from a Sentinel-2 MSI image. Both, the Sentinel-1 and Sentinel-2 images were obtained after Willa landfall. While the LULC map reached an accuracy of 92%, validated using data collected during field surveys, the flood map achieved 90% overall accuracy, validated using locations extracted from social network data, that were manually georeferenced. The agriculture class was the dominant land use (about 2,624 km2), followed by deciduous forest (1,591 km2) and sub-perennial forest (1,317 km2). About 1,608 km2 represents the permanent wetlands (mangrove, salt marsh, lagoon and estuaries, and littoral classes), but only 489 km2 of this area belongs to aquatic surfaces (lagoons and estuaries). The flooded area was 1,225 km2, with the agricultural class as the most impacted (735 km2). Our analysis detected the saltmarsh class occupied 541 km2in the LULC map, and around 328 km2 were flooded during Hurricane Willa. Since the water flow receded relatively quickly, obtaining representative imagery to assess the flood event was a challenge. Still, the high overall accuracies obtained in this study allow us to assume that the outputs are reliable and can be used in the implementation of effective strategies for the protection, restoration, and management of wetlands. In addition, they will improve the capacity of local governments and residents of Marismas Nacionales to make informed decisions for the protection of vulnerable areas to the different…
format: application/pdf
format: text/html
creator: Rafael Hernández-Guzmán
creator: Arturo Ruiz-Luna
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.17319
publisher: PeerJ Inc.
rights: © 2024 Hernández-Guzmán and Ruiz-Luna
abstract: In this study, multisensor remote sensing datasets were used to characterize the land use and land covers (LULC) flooded by Hurricane Willa which made landfall on October 24, 2018. The landscape characterization was done using an unsupervised K-means algorithm of a cloud-free Sentinel-2 MultiSpectral Instrument (MSI) image, acquired during the dry season before Hurricane Willa. A flood map was derived using the histogram thresholding technique over a Synthetic Aperture Radar (SAR) Sentinel-1 C-band and combined with a flood map derived from a Sentinel-2 MSI image. Both, the Sentinel-1 and Sentinel-2 images were obtained after Willa landfall. While the LULC map reached an accuracy of 92%, validated using data collected during field surveys, the flood map achieved 90% overall accuracy, validated using locations extracted from social network data, that were manually georeferenced. The agriculture class was the dominant land use (about 2,624 km2), followed by deciduous forest (1,591 km2) and sub-perennial forest (1,317 km2). About 1,608 km2 represents the permanent wetlands (mangrove, salt marsh, lagoon and estuaries, and littoral classes), but only 489 km2 of this area belongs to aquatic surfaces (lagoons and estuaries). The flooded area was 1,225 km2, with the agricultural class as the most impacted (735 km2). Our analysis detected the saltmarsh class occupied 541 km2in the LULC map, and around 328 km2 were flooded during Hurricane Willa. Since the water flow receded relatively quickly, obtaining representative imagery to assess the flood event was a challenge. Still, the high overall accuracies obtained in this study allow us to assume that the outputs are reliable and can be used in the implementation of effective strategies for the protection, restoration, and management of wetlands. In addition, they will improve the capacity of local governments and residents of Marismas Nacionales to make informed decisions for the protection of vulnerable areas to the different…
bibliographic citation: Hernández-Guzmán et al. (2024) Combining multisensor images and social network data to assess the area flooded by a hurricane event. PeerJ 12:e17319 https://doi.org/10.7717/peerj.17319
date submitted: 2023-11-24
date accepted: 2024-04-09
issued: 2024-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Guzmán
  given name: Rafael
author list: Agent
  family name: Ruiz-Luna
  given name: Arturo
doi: 10.7717/peerj.17319
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-29
copyright: ©2024 Hernández-Guzmán and Ruiz-Luna
attribution name: Hernández-Guzmán and Ruiz-Luna

The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area
type: item
type: AcademicArticle
