PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells
items: Iron (oxyhydr)oxides are responsible for the stabilization of Cu and Zn in AMD after treatment with limestone
items: Modeling knot features using branch scars from Mongolian oak (Quercus mongolica)
items: The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research
items: Effects of lower and upper body fatigue in striking response time of amateur karate athletes
items: Simultaneous functioning of different light-harvesting complexes—a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions
items: Adjuvant Pam3CSk4 does not improve the immunization against Cryptococcus gattii infection in C57BL/6 mice
items: Bidirectional effect of vitamin D on brown adipogenesis of C3H10T1/2 fibroblast-like cells
items: Hereditary etiology of non-syndromic sensorineural hearing loss in the Republic of North Ossetia–Alania
items: Alien species revises systematic status: integrative species delimitation of two similar taxa of Symbrenthia Hübner, [1819] (Lepidoptera, Nymphalidae)

Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells
type: item
type: AcademicArticle
description: Mathematical modeling is widely used to study within-host viral dynamics. However, to the best of our knowledge, for the case of SARS-CoV-2 such analyses were mainly conducted with the use of viral load data and for the wild type (WT) variant of the virus. In addition, only few studies analyzed models for in vitro data, which are less noisy and more reproducible. In this work we collected multiple data types for SARS-CoV-2-infected Caco-2 cell lines, including infectious virus titers, measurements of intracellular viral RNA, cell viability data and percentage of infected cells for the WT and Delta variants. We showed that standard models cannot explain some key observations given the absence of cytopathic effect in human cell lines. We propose a novel mathematical model for in vitro SARS-CoV-2 dynamics, which included explicit modeling of intracellular events such as exhaustion of cellular resources required for virus production. The model also explicitly considers innate immune response. The proposed model accurately explained experimental data. Attenuated replication of the Delta variant in Caco-2 cells could be explained by our model on the basis of just two parameters: decreased cell entry rate and increased cytokine production rate.
format: application/pdf
format: text/html
creator: Vladimir Staroverov
creator: Stepan Nersisyan
creator: Alexei Galatenko
creator: Dmitriy Alekseev
creator: Sofya Lukashevich
creator: Fedor Polyakov
creator: Nikita Anisimov
creator: Alexander Tonevitsky
subject: Cell Biology
subject: Computational Biology
subject: Mathematical Biology
subject: Virology
subject: COVID-19
description: doi:10.7717/peerj.14828
publisher: PeerJ Inc.
rights: © 2023 Staroverov et al.
abstract: Mathematical modeling is widely used to study within-host viral dynamics. However, to the best of our knowledge, for the case of SARS-CoV-2 such analyses were mainly conducted with the use of viral load data and for the wild type (WT) variant of the virus. In addition, only few studies analyzed models for in vitro data, which are less noisy and more reproducible. In this work we collected multiple data types for SARS-CoV-2-infected Caco-2 cell lines, including infectious virus titers, measurements of intracellular viral RNA, cell viability data and percentage of infected cells for the WT and Delta variants. We showed that standard models cannot explain some key observations given the absence of cytopathic effect in human cell lines. We propose a novel mathematical model for in vitro SARS-CoV-2 dynamics, which included explicit modeling of intracellular events such as exhaustion of cellular resources required for virus production. The model also explicitly considers innate immune response. The proposed model accurately explained experimental data. Attenuated replication of the Delta variant in Caco-2 cells could be explained by our model on the basis of just two parameters: decreased cell entry rate and increased cytokine production rate.
bibliographic citation: Staroverov et al. (2023) Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells. PeerJ 11:e14828 https://doi.org/10.7717/peerj.14828
date submitted: 2022-10-18
date accepted: 2023-01-09
issued: 2023-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Staroverov
  given name: Vladimir
author list: Agent
  family name: Nersisyan
  given name: Stepan
author list: Agent
  family name: Galatenko
  given name: Alexei
author list: Agent
  family name: Alekseev
  given name: Dmitriy
author list: Agent
  family name: Lukashevich
  given name: Sofya
author list: Agent
  family name: Polyakov
  given name: Fedor
author list: Agent
  family name: Anisimov
  given name: Nikita
author list: Agent
  family name: Tonevitsky
  given name: Alexander
doi: 10.7717/peerj.14828
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-01
copyright: © 2023 Staroverov et al.
attribution name: Staroverov et al.

