PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of erythromycin residuals in food on the development of resistance in Streptococcus pneumoniae: an in vivo study in Galleria mellonella
items: Impact of biological manure substitution on grain yield, nitrogen recovery efficiency, and soil biochemical properties
items: Estimating body volumes and surface areas of animals from cross-sections
items: Epigallocatechin gallate protects MC3T3-E1 cells from cadmium-induced apoptosis and dysfunction via modulating PI3K/AKT/mTOR and Nrf2/HO-1 pathways
items: Identification and analysis of immunoreactive proteins of Shigella flexneri in human sera and stool specimens
items: Elevational variation in morphology and biomass allocation in carpathian snowbell Soldanella carpatica (Primulaceae)
items: Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae
items: The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq
items: Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas
items: Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens

Effect of erythromycin residuals in food on the development of resistance in Streptococcus pneumoniae: an in vivo study in Galleria mellonella
type: item
type: AcademicArticle
description: Background The use of antimicrobials to treat food animals may result in antimicrobial residues in foodstuffs of animal origin. The European Medicines Association (EMA) and World Health Organization (WHO) define safe antimicrobial concentrations in food based on acceptable daily intakes (ADIs). It is unknown if ADI doses of antimicrobials in food could influence the antimicrobial susceptibility of human-associated bacteria. Objectives This aim of this study was to evaluate if the consumption of ADI doses of erythromycin could select for erythromycin resistance in a Galleria mellonella model of Streptococcus pneumoniae infection. Methods A chronic model of S. pneumoniae infection in G. mellonella larvae was used for the experiment. Inoculation of larvae with S. pneumoniae was followed by injections of erythromycin ADI doses (0.0875 and 0.012 μg/ml according to EMA and WHO, respectively). Isolation of S. pneumoniae colonies was then performed on selective agar plates. Minimum inhibitory concentrations (MICs) of resistant colonies were measured, and whole genome sequencing (WGS) was performed followed by variant calling to determine the genetic modifications. Results Exposure to single doses of both EMA and WHO ADI doses of erythromycin resulted in the emergence of erythromycin resistance in S. pneumoniae. Emergent resistance to erythromycin was associated with a mutation in rplA, which codes for the L1 ribosomal protein and has been linked to macrolide resistance in previous studies. Conclusion In our in vivo model, even single doses of erythromycin that are classified as acceptable by the WHO and EMA induced significant increases in erythromycin MICs in S. pneumoniae. These results suggest the need to include the induction of antimicrobial resistance (AMR) as a significant criterion for determining ADIs.
format: application/pdf
format: text/html
creator: Yuliia Baranchyk
creator: Zina Gestels
creator: Dorien Van den Bossche
creator: Saïd Abdellati
creator: Basil Britto Xavier
creator: Sheeba Santhini Manoharan-Basil
creator: Chris Kenyon
subject: Microbiology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.17463
publisher: PeerJ Inc.
rights: © 2024 Baranchyk et al.
abstract: Background The use of antimicrobials to treat food animals may result in antimicrobial residues in foodstuffs of animal origin. The European Medicines Association (EMA) and World Health Organization (WHO) define safe antimicrobial concentrations in food based on acceptable daily intakes (ADIs). It is unknown if ADI doses of antimicrobials in food could influence the antimicrobial susceptibility of human-associated bacteria. Objectives This aim of this study was to evaluate if the consumption of ADI doses of erythromycin could select for erythromycin resistance in a Galleria mellonella model of Streptococcus pneumoniae infection. Methods A chronic model of S. pneumoniae infection in G. mellonella larvae was used for the experiment. Inoculation of larvae with S. pneumoniae was followed by injections of erythromycin ADI doses (0.0875 and 0.012 μg/ml according to EMA and WHO, respectively). Isolation of S. pneumoniae colonies was then performed on selective agar plates. Minimum inhibitory concentrations (MICs) of resistant colonies were measured, and whole genome sequencing (WGS) was performed followed by variant calling to determine the genetic modifications. Results Exposure to single doses of both EMA and WHO ADI doses of erythromycin resulted in the emergence of erythromycin resistance in S. pneumoniae. Emergent resistance to erythromycin was associated with a mutation in rplA, which codes for the L1 ribosomal protein and has been linked to macrolide resistance in previous studies. Conclusion In our in vivo model, even single doses of erythromycin that are classified as acceptable by the WHO and EMA induced significant increases in erythromycin MICs in S. pneumoniae. These results suggest the need to include the induction of antimicrobial resistance (AMR) as a significant criterion for determining ADIs.