description: Environmental heterogeneity poses a significant influence on the functional characteristics of species and communities at local scales. Environmental transition zones, such as at the savanna-forest borders, can act as regions of ecological tension when subjected to sharp variations in the microclimate. For ectothermic organisms, such as lizards, environmental temperatures directly influence physiological capabilities, and some species use different thermoregulation strategies that produce varied responses to local climatic conditions, which in turn affect species occurrence and community dynamics. In the context of global warming, these various strategies confer different types of vulnerability as well as risks of extinction. To assess the vulnerability of a species and understand the relationships between environmental variations, thermal tolerance of a species and community structure, lizard communities in forest-savanna transition areas of two national parks in the southwestern Amazon were sampled and their thermal functional traits were characterized. Then, we investigated how community structure and functional thermal variation were shaped by two environmental predictors (i.e., microclimates estimated locally and vegetation structure estimated from remote sensing). It was found that the community structure was more strongly predicted by the canopy surface reflectance values obtained via remote sensing than by microclimate variables. Environmental temperatures were not the most important factor affecting the occurrence of species, and the variations in ecothermal traits demonstrated a pattern within the taxonomic hierarchy at the family level. This pattern may indicate a tendency for evolutionary history to indirectly influence these functional features. Considering the estimates of the thermal tolerance range and warming tolerance, thermoconformer lizards are likely to be more vulnerable and at greater risk of extinction due to global warming than thermoregulat…
format: application/pdf
format: text/html
creator: Alan F. Souza-Oliveira
creator: Gabriela Zuquim
creator: Lidia F. Martins
creator: Lucas N. Bandeira
creator: Luisa Maria Diele-Viegas
creator: Victor H.G.L. Cavalcante
creator: Fabricio Baccaro
creator: Guarino Rinaldi Colli
creator: Hanna Tuomisto
creator: Fernanda P. Werneck
subject: Biodiversity
subject: Ecology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.16986
publisher: PeerJ Inc.
rights: © 2024 Souza-Oliveira et al.
abstract: Environmental heterogeneity poses a significant influence on the functional characteristics of species and communities at local scales. Environmental transition zones, such as at the savanna-forest borders, can act as regions of ecological tension when subjected to sharp variations in the microclimate. For ectothermic organisms, such as lizards, environmental temperatures directly influence physiological capabilities, and some species use different thermoregulation strategies that produce varied responses to local climatic conditions, which in turn affect species occurrence and community dynamics. In the context of global warming, these various strategies confer different types of vulnerability as well as risks of extinction. To assess the vulnerability of a species and understand the relationships between environmental variations, thermal tolerance of a species and community structure, lizard communities in forest-savanna transition areas of two national parks in the southwestern Amazon were sampled and their thermal functional traits were characterized. Then, we investigated how community structure and functional thermal variation were shaped by two environmental predictors (i.e., microclimates estimated locally and vegetation structure estimated from remote sensing). It was found that the community structure was more strongly predicted by the canopy surface reflectance values obtained via remote sensing than by microclimate variables. Environmental temperatures were not the most important factor affecting the occurrence of species, and the variations in ecothermal traits demonstrated a pattern within the taxonomic hierarchy at the family level. This pattern may indicate a tendency for evolutionary history to indirectly influence these functional features. Considering the estimates of the thermal tolerance range and warming tolerance, thermoconformer lizards are likely to be more vulnerable and at greater risk of extinction due to global warming than thermoregulat…
bibliographic citation: Souza-Oliveira et al. (2024) The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area. PeerJ 12:e16986 https://doi.org/10.7717/peerj.16986
date submitted: 2023-01-10
date accepted: 2024-01-30
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Souza-Oliveira
  given name: Alan F.
author list: Agent
  family name: Zuquim
  given name: Gabriela
author list: Agent
  family name: Martins
  given name: Lidia F.
author list: Agent
  family name: Bandeira
  given name: Lucas N.
author list: Agent
  family name: Diele-Viegas
  given name: Luisa Maria
author list: Agent
  family name: Cavalcante
  given name: Victor H.G.L.
author list: Agent
  family name: Baccaro
  given name: Fabricio
author list: Agent
  family name: Colli
  given name: Guarino Rinaldi
author list: Agent
  family name: Tuomisto
  given name: Hanna
author list: Agent
  family name: Werneck
  given name: Fernanda P.
doi: 10.7717/peerj.16986
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: ©2024 Souza-Oliveira et al.
attribution name: Souza-Oliveira et al.