Iron (oxyhydr)oxides are responsible for the stabilization of Cu and Zn in AMD after treatment with limestone
type: item
type: AcademicArticle
description: The formation and transformation of secondary iron (oxyhydr)oxides and their role in the stabilization of copper (Cu) and zinc (Zn) in acid mine drainage (AMD) after limestone treatment are worth studying to better understand the impacts of limestone AMD treatment. In this study, the wastewater from a copper mine ditch was sampled. Two different doses of limestone (S: 5.33 g L−1 and SS: 8.00 g L−1) were applied to adjust the pH range of the sampled AMD. The concentrations of Fe, Cu and Zn in the supernatant and the levels of iron (oxyhydr)oxides and heavy metals in AMD sediments were dynamically monitored for 300 days to analyze the transformation of the secondary iron mineral phase and the role iron (oxyhydr)oxides play in the removal and stabilization of Cu and Zn. The results showed that the pH rose rapidly to 6.82, decreased to 5.82 on the 150th day, and finally decreased to approximately 4.63 by the 300th day, when the dosage of limestone (S) was 5.33 g L−1. Goethite was the main form of iron oxides in the sediments. As the incubation time increased, so did the content of crystalline Fe (oxyhydr)oxides. In addition, the Cu and Zn content in the fraction of crystalline Fe (oxyhydr)oxides increased as the corresponding iron (oxyhydr)oxide increased. When the high dosage of limestone (8.00 g L−1 or SS) was applied, the pH remained at approximately at 7.46 during the whole period and goethite and lepidocrocite were present in the sediment. Amorphous/ poorly crystalline Fe-oxyhydroxide was the main product after SS limestone dosage, indicating that the risk of Cu and Zn reactivation in the sediment was higher with a higher limestone treatment dosage.
format: application/pdf
format: text/html
creator: Yuan Ding
creator: Yan Long
creator: Weiya Wang
creator: Zhe Wei
creator: Shuo Cai
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.14663
publisher: PeerJ Inc.
rights: © 2023 Ding et al.
abstract: The formation and transformation of secondary iron (oxyhydr)oxides and their role in the stabilization of copper (Cu) and zinc (Zn) in acid mine drainage (AMD) after limestone treatment are worth studying to better understand the impacts of limestone AMD treatment. In this study, the wastewater from a copper mine ditch was sampled. Two different doses of limestone (S: 5.33 g L−1 and SS: 8.00 g L−1) were applied to adjust the pH range of the sampled AMD. The concentrations of Fe, Cu and Zn in the supernatant and the levels of iron (oxyhydr)oxides and heavy metals in AMD sediments were dynamically monitored for 300 days to analyze the transformation of the secondary iron mineral phase and the role iron (oxyhydr)oxides play in the removal and stabilization of Cu and Zn. The results showed that the pH rose rapidly to 6.82, decreased to 5.82 on the 150th day, and finally decreased to approximately 4.63 by the 300th day, when the dosage of limestone (S) was 5.33 g L−1. Goethite was the main form of iron oxides in the sediments. As the incubation time increased, so did the content of crystalline Fe (oxyhydr)oxides. In addition, the Cu and Zn content in the fraction of crystalline Fe (oxyhydr)oxides increased as the corresponding iron (oxyhydr)oxide increased. When the high dosage of limestone (8.00 g L−1 or SS) was applied, the pH remained at approximately at 7.46 during the whole period and goethite and lepidocrocite were present in the sediment. Amorphous/ poorly crystalline Fe-oxyhydroxide was the main product after SS limestone dosage, indicating that the risk of Cu and Zn reactivation in the sediment was higher with a higher limestone treatment dosage.
bibliographic citation: Ding et al. (2023) Iron (oxyhydr)oxides are responsible for the stabilization of Cu and Zn in AMD after treatment with limestone. PeerJ 11:e14663 https://doi.org/10.7717/peerj.14663
date submitted: 2022-09-12
date accepted: 2022-12-09
issued: 2023-01-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Yuan
author list: Agent
  family name: Long
  given name: Yan
author list: Agent
  family name: Wang
  given name: Weiya
author list: Agent
  family name: Wei
  given name: Zhe
author list: Agent
  family name: Cai
  given name: Shuo
doi: 10.7717/peerj.14663
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-30
copyright: ©2023 Ding et al.
attribution name: Ding et al.