bibliographic citation: Baranchyk et al. (2024) Effect of erythromycin residuals in food on the development of resistance in Streptococcus pneumoniae: an in vivo study in Galleria mellonella. PeerJ 12:e17463 https://doi.org/10.7717/peerj.17463
date submitted: 2024-01-25
date accepted: 2024-05-05
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baranchyk
  given name: Yuliia
author list: Agent
  family name: Gestels
  given name: Zina
author list: Agent
  family name: Van den Bossche
  given name: Dorien
author list: Agent
  family name: Abdellati
  given name: Saïd
author list: Agent
  family name: Britto Xavier
  given name: Basil
author list: Agent
  family name: Manoharan-Basil
  given name: Sheeba Santhini
author list: Agent
  family name: Kenyon
  given name: Chris
doi: 10.7717/peerj.17463
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: © 2024 Baranchyk et al.
attribution name: Baranchyk et al.

Impact of biological manure substitution on grain yield, nitrogen recovery efficiency, and soil biochemical properties
type: item
type: AcademicArticle
description: Fertilization plays a crucial role in ensuring global food security and ecological balance. This study investigated the impact of substituting innovative biological manure for chemical fertilization on rice (Oryza sativa L) productivity and soil biochemical properties based on a three-year experiment. Our results suggested rice yield and straw weight were increased under manure addition treatment. Specifically, 70% of total nitrogen (N) fertilizer substituted by biological manure derived from straw, animal waste and microbiome, led to a substantial 13.6% increase in rice yield and a remarkable 34.2% boost in straw weight. In comparison to the conventional local farmer practice of applying 165 kg N ha−1, adopting 70% of total N plus biological manure demonstrated superior outcomes, particularly in enhancing yield components and spike morphology. Fertilization treatments led to elevated levels of soil microbial biomass carbon and N. However, a nuanced comparison with local practices indicated that applying biological manure alongside urea resulted in a slight reduction in N content in vegetative and economic organs, along with decreases of 10.4%, 11.2%, and 6.1% in N recovery efficiency (NRE), respectively. Prudent N management through the judicious application of partial biological manure fertilizer in rice systems could be imperative for sustaining productivity and soil fertility in southern China.
format: application/pdf
format: text/html
creator: Zhili Sun
creator: Chengshun Wang
creator: Jiabao Wang
creator: Gang Wu
creator: Manman Yuan
creator: Haiming Zou
creator: Yixiang Sun
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.17475
publisher: PeerJ Inc.
rights: © 2024 Sun et al.
abstract: Fertilization plays a crucial role in ensuring global food security and ecological balance. This study investigated the impact of substituting innovative biological manure for chemical fertilization on rice (Oryza sativa L) productivity and soil biochemical properties based on a three-year experiment. Our results suggested rice yield and straw weight were increased under manure addition treatment. Specifically, 70% of total nitrogen (N) fertilizer substituted by biological manure derived from straw, animal waste and microbiome, led to a substantial 13.6% increase in rice yield and a remarkable 34.2% boost in straw weight. In comparison to the conventional local farmer practice of applying 165 kg N ha−1, adopting 70% of total N plus biological manure demonstrated superior outcomes, particularly in enhancing yield components and spike morphology. Fertilization treatments led to elevated levels of soil microbial biomass carbon and N. However, a nuanced comparison with local practices indicated that applying biological manure alongside urea resulted in a slight reduction in N content in vegetative and economic organs, along with decreases of 10.4%, 11.2%, and 6.1% in N recovery efficiency (NRE), respectively. Prudent N management through the judicious application of partial biological manure fertilizer in rice systems could be imperative for sustaining productivity and soil fertility in southern China.