Transcriptome differential expression analysis of defoliation of two different lemon varieties
type: item
type: AcademicArticle
description: ‘Allen Eureka’ is a bud variety of Eureka lemon with excellent fruiting traits. However, it suffers from severe winter defoliation that leads to a large loss of organic nutrients and seriously affects the tree’s growth and development as well as the yield of the following year, and the mechanism of its response to defoliation is still unclear. In order to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemon, two lemon cultivars (‘Allen Eureka’ and ‘Yunning No. 1’) with different defoliation traits were used as materials. The petiole abscission zone (AZ) was collected at three different defoliation stages, namely, the pre-defoliation stage (CQ), the mid-defoliation stage (CZ), and the post-defoliation stage (CH). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 898, 4,856, and 3,126 differentially expressed genes (DEGs) were obtained in CQ, CZ, and CH, respectively, and the number of DEGs in CZ was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to oxidoreductase, hydrolase, DNA binding transcription factor, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in CZ and involved plant hormone signal transduction, phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. The expression trends of some DEGs suggested their roles in regulating defoliation in lemon. Eight gene families were obtained by combining DEG clustering analysis and weighted gene co-expression network analysis (WGCNA), including β-glucosidase, AUX/IAA, SAUR, GH3, POD, and WRKY, suggesting that these genes may be involved in the regulation of lemon leaf abscission. The above conclusions enrich the research related to lemon leaf abscission and provide reliable data for the screening of lemon defoliation candidate genes and ana…
format: application/pdf
format: text/html
creator: Meichao Dong
creator: Tuo Yin
creator: Junyan Gao
creator: Hanyao Zhang
creator: Fan Yang
creator: Shaohua Wang
creator: Chunrui Long
creator: Xiaomeng Fu
creator: Hongming Liu
creator: Lina Guo
creator: Dongguo Zhou
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.17218
publisher: PeerJ Inc.
rights: © 2024 Dong et al.
abstract: ‘Allen Eureka’ is a bud variety of Eureka lemon with excellent fruiting traits. However, it suffers from severe winter defoliation that leads to a large loss of organic nutrients and seriously affects the tree’s growth and development as well as the yield of the following year, and the mechanism of its response to defoliation is still unclear. In order to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemon, two lemon cultivars (‘Allen Eureka’ and ‘Yunning No. 1’) with different defoliation traits were used as materials. The petiole abscission zone (AZ) was collected at three different defoliation stages, namely, the pre-defoliation stage (CQ), the mid-defoliation stage (CZ), and the post-defoliation stage (CH). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 898, 4,856, and 3,126 differentially expressed genes (DEGs) were obtained in CQ, CZ, and CH, respectively, and the number of DEGs in CZ was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to oxidoreductase, hydrolase, DNA binding transcription factor, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in CZ and involved plant hormone signal transduction, phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. The expression trends of some DEGs suggested their roles in regulating defoliation in lemon. Eight gene families were obtained by combining DEG clustering analysis and weighted gene co-expression network analysis (WGCNA), including β-glucosidase, AUX/IAA, SAUR, GH3, POD, and WRKY, suggesting that these genes may be involved in the regulation of lemon leaf abscission. The above conclusions enrich the research related to lemon leaf abscission and provide reliable data for the screening of lemon defoliation candidate genes and ana…
bibliographic citation: Dong et al. (2024) Transcriptome differential expression analysis of defoliation of two different lemon varieties. PeerJ 12:e17218 https://doi.org/10.7717/peerj.17218
date submitted: 2023-11-28
date accepted: 2024-03-20
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Meichao
author list: Agent
  family name: Yin
  given name: Tuo
author list: Agent
  family name: Gao
  given name: Junyan
author list: Agent
  family name: Zhang
  given name: Hanyao
author list: Agent
  family name: Yang
  given name: Fan
author list: Agent
  family name: Wang
  given name: Shaohua
author list: Agent
  family name: Long
  given name: Chunrui
author list: Agent
  family name: Fu
  given name: Xiaomeng
author list: Agent
  family name: Liu
  given name: Hongming
author list: Agent
  family name: Guo
  given name: Lina
author list: Agent
  family name: Zhou
  given name: Dongguo
doi: 10.7717/peerj.17218
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: © 2024 Dong et al.
attribution name: Dong et al.

Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites
type: item
type: AcademicArticle
description: Background Schisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera? Methods In this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed. Results The major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new oppor…
format: application/pdf
format: text/html
creator: Xiaolu Qin
creator: Han Pu
creator: Xilin Fang
creator: Qianqian Shang
creator: Jianhua Li
creator: Qiaozhu Zhao
creator: Xiaorui Wang
creator: Wei Gu
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17240
publisher: PeerJ Inc.
rights: © 2024 Qin et al.
abstract: Background Schisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera? Methods In this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed. Results The major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new oppor…
bibliographic citation: Qin et al. (2024) Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites. PeerJ 12:e17240 https://doi.org/10.7717/peerj.17240
date submitted: 2023-09-06
date accepted: 2024-03-25
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Xiaolu
author list: Agent
  family name: Pu
  given name: Han
author list: Agent
  family name: Fang
  given name: Xilin
author list: Agent
  family name: Shang
  given name: Qianqian
author list: Agent
  family name: Li
  given name: Jianhua
author list: Agent
  family name: Zhao
  given name: Qiaozhu
author list: Agent
  family name: Wang
  given name: Xiaorui
author list: Agent
  family name: Gu
  given name: Wei
doi: 10.7717/peerj.17240
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: ©2024 Qin et al.
attribution name: Qin et al.

Influence of honey bee (Apis mellifera) breeding on wing venation in Serbia and neighbouring countries
type: item
type: AcademicArticle
description: In order to improve the productivity of honey bees (Apis mellifera), some of their traits are selected by breeding. On one hand, breeding is mainly based on the natural geographical variation of this species; on the other hand, mass production and distribution of artificially selected queens can significantly affect the natural geographic variation of honey bees. In this study, we have compared honey bee wings originating from breeding and non-breeding populations in Serbia. In the comparison, we have also used data from a large area of south-eastern Europe. The wings were measured using the 19 landmarks indicated on the wing images. The coordinates were analysed using the methodology of geometric morphometrics. We found that honey bees obtained from honey bee queen breeder differed in wing venation from surrounding populations, which are under natural selection. Therefore, we argue against including populations under artificial selection in the analysis of the natural geographical variation of honey bees. In our analysis of non-breeding samples, we found that in south-eastern Europe there is continuous variation in wing venation and no clear boundaries between A. m. carnica, A. m. cecropia, and A. m. macedonica.
format: application/pdf
format: text/html
creator: Hardeep Kaur
creator: Nebojša Nedić
creator: Adam Tofilski
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.17247
publisher: PeerJ Inc.
rights: © 2024 Kaur et al.
abstract: In order to improve the productivity of honey bees (Apis mellifera), some of their traits are selected by breeding. On one hand, breeding is mainly based on the natural geographical variation of this species; on the other hand, mass production and distribution of artificially selected queens can significantly affect the natural geographic variation of honey bees. In this study, we have compared honey bee wings originating from breeding and non-breeding populations in Serbia. In the comparison, we have also used data from a large area of south-eastern Europe. The wings were measured using the 19 landmarks indicated on the wing images. The coordinates were analysed using the methodology of geometric morphometrics. We found that honey bees obtained from honey bee queen breeder differed in wing venation from surrounding populations, which are under natural selection. Therefore, we argue against including populations under artificial selection in the analysis of the natural geographical variation of honey bees. In our analysis of non-breeding samples, we found that in south-eastern Europe there is continuous variation in wing venation and no clear boundaries between A. m. carnica, A. m. cecropia, and A. m. macedonica.
bibliographic citation: Kaur et al. (2024) Influence of honey bee (Apis mellifera) breeding on wing venation in Serbia and neighbouring countries. PeerJ 12:e17247 https://doi.org/10.7717/peerj.17247
date submitted: 2023-12-27
date accepted: 2024-03-25
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaur
  given name: Hardeep
author list: Agent
  family name: Nedić
  given name: Nebojša
author list: Agent
  family name: Tofilski
  given name: Adam
doi: 10.7717/peerj.17247
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: © 2024 Kaur et al.
attribution name: Kaur et al.