Modeling knot features using branch scars from Mongolian oak (Quercus mongolica)
type: item
type: AcademicArticle
description: Wood quality is an important indicator for modern sawmills. Internal wood characteristics can be derived from their correlations with external appearances. In this study, we developed linear regression models to predict knot size from surface features of Mongolian oak (Quercus mongolica) using data collected from 53 trees. For this, manual measurements and X-ray computed tomography scanning technology was respectively used to obtain internal and external features of 1,297 knots. Our results showed that Mongolian oak knots were generally concentrated in the middle part of oak stems, with fewer knots observed at the top and base. The parameters of knot and scar showed significant correlations (P < 0.01), where length and diameter of the corresponding external scar increase with increasing the length and diameter of a knot. The corresponding external scar can be used as an effective indicator to predict the internal value of oak logs. The accuracy of our constructed model is more than 95% when assessed against independent test samples. These models thus can be applied to improve the practical production of oak timber and reduce commercial loss caused by knots. These additional data can improve the estimation of the influence of knots on wood quality and provide a theoretical foundation for investigating the characteristics of hardwood knots.
format: application/pdf
format: text/html
creator: Xiu-jun Lu
creator: Lei Wang
creator: Hui-lin Gao
creator: Hao Zhan
creator: Xiao-lin Zhang
subject: Ecology
subject: Plant Science
subject: Computational Science
subject: Forestry
description: doi:10.7717/peerj.14755
publisher: PeerJ Inc.
rights: © 2023 Lu et al.
abstract: Wood quality is an important indicator for modern sawmills. Internal wood characteristics can be derived from their correlations with external appearances. In this study, we developed linear regression models to predict knot size from surface features of Mongolian oak (Quercus mongolica) using data collected from 53 trees. For this, manual measurements and X-ray computed tomography scanning technology was respectively used to obtain internal and external features of 1,297 knots. Our results showed that Mongolian oak knots were generally concentrated in the middle part of oak stems, with fewer knots observed at the top and base. The parameters of knot and scar showed significant correlations (P < 0.01), where length and diameter of the corresponding external scar increase with increasing the length and diameter of a knot. The corresponding external scar can be used as an effective indicator to predict the internal value of oak logs. The accuracy of our constructed model is more than 95% when assessed against independent test samples. These models thus can be applied to improve the practical production of oak timber and reduce commercial loss caused by knots. These additional data can improve the estimation of the influence of knots on wood quality and provide a theoretical foundation for investigating the characteristics of hardwood knots.
bibliographic citation: Lu et al. (2023) Modeling knot features using branch scars from Mongolian oak (Quercus mongolica). PeerJ 11:e14755 https://doi.org/10.7717/peerj.14755
date submitted: 2022-07-19
date accepted: 2022-12-27
issued: 2023-01-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Xiu-jun
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Gao
  given name: Hui-lin
author list: Agent
  family name: Zhan
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Xiao-lin
doi: 10.7717/peerj.14755
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-31
copyright: ©2023 Lu et al.
attribution name: Lu et al.

The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research
type: item
type: AcademicArticle
description: Background Continuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields. Methods In this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd). Results Soil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi. Conclusions Preliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots.
format: application/pdf
format: text/html
creator: Yuqing Li
creator: Feyisike Gbolayori Jones
creator: Bing Zhang
creator: Juntao Cui
creator: Wei Zhang
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.14758
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Continuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields. Methods In this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd). Results Soil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi. Conclusions Preliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots.
bibliographic citation: Li et al. (2023) The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research. PeerJ 11:e14758 https://doi.org/10.7717/peerj.14758
date submitted: 2022-01-31
date accepted: 2022-12-27
issued: 2023-01-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yuqing
author list: Agent
  family name: Jones
  given name: Feyisike Gbolayori
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Cui
  given name: Juntao
author list: Agent
  family name: Zhang
  given name: Wei
doi: 10.7717/peerj.14758
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-31
copyright: ©2023 Li et al.
attribution name: Li et al.