bibliographic citation: Sun et al. (2024) Impact of biological manure substitution on grain yield, nitrogen recovery efficiency, and soil biochemical properties. PeerJ 12:e17475 https://doi.org/10.7717/peerj.17475
date submitted: 2024-02-13
date accepted: 2024-05-06
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zhili
author list: Agent
  family name: Wang
  given name: Chengshun
author list: Agent
  family name: Wang
  given name: Jiabao
author list: Agent
  family name: Wu
  given name: Gang
author list: Agent
  family name: Yuan
  given name: Manman
author list: Agent
  family name: Zou
  given name: Haiming
author list: Agent
  family name: Sun
  given name: Yixiang
doi: 10.7717/peerj.17475
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: ©2024 Sun et al.
attribution name: Sun et al.

Estimating body volumes and surface areas of animals from cross-sections
type: item
type: AcademicArticle
description: Background Body mass and surface area are among the most important biological properties, but such information is lacking for some extant organisms and most extinct species. Numerous methods have been developed for body size estimation of animals for this reason. There are two main categories of mass-estimating approaches: extant-scaling approaches and volumetric-density approaches. Extant-scaling approaches determine the relationships between linear skeletal measurements and body mass using regression equations. Volumetric-density approaches, on the other hand, are all based on models. The models are of various types, including physical models, 2D images, and 3D virtual reconstructions. Once the models are constructed, their volumes are acquired using Archimedes’ Principle, math formulae, or 3D software. Then densities are assigned to convert volumes to masses. The acquisition of surface area is similar to volume estimation by changing math formulae or software commands. This article presents a new 2D volumetric-density approach called the cross-sectional method (CSM). Methods The CSM integrates biological cross-sections to estimate volume and surface area accurately. It requires a side view or dorsal/ventral view image, a series of cross-sectional silhouettes and some measurements to perform the calculation. To evaluate the performance of the CSM, two other 2D volumetric-density approaches (Graphic Double Integration (GDI) and Paleomass) are compared with it. Results The CSM produces very accurate results, with average error rates around 0.20% in volume and 1.21% in area respectively. It has higher accuracy than GDI or Paleomass in estimating the volumes and areas of irregular-shaped biological structures. Discussion Most previous 2D volumetric-density approaches assume an elliptical or superelliptical approximation of animal cross-sections. Such an approximation does not always have good performance. The CSM processes the true profiles directly rather than approx…
format: application/pdf
format: text/html
creator: Ruizhe Jackevan Zhao
subject: Computational Biology
subject: Evolutionary Studies
subject: Marine Biology
subject: Mathematical Biology
subject: Paleontology
description: doi:10.7717/peerj.17479
publisher: PeerJ Inc.
rights: © 2024 Zhao
abstract: Background Body mass and surface area are among the most important biological properties, but such information is lacking for some extant organisms and most extinct species. Numerous methods have been developed for body size estimation of animals for this reason. There are two main categories of mass-estimating approaches: extant-scaling approaches and volumetric-density approaches. Extant-scaling approaches determine the relationships between linear skeletal measurements and body mass using regression equations. Volumetric-density approaches, on the other hand, are all based on models. The models are of various types, including physical models, 2D images, and 3D virtual reconstructions. Once the models are constructed, their volumes are acquired using Archimedes’ Principle, math formulae, or 3D software. Then densities are assigned to convert volumes to masses. The acquisition of surface area is similar to volume estimation by changing math formulae or software commands. This article presents a new 2D volumetric-density approach called the cross-sectional method (CSM). Methods The CSM integrates biological cross-sections to estimate volume and surface area accurately. It requires a side view or dorsal/ventral view image, a series of cross-sectional silhouettes and some measurements to perform the calculation. To evaluate the performance of the CSM, two other 2D volumetric-density approaches (Graphic Double Integration (GDI) and Paleomass) are compared with it. Results The CSM produces very accurate results, with average error rates around 0.20% in volume and 1.21% in area respectively. It has higher accuracy than GDI or Paleomass in estimating the volumes and areas of irregular-shaped biological structures. Discussion Most previous 2D volumetric-density approaches assume an elliptical or superelliptical approximation of animal cross-sections. Such an approximation does not always have good performance. The CSM processes the true profiles directly rather than approx…