Genome-wide identification and analysis of ascorbate peroxidase (APX) gene family in hemp (Cannabis sativa L.) under various abiotic stresses
type: item
type: AcademicArticle
description: Ascorbate peroxidase (APX) plays a critical role in molecular mechanisms such as plant development and defense against abiotic stresses. As an important economic crop, hemp (Cannabis sativa L.) is vulnerable to adverse environmental conditions, such as drought, cold, salt, and oxidative stress, which lead to a decline in yield and quality. Although APX genes have been characterized in a variety of plants, members of the APX gene family in hemp have not been completely identified. In this study, we (1) identified eight members of the CsAPX gene family in hemp and mapped their locations on the chromosomes using bioinformatics analysis; (2) examined the physicochemical characteristics of the proteins encoded by these CsAPX gene family members; (3) investigated their intraspecific collinearity, gene structure, conserved domains, conserved motifs, and cis-acting elements; (4) constructed a phylogenetic tree and analyzed interspecific collinearity; and (5) ascertained expression differences in leaf tissue subjected to cold, drought, salt, and oxidative stresses using quantitative real-time-PCR (qRT-PCR). Under all four stresses, CsAPX6, CsAPX7, and CsAPX8 consistently exhibited significant upregulation, whereas CsAPX2 displayed notably higher expression levels under drought stress than under the other stresses. Taken together, the results of this study provide basic genomic information on the expression of the APX gene family and pave the way for studying the role of APX genes in abiotic stress.
format: application/pdf
format: text/html
creator: Zixiao Liang
creator: Hongguo Xu
creator: Hongying Qi
creator: Yiying Fei
creator: Jiaying Cui
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.17249
publisher: PeerJ Inc.
rights: © 2024 Liang et al.
abstract: Ascorbate peroxidase (APX) plays a critical role in molecular mechanisms such as plant development and defense against abiotic stresses. As an important economic crop, hemp (Cannabis sativa L.) is vulnerable to adverse environmental conditions, such as drought, cold, salt, and oxidative stress, which lead to a decline in yield and quality. Although APX genes have been characterized in a variety of plants, members of the APX gene family in hemp have not been completely identified. In this study, we (1) identified eight members of the CsAPX gene family in hemp and mapped their locations on the chromosomes using bioinformatics analysis; (2) examined the physicochemical characteristics of the proteins encoded by these CsAPX gene family members; (3) investigated their intraspecific collinearity, gene structure, conserved domains, conserved motifs, and cis-acting elements; (4) constructed a phylogenetic tree and analyzed interspecific collinearity; and (5) ascertained expression differences in leaf tissue subjected to cold, drought, salt, and oxidative stresses using quantitative real-time-PCR (qRT-PCR). Under all four stresses, CsAPX6, CsAPX7, and CsAPX8 consistently exhibited significant upregulation, whereas CsAPX2 displayed notably higher expression levels under drought stress than under the other stresses. Taken together, the results of this study provide basic genomic information on the expression of the APX gene family and pave the way for studying the role of APX genes in abiotic stress.
bibliographic citation: Liang et al. (2024) Genome-wide identification and analysis of ascorbate peroxidase (APX) gene family in hemp (Cannabis sativa L.) under various abiotic stresses. PeerJ 12:e17249 https://doi.org/10.7717/peerj.17249
date submitted: 2023-11-29
date accepted: 2024-03-25
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Zixiao
author list: Agent
  family name: Xu
  given name: Hongguo
author list: Agent
  family name: Qi
  given name: Hongying
author list: Agent
  family name: Fei
  given name: Yiying
author list: Agent
  family name: Cui
  given name: Jiaying
doi: 10.7717/peerj.17249
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: ©2024 Liang et al.
attribution name: Liang et al.