Effects of lower and upper body fatigue in striking response time of amateur karate athletes
type: item
type: AcademicArticle
description: In combat sports, strikes or counter-strikes response time (RT) can be related to performance and sporting success. Moreover, training sessions are usually highly fatiguing, which is expected to impair basic skills, such as RT. Thus, this study aimed to investigate the effect of fatigue on punch and kick RTs of karate practitioners. Twelve individuals of both sexes from different levels (three yellow belts, three red belts, two orange belts, two green belts, one brown belt, and one black belt) were selected. Participants were aged 22 ± 3 years old, with a stature of 169.1 ± 6.5 cm, and a body mass of 65.5 ± 10 kg. Six visits were held with each participant. On the first 2 days, the RT of punches and kicks was measured by a validated smartphone app (TReaction). For the subsequent visits, a randomized incremental test for the upper or lower body was adopted as motor fatigue protocol, immediately followed by punches and kicks RT tests, also in random order. For induction of lower and upper body-specific muscle fatigue, the ITStriker app was used, which operates by emitting sound signals transmitted by a smartphone. One-way repeated measures ANOVA was performed, and significance was set at p ≤ 0.05. Regarding the mean punches RT, significant effects between situations for the upper (F(2,22) = 11.5; ω2 = 0.23; p < 0.001) and lower body (F(2,22) = 14.2; ω2 = 0.18; p < 0.001) fatigue protocols were found. The negative effect of the lower body fatigue protocol in punches RT was evident regardless of the order of the tests (punch RT first: Δ = 10.5%; t = 4.4; p < 0.001; d = 1.0; kick RT first: Δ = 11.4%; t = 4.8; p < 0.001; d = 1.1). Regarding mean kicks RT, significant effects were found between situations for the lower (F(2,22) = 16.6; ω2 = 0.27; p < 0.001) but not for the upper (F(2,22) = 2.3; ω2 = 0.02; p = 0.12) body fatigue protocols. Kick RTs were negatively affected by the lower body fatigue protocol regardless of the RT order applied (punch RT first: Δ = 7.5%; t = 3…
format: application/pdf
format: text/html
creator: Júlio Cesar Carvalho Rodrigues
creator: Eduardo Macedo Penna
creator: Hugo Enrico Souza Machado
creator: Jader Sant’Ana
creator: Fernando Diefenthaeler
creator: Victor S. Coswig
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.14764
publisher: PeerJ Inc.
rights: © 2023 Rodrigues et al.
abstract: In combat sports, strikes or counter-strikes response time (RT) can be related to performance and sporting success. Moreover, training sessions are usually highly fatiguing, which is expected to impair basic skills, such as RT. Thus, this study aimed to investigate the effect of fatigue on punch and kick RTs of karate practitioners. Twelve individuals of both sexes from different levels (three yellow belts, three red belts, two orange belts, two green belts, one brown belt, and one black belt) were selected. Participants were aged 22 ± 3 years old, with a stature of 169.1 ± 6.5 cm, and a body mass of 65.5 ± 10 kg. Six visits were held with each participant. On the first 2 days, the RT of punches and kicks was measured by a validated smartphone app (TReaction). For the subsequent visits, a randomized incremental test for the upper or lower body was adopted as motor fatigue protocol, immediately followed by punches and kicks RT tests, also in random order. For induction of lower and upper body-specific muscle fatigue, the ITStriker app was used, which operates by emitting sound signals transmitted by a smartphone. One-way repeated measures ANOVA was performed, and significance was set at p ≤ 0.05. Regarding the mean punches RT, significant effects between situations for the upper (F(2,22) = 11.5; ω2 = 0.23; p < 0.001) and lower body (F(2,22) = 14.2; ω2 = 0.18; p < 0.001) fatigue protocols were found. The negative effect of the lower body fatigue protocol in punches RT was evident regardless of the order of the tests (punch RT first: Δ = 10.5%; t = 4.4; p < 0.001; d = 1.0; kick RT first: Δ = 11.4%; t = 4.8; p < 0.001; d = 1.1). Regarding mean kicks RT, significant effects were found between situations for the lower (F(2,22) = 16.6; ω2 = 0.27; p < 0.001) but not for the upper (F(2,22) = 2.3; ω2 = 0.02; p = 0.12) body fatigue protocols. Kick RTs were negatively affected by the lower body fatigue protocol regardless of the RT order applied (punch RT first: Δ = 7.5%; t = 3…
bibliographic citation: Rodrigues et al. (2023) Effects of lower and upper body fatigue in striking response time of amateur karate athletes. PeerJ 11:e14764 https://doi.org/10.7717/peerj.14764
date submitted: 2022-09-27
date accepted: 2022-12-27
issued: 2023-01-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodrigues
  given name: Júlio Cesar Carvalho
author list: Agent
  family name: Penna
  given name: Eduardo Macedo
author list: Agent
  family name: Machado
  given name: Hugo Enrico Souza
author list: Agent
  family name: Sant’Ana
  given name: Jader
author list: Agent
  family name: Diefenthaeler
  given name: Fernando
author list: Agent
  family name: Coswig
  given name: Victor S.