bibliographic citation: Zhao (2024) Estimating body volumes and surface areas of animals from cross-sections. PeerJ 12:e17479 https://doi.org/10.7717/peerj.17479
date submitted: 2023-12-09
date accepted: 2024-05-07
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Ruizhe Jackevan
doi: 10.7717/peerj.17479
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: © 2024 Zhao
attribution name: Zhao

Epigallocatechin gallate protects MC3T3-E1 cells from cadmium-induced apoptosis and dysfunction via modulating PI3K/AKT/mTOR and Nrf2/HO-1 pathways
type: item
type: AcademicArticle
description: Epigallocatechin gallate (EGCG), an active constituent of tea, is recognized for its anticancer and anti-inflammatory properties. However, the specific mechanism by which EGCG protects osteoblasts from cadmium-induced damage remains incompletely understood. Here, the action of EGCG was investigated by exposing MC3T3-E1 osteoblasts to EGCG and CdCl2 and examining their growth, apoptosis, and differentiation. It was found that EGCG promoted the viability of cadmium-exposed MC3T3-E1 cells, mitigated apoptosis, and promoted both maturation and mineralization. Additionally, CdCl2 has been reported to inhibit both the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) and nuclear factor erythroid 2-related factor 2/heme oxygenase-1(Nrf2/HO-1) signaling pathways. EGCG treatment attenuated cadmium-induced apoptosis in osteoblasts and restored their function by upregulating both signaling pathways. The findings provide compelling evidence for EGCG’s role in attenuating cadmium-induced osteoblast apoptosis and dysfunction through activating the PI3K/AKT/mTOR and Nrf2/HO-1 pathways. This suggests the potential of using EGCG for treating cadmium-induced osteoblast dysfunction.
format: application/pdf
format: text/html
creator: Fanhao Wei
creator: Kai Lin
creator: Binjia Ruan
creator: Chaoyong Wang
creator: Lixun Yang
creator: Hongwei Wang
creator: Yongxiang Wang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.17488
publisher: PeerJ Inc.
rights: © 2024 Wei et al.
abstract: Epigallocatechin gallate (EGCG), an active constituent of tea, is recognized for its anticancer and anti-inflammatory properties. However, the specific mechanism by which EGCG protects osteoblasts from cadmium-induced damage remains incompletely understood. Here, the action of EGCG was investigated by exposing MC3T3-E1 osteoblasts to EGCG and CdCl2 and examining their growth, apoptosis, and differentiation. It was found that EGCG promoted the viability of cadmium-exposed MC3T3-E1 cells, mitigated apoptosis, and promoted both maturation and mineralization. Additionally, CdCl2 has been reported to inhibit both the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) and nuclear factor erythroid 2-related factor 2/heme oxygenase-1(Nrf2/HO-1) signaling pathways. EGCG treatment attenuated cadmium-induced apoptosis in osteoblasts and restored their function by upregulating both signaling pathways. The findings provide compelling evidence for EGCG’s role in attenuating cadmium-induced osteoblast apoptosis and dysfunction through activating the PI3K/AKT/mTOR and Nrf2/HO-1 pathways. This suggests the potential of using EGCG for treating cadmium-induced osteoblast dysfunction.
bibliographic citation: Wei et al. (2024) Epigallocatechin gallate protects MC3T3-E1 cells from cadmium-induced apoptosis and dysfunction via modulating PI3K/AKT/mTOR and Nrf2/HO-1 pathways. PeerJ 12:e17488 https://doi.org/10.7717/peerj.17488
date submitted: 2023-12-05
date accepted: 2024-05-09
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Fanhao
author list: Agent
  family name: Lin
  given name: Kai
author list: Agent
  family name: Ruan
  given name: Binjia
author list: Agent
  family name: Wang
  given name: Chaoyong
author list: Agent
  family name: Yang
  given name: Lixun
author list: Agent
  family name: Wang
  given name: Hongwei
author list: Agent
  family name: Wang
  given name: Yongxiang
doi: 10.7717/peerj.17488
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: ©2024 Wei et al.
attribution name: Wei et al.