A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer
type: item
type: AcademicArticle
description: Background Occult lymph node metastasis (OLNM) is an essential prognostic factor for early-stage tongue cancer (cT1-2N0M0) and a determinant of treatment decisions. Therefore, accurate prediction of OLNM can significantly impact the clinical management and outcomes of patients with tongue cancer. The aim of this study was to develop and validate a multiomics-based model to predict OLNM in patients with early-stage tongue cancer. Methods The data of 125 patients diagnosed with early-stage tongue cancer (cT1-2N0M0) who underwent primary surgical treatment and elective neck dissection were retrospectively analyzed. A total of 100 patients were randomly assigned to the training set and 25 to the test set. The preoperative contrast-enhanced computed tomography (CT) and clinical data on these patients were collected. Radiomics features were extracted from the primary tumor as the region of interest (ROI) on CT images, and correlation analysis and the least absolute shrinkage and selection operator (LASSO) method were used to identify the most relevant features. A support vector machine (SVM) classifier was constructed and compared with other machine learning algorithms. With the same method, a clinical model was built and the peri-tumoral and intra-tumoral images were selected as the input for the deep learning model. The stacking ensemble technique was used to combine the multiple models. The predictive performance of the integrated model was evaluated for accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC-ROC), and compared with expert assessment. Internal validation was performed using a stratified five-fold cross-validation approach. Results Of the 125 patients, 41 (32.8%) showed OLNM on postoperative pathological examination. The integrated model achieved higher predictive performance compared with the individual models, with an accuracy of 84%, a sensitivity of 100%, a specificity of 76.5%, and an AUC-ROC of 0.949…
format: application/pdf
format: text/html
creator: Wei Han
creator: Yingshu Wang
creator: Tao Li
creator: Yuke Dong
creator: Yanwei Dang
creator: Liang He
creator: Lianfang Xu
creator: Yuhao Zhou
creator: Yujie Li
creator: Xudong Wang
subject: Oncology
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17254
publisher: PeerJ Inc.
rights: © 2024 Han et al.
abstract: Background Occult lymph node metastasis (OLNM) is an essential prognostic factor for early-stage tongue cancer (cT1-2N0M0) and a determinant of treatment decisions. Therefore, accurate prediction of OLNM can significantly impact the clinical management and outcomes of patients with tongue cancer. The aim of this study was to develop and validate a multiomics-based model to predict OLNM in patients with early-stage tongue cancer. Methods The data of 125 patients diagnosed with early-stage tongue cancer (cT1-2N0M0) who underwent primary surgical treatment and elective neck dissection were retrospectively analyzed. A total of 100 patients were randomly assigned to the training set and 25 to the test set. The preoperative contrast-enhanced computed tomography (CT) and clinical data on these patients were collected. Radiomics features were extracted from the primary tumor as the region of interest (ROI) on CT images, and correlation analysis and the least absolute shrinkage and selection operator (LASSO) method were used to identify the most relevant features. A support vector machine (SVM) classifier was constructed and compared with other machine learning algorithms. With the same method, a clinical model was built and the peri-tumoral and intra-tumoral images were selected as the input for the deep learning model. The stacking ensemble technique was used to combine the multiple models. The predictive performance of the integrated model was evaluated for accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC-ROC), and compared with expert assessment. Internal validation was performed using a stratified five-fold cross-validation approach. Results Of the 125 patients, 41 (32.8%) showed OLNM on postoperative pathological examination. The integrated model achieved higher predictive performance compared with the individual models, with an accuracy of 84%, a sensitivity of 100%, a specificity of 76.5%, and an AUC-ROC of 0.949…
bibliographic citation: Han et al. (2024) A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer. PeerJ 12:e17254 https://doi.org/10.7717/peerj.17254
date submitted: 2023-11-29
date accepted: 2024-03-26
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Wei
author list: Agent
  family name: Wang
  given name: Yingshu
author list: Agent
  family name: Li
  given name: Tao
author list: Agent
  family name: Dong
  given name: Yuke
author list: Agent
  family name: Dang
  given name: Yanwei
author list: Agent
  family name: He
  given name: Liang
author list: Agent
  family name: Xu
  given name: Lianfang
author list: Agent
  family name: Zhou
  given name: Yuhao
author list: Agent
  family name: Li
  given name: Yujie
author list: Agent
  family name: Wang
  given name: Xudong
doi: 10.7717/peerj.17254
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: © 2024 Han et al.
attribution name: Han et al.

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