doi: 10.7717/peerj.14764
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-31
copyright: © 2023 Rodrigues et al.
attribution name: Rodrigues et al.

Simultaneous functioning of different light-harvesting complexes—a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions
type: item
type: AcademicArticle
description: Novel peripheral light-harvesting (LH) complex designated as LL LH2 was isolated along with LH4 complex from Rhodopseudomonas palustris cells grown under low light intensity (LL). FPLC-MS/MS allowed to reveal PucABd and PucBabc apoproteins in LL LH2 complex, which is different from previously described LH4 complex containing PucABd, PucABa and PucBb. The main carotenoids in LL LH2 complex were rhodopin and 3,4-didehydrorhodopin. Three-dimensional modeling demonstrated which amino acid residues of all the β-subunits could interact with carotenoids (Car) and bacteriochlorophyll a (BChl a). Analysis of amino acid sequences of α-subunits of both LL complexes showed presence of different C-terminal motifs, IESSVNVG in αa subunit and IESSIKAV in αd subunit, in the same positions of C-termini, which could reflect different retention force of LL LH2 and LH4 on hydroxyl apatite, facilitating successful isolation of these complexes. Differences of these LL complexes in protein and carotenoid composition, in efficiency of energy transfer from Car to BChl a, which is two times lower in LL LH2 than in LH4, allow to assign it to a novel type of light-harvesting complex in Rhodopseudomonas palustris.
format: application/pdf
format: text/html
creator: Olga Petrovna Serdyuk
creator: Azat Vadimovich Abdullatypov
creator: Lidiya Dmitrievna Smolygina
creator: Aleksandr Aleksandrovich Ashikhmin
creator: Maxim Alexandrovich Bolshakov
subject: Computational Biology
subject: Microbiology
description: doi:10.7717/peerj.14769
publisher: PeerJ Inc.
rights: © 2023 Serdyuk et al.
abstract: Novel peripheral light-harvesting (LH) complex designated as LL LH2 was isolated along with LH4 complex from Rhodopseudomonas palustris cells grown under low light intensity (LL). FPLC-MS/MS allowed to reveal PucABd and PucBabc apoproteins in LL LH2 complex, which is different from previously described LH4 complex containing PucABd, PucABa and PucBb. The main carotenoids in LL LH2 complex were rhodopin and 3,4-didehydrorhodopin. Three-dimensional modeling demonstrated which amino acid residues of all the β-subunits could interact with carotenoids (Car) and bacteriochlorophyll a (BChl a). Analysis of amino acid sequences of α-subunits of both LL complexes showed presence of different C-terminal motifs, IESSVNVG in αa subunit and IESSIKAV in αd subunit, in the same positions of C-termini, which could reflect different retention force of LL LH2 and LH4 on hydroxyl apatite, facilitating successful isolation of these complexes. Differences of these LL complexes in protein and carotenoid composition, in efficiency of energy transfer from Car to BChl a, which is two times lower in LL LH2 than in LH4, allow to assign it to a novel type of light-harvesting complex in Rhodopseudomonas palustris.