Identification and analysis of immunoreactive proteins of Shigella flexneri in human sera and stool specimens
type: item
type: AcademicArticle
description: Background The method currently available to diagnose shigellosis is insensitive and has many limitations. Thus, this study was designed to identify specific antigenic protein(s) among the cell surface associated proteins (SAPs) of Shigella that would be valuable in the development of an alternative diagnostic assay for shigellosis, particularly one that could be run using a stool sample rather than serum. Methods The SAPs of clinical isolates of S. dysenteriae, S. boydii, Shigella flexneri, and S. sonnei were extracted from an overnight culture grown at 37 °C using acidified-glycine extraction methods. Protein profiles were observed by SDS-PAGE. To determine if antibodies specific to certain Shigella SAPs were present in both sera and stool suspensions, Western blot analysis was used to detect the presence of IgA, IgG, and IgM. Results Immunoblot analysis revealed that sera from patients infected with S. flexneri recognized 31 proteins. These SAP antigens are recognized by the host humoral response during Shigella infection. Specific antibodies against these antigens were also observed in intestinal secretions of shigellosis patients. Of these 31 S. flexneri proteins, the 35 kDa protein specifically reacted against IgA present in patients’ stool suspensions. Further study illustrated the immunoreactivity of this protein in S. dysenteriae, S. boydii, and S. sonnei. This is the first report that demonstrates the presence of immunoreactive Shigella SAPs in stool suspensions. The SAPSs could be very useful in developing a simple and rapid serodiagnostic assay for shigellosis directly from stool specimens.
format: application/pdf
format: text/html
creator: Kirnpal Kaur Banga Singh
creator: Mohd Zaki Salleh
creator: Naveed Ahmed
creator: Chan Yean Yean
creator: Asma Ismail
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.17498
publisher: PeerJ Inc.
rights: © 2024 Singh et al.
abstract: Background The method currently available to diagnose shigellosis is insensitive and has many limitations. Thus, this study was designed to identify specific antigenic protein(s) among the cell surface associated proteins (SAPs) of Shigella that would be valuable in the development of an alternative diagnostic assay for shigellosis, particularly one that could be run using a stool sample rather than serum. Methods The SAPs of clinical isolates of S. dysenteriae, S. boydii, Shigella flexneri, and S. sonnei were extracted from an overnight culture grown at 37 °C using acidified-glycine extraction methods. Protein profiles were observed by SDS-PAGE. To determine if antibodies specific to certain Shigella SAPs were present in both sera and stool suspensions, Western blot analysis was used to detect the presence of IgA, IgG, and IgM. Results Immunoblot analysis revealed that sera from patients infected with S. flexneri recognized 31 proteins. These SAP antigens are recognized by the host humoral response during Shigella infection. Specific antibodies against these antigens were also observed in intestinal secretions of shigellosis patients. Of these 31 S. flexneri proteins, the 35 kDa protein specifically reacted against IgA present in patients’ stool suspensions. Further study illustrated the immunoreactivity of this protein in S. dysenteriae, S. boydii, and S. sonnei. This is the first report that demonstrates the presence of immunoreactive Shigella SAPs in stool suspensions. The SAPSs could be very useful in developing a simple and rapid serodiagnostic assay for shigellosis directly from stool specimens.
bibliographic citation: Singh et al. (2024) Identification and analysis of immunoreactive proteins of Shigella flexneri in human sera and stool specimens. PeerJ 12:e17498 https://doi.org/10.7717/peerj.17498
date submitted: 2023-12-01
date accepted: 2024-05-10
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Singh
  given name: Kirnpal Kaur Banga
author list: Agent
  family name: Salleh
  given name: Mohd Zaki
author list: Agent
  family name: Ahmed
  given name: Naveed
author list: Agent
  family name: Yean Yean
  given name: Chan
author list: Agent
  family name: Ismail
  given name: Asma
doi: 10.7717/peerj.17498
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: © 2024 Singh et al.
attribution name: Singh et al.

Elevational variation in morphology and biomass allocation in carpathian snowbell Soldanella carpatica (Primulaceae)
type: item
type: AcademicArticle
description: Plants growing along wide elevation gradients in mountains experience considerable variations in environmental factors that vary across elevations. The most pronounced elevational changes are in climate conditions with characteristic decrease in air temperature with an increase in elevation. Studying intraspecific elevational variations in plant morphological traits and biomass allocation gives opportunity to understand how plants adapted to steep environmental gradients that change with elevation and how they may respond to climate changes related to global warming. In this study, phenotypic variation of an alpine plant Soldanella carpatica Vierh. (Primulaceae) was investigated on 40 sites distributed continuously across a 1,480-m elevation gradient in the Tatra Mountains, Central Europe. Mixed-effects models, by which plant traits were fitted to elevation, revealed that on most part of the gradient total leaf mass, leaf size and scape height decreased gradually with an increase in elevation, whereas dry mass investment in roots and flowers as well as individual flower mass did not vary with elevation. Unexpectedly, in the uppermost part of the elevation gradient overall plant size, including both below-and aboveground plant parts, decreased rapidly causing abrupt plant miniaturization. Despite the plant miniaturization at the highest elevations, biomass partitioning traits changed gradually across the entire species elevation range, namely, the leaf mass fraction decreased continuously, whereas the flower mass fraction and the root:shoot ratio increased steadily from the lowest to the highest elevations. Observed variations in S. carpatica phenotypes are seen as structural adjustments to environmental changes across elevations that increase chances of plant survival and reproduction at different elevations. Moreover, results of the present study agreed with the observations that populations of species from the ‘Soldanella’ intrageneric group adapted to alpine and …
format: application/pdf
format: text/html
creator: Piotr Kiełtyk
subject: Ecology
subject: Environmental Sciences
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.17500
publisher: PeerJ Inc.
rights: © 2024 Kiełtyk
abstract: Plants growing along wide elevation gradients in mountains experience considerable variations in environmental factors that vary across elevations. The most pronounced elevational changes are in climate conditions with characteristic decrease in air temperature with an increase in elevation. Studying intraspecific elevational variations in plant morphological traits and biomass allocation gives opportunity to understand how plants adapted to steep environmental gradients that change with elevation and how they may respond to climate changes related to global warming. In this study, phenotypic variation of an alpine plant Soldanella carpatica Vierh. (Primulaceae) was investigated on 40 sites distributed continuously across a 1,480-m elevation gradient in the Tatra Mountains, Central Europe. Mixed-effects models, by which plant traits were fitted to elevation, revealed that on most part of the gradient total leaf mass, leaf size and scape height decreased gradually with an increase in elevation, whereas dry mass investment in roots and flowers as well as individual flower mass did not vary with elevation. Unexpectedly, in the uppermost part of the elevation gradient overall plant size, including both below-and aboveground plant parts, decreased rapidly causing abrupt plant miniaturization. Despite the plant miniaturization at the highest elevations, biomass partitioning traits changed gradually across the entire species elevation range, namely, the leaf mass fraction decreased continuously, whereas the flower mass fraction and the root:shoot ratio increased steadily from the lowest to the highest elevations. Observed variations in S. carpatica phenotypes are seen as structural adjustments to environmental changes across elevations that increase chances of plant survival and reproduction at different elevations. Moreover, results of the present study agreed with the observations that populations of species from the ‘Soldanella’ intrageneric group adapted to alpine and …
bibliographic citation: Kiełtyk (2024) Elevational variation in morphology and biomass allocation in carpathian snowbell Soldanella carpatica (Primulaceae). PeerJ 12:e17500 https://doi.org/10.7717/peerj.17500
date submitted: 2024-01-16
date accepted: 2024-05-10
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kiełtyk
  given name: Piotr
doi: 10.7717/peerj.17500
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: ©2024 Kiełtyk
attribution name: Kiełtyk

Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae
type: item
type: AcademicArticle
description: Background & Objectives American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee. Methods We investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand. Results Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae. Conclusions Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
format: application/pdf
format: text/html
creator: Sawsen Rebhi
creator: Zarrin Basharat
creator: Calvin R. Wei
creator: Salim Lebbal
creator: Hanen Najjaa
creator: Najla Sadfi-Zouaoui
creator: Abdelmonaem Messaoudi
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.17292
publisher: PeerJ Inc.
rights: © 2024 Rebhi et al.
abstract: Background & Objectives American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee. Methods We investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand. Results Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae. Conclusions Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
bibliographic citation: Rebhi et al. (2024) Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae. PeerJ 12:e17292 https://doi.org/10.7717/peerj.17292
date submitted: 2023-11-16
date accepted: 2024-04-02
issued: 2024-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rebhi
  given name: Sawsen
author list: Agent
  family name: Basharat
  given name: Zarrin
author list: Agent
  family name: Wei
  given name: Calvin R.
author list: Agent
  family name: Lebbal
  given name: Salim
author list: Agent
  family name: Najjaa
  given name: Hanen
author list: Agent
  family name: Sadfi-Zouaoui
  given name: Najla
author list: Agent
  family name: Messaoudi
  given name: Abdelmonaem
doi: 10.7717/peerj.17292
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-27
copyright: ©2024 Rebhi et al.
attribution name: Rebhi et al.

The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq
type: item
type: AcademicArticle
description: Background The chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits. Methods Two parental E. guineensis individuals and 23 of their F1 progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome. Results The chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F1 progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F1 progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops’ scientists who consider using chloroplast genome for agronomic trait modifications.
format: application/pdf
format: text/html
creator: Nurul Shakina Mohd Talkah
creator: Nur Afieqah Kaz Abdul Aziz
creator: Muhammad Farid Abdul Rahim
creator: Nurul Fatiha Farhana Hanafi
creator: Mohd Azinuddin Ahmad Mokhtar
creator: Ahmad Sofiman Othman
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.17335
publisher: PeerJ Inc.
rights: © 2024 Mohd Talkah et al.
abstract: Background The chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits. Methods Two parental E. guineensis individuals and 23 of their F1 progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome. Results The chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F1 progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F1 progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops’ scientists who consider using chloroplast genome for agronomic trait modifications.
bibliographic citation: Mohd Talkah et al. (2024) The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq. PeerJ 12:e17335 https://doi.org/10.7717/peerj.17335
date submitted: 2023-12-10
date accepted: 2024-04-15
issued: 2024-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohd Talkah
  given name: Nurul Shakina
author list: Agent
  family name: Aziz
  given name: Nur Afieqah Kaz Abdul
author list: Agent
  family name: Rahim
  given name: Muhammad Farid Abdul
author list: Agent
  family name: Hanafi
  given name: Nurul Fatiha Farhana
author list: Agent
  family name: Ahmad Mokhtar
  given name: Mohd Azinuddin
author list: Agent
  family name: Othman
  given name: Ahmad Sofiman
doi: 10.7717/peerj.17335
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-27
copyright: ©2024 Mohd Talkah et al.
attribution name: Mohd Talkah et al.

Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas
type: item
type: AcademicArticle
description: Background Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection. Methods Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala’s gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection. Results and Discussion This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabol…
format: application/pdf
format: text/html
creator: Kotaro Kondo
creator: Mirei Suzuki
creator: Mana Amadaira
creator: Chiharu Araki
creator: Rie Watanabe
creator: Koichi Murakami
creator: Shinsaku Ochiai
creator: Tadatoshi Ogura
creator: Takashi Hayakawa
subject: Animal Behavior
subject: Biogeography
subject: Genetics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.17385
publisher: PeerJ Inc.
rights: © 2024 Kondo et al.
abstract: Background Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection. Methods Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala’s gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection. Results and Discussion This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabol…
bibliographic citation: Kondo et al. (2024) Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas. PeerJ 12:e17385 https://doi.org/10.7717/peerj.17385
date submitted: 2024-02-02
date accepted: 2024-04-23
issued: 2024-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kondo
  given name: Kotaro
author list: Agent
  family name: Suzuki
  given name: Mirei
author list: Agent
  family name: Amadaira
  given name: Mana
author list: Agent
  family name: Araki
  given name: Chiharu
author list: Agent
  family name: Watanabe
  given name: Rie
author list: Agent
  family name: Murakami
  given name: Koichi
author list: Agent
  family name: Ochiai
  given name: Shinsaku
author list: Agent
  family name: Ogura
  given name: Tadatoshi
author list: Agent
  family name: Hayakawa
  given name: Takashi
doi: 10.7717/peerj.17385
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-27
copyright: ©2024 Kondo et al.
attribution name: Kondo et al.

Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens
type: item
type: AcademicArticle
description: The basic helix-loop-helix (bHLH) gene family is integral to various aspects of plant development and the orchestration of stress response. This study focuses on the bHLH genes within Populus × canescens, a poplar species noted for its significant tolerance to cadmium (Cd) stress. Through our comprehensive genomic analysis, we have identified and characterized 170 bHLH genes within the P. canescens genome. These genes have been systematically classified into 22 distant subfamilies based on their evolutionary relationships. A notable conservation in gene structure and motif compositions were conserved across these subfamilies. Further analysis of the promoter regions of these genes revealed an abundance of essential cis-acting element, which are associated with plant hormonal regulation, development processes, and stress response pathway. Utilizing quantitative PCR (qPCR), we have documented the differential regulation of PcbHLHs in response to elevated Cd concentrations, with distinct expression patterns observed across various tissues. This study is poised to unravel the molecular mechanism underpinning Cd tolerance in P. canescens, offering valuable insights for the development of new cultivars with enhanced Cd accumulation capacity and tolerance. Such advancements are crucial for implementing effective phytoremediation strategies to mitigate soil pollution caused by Cd.
format: application/pdf
format: text/html
creator: Yuneng Yao
creator: Zhengquan He
creator: Xinmeng Li
creator: Jing Xu
creator: Xiaojiao Han
creator: Hongwei Liang
creator: Renying Zhuo
creator: Wenmin Qiu
subject: Bioinformatics
subject: Plant Science
subject: Soil Science
subject: Environmental Contamination and Remediation
subject: Forestry
description: doi:10.7717/peerj.17410
publisher: PeerJ Inc.
rights: © 2024 Yao et al.
abstract: The basic helix-loop-helix (bHLH) gene family is integral to various aspects of plant development and the orchestration of stress response. This study focuses on the bHLH genes within Populus × canescens, a poplar species noted for its significant tolerance to cadmium (Cd) stress. Through our comprehensive genomic analysis, we have identified and characterized 170 bHLH genes within the P. canescens genome. These genes have been systematically classified into 22 distant subfamilies based on their evolutionary relationships. A notable conservation in gene structure and motif compositions were conserved across these subfamilies. Further analysis of the promoter regions of these genes revealed an abundance of essential cis-acting element, which are associated with plant hormonal regulation, development processes, and stress response pathway. Utilizing quantitative PCR (qPCR), we have documented the differential regulation of PcbHLHs in response to elevated Cd concentrations, with distinct expression patterns observed across various tissues. This study is poised to unravel the molecular mechanism underpinning Cd tolerance in P. canescens, offering valuable insights for the development of new cultivars with enhanced Cd accumulation capacity and tolerance. Such advancements are crucial for implementing effective phytoremediation strategies to mitigate soil pollution caused by Cd.
bibliographic citation: Yao et al. (2024) Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens. PeerJ 12:e17410 https://doi.org/10.7717/peerj.17410
date submitted: 2024-02-08
date accepted: 2024-04-26
issued: 2024-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yao
  given name: Yuneng
author list: Agent
  family name: He
  given name: Zhengquan
author list: Agent
  family name: Li
  given name: Xinmeng
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Han
  given name: Xiaojiao
author list: Agent
  family name: Liang
  given name: Hongwei
author list: Agent
  family name: Zhuo
  given name: Renying
author list: Agent
  family name: Qiu
  given name: Wenmin
doi: 10.7717/peerj.17410
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-27
copyright: ©2024 Yao et al.
attribution name: Yao et al.

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