bibliographic citation: Serdyuk et al. (2023) Simultaneous functioning of different light-harvesting complexes—a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions. PeerJ 11:e14769 https://doi.org/10.7717/peerj.14769
date submitted: 2022-09-15
date accepted: 2022-12-29
issued: 2023-01-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serdyuk
  given name: Olga Petrovna
author list: Agent
  family name: Abdullatypov
  given name: Azat Vadimovich
author list: Agent
  family name: Smolygina
  given name: Lidiya Dmitrievna
author list: Agent
  family name: Ashikhmin
  given name: Aleksandr Aleksandrovich
author list: Agent
  family name: Bolshakov
  given name: Maxim Alexandrovich
doi: 10.7717/peerj.14769
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-31
copyright: ©2023 Serdyuk et al.
attribution name: Serdyuk et al.

Adjuvant Pam3CSk4 does not improve the immunization against Cryptococcus gattii infection in C57BL/6 mice
type: item
type: AcademicArticle
description: Background Cryptococcosis is a relevant invasive fungal infection that affects immunocompromised and immunocompetent individuals when caused by Cryptococcus gattii. Host innate and adaptive immune responses can be subverted by C. gattii, that blocks the differentiation of T helper (Th) 1 and Th17 cells, which are involved in the protection against cryptococcosis. Moreover, the macrophage polarization is modulated by C. gattii infection that requires a balance in the macrophage subsets to control the C. gattii infection. Toll-like receptor (TLR) 2 agonists are important immunomodulators favoring a pro-inflammatory response with potential fungicidal activity, and TLR2 agonists have been used as adjuvants in vaccines against infections caused by bacteria or viruses. Therefore, this work aimed to evaluate the immunomodulatory effect of the tripalmitoyl lipopeptide S-glycerol cysteine (Pam3CSK4 or P3C4), a TLR2 agonist, as an adjuvant in the vaccination against C. gattii infection. Methods and Results C57BL/6 mice were immunized with 2 × 107 inactivated yeasts of C. gattii via intranasal route on day 1, 14 and 28 (Immunized group). Immunization was associated with 1µg or 10µg of adjuvant P3C4 (Immunized+P3C4-1µg or Immunized+P3C4-10 µg), followed by C. gattii infection on day 42 after the immunization protocol. Immunized+P3C4-1 µg group had reduced levels of IgG1, IgG2a and IgA and no significant difference in the IgG and IgM anti-GXM antibody titer was detected, compared to the Immunized group. High levels of IL-17 and IL-1β in lung tissue of mice from the Immunized+P3C4-1µg group did not promote a predominance of Th17 cells, in contrast, the frequency of TLR2+ cells was increased in immunized mice that received 1 µg of P3C4. The reduction in the relative expression of T-bet and high levels of Foxp3 detected in the lungs of the Immunized+P3C4-1µg group suggest a prevalence of regulatory T cells in the tissue, which did not contribute to the control of C. gattii infectio…
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creator: Gabriela Yamazaki de Campos
creator: Patrícia Kellen Martins Oliveira-Brito
creator: Júlia Garcia Guimarães
creator: Letícia Serafim da Costa
creator: Javier Emílio Lazo Chica
creator: Thiago Aparecido da Silva
subject: Cell Biology
subject: Mycology
description: doi:10.7717/peerj.14778
publisher: PeerJ Inc.
rights: © 2023 de Campos et al.
abstract: Background Cryptococcosis is a relevant invasive fungal infection that affects immunocompromised and immunocompetent individuals when caused by Cryptococcus gattii. Host innate and adaptive immune responses can be subverted by C. gattii, that blocks the differentiation of T helper (Th) 1 and Th17 cells, which are involved in the protection against cryptococcosis. Moreover, the macrophage polarization is modulated by C. gattii infection that requires a balance in the macrophage subsets to control the C. gattii infection. Toll-like receptor (TLR) 2 agonists are important immunomodulators favoring a pro-inflammatory response with potential fungicidal activity, and TLR2 agonists have been used as adjuvants in vaccines against infections caused by bacteria or viruses. Therefore, this work aimed to evaluate the immunomodulatory effect of the tripalmitoyl lipopeptide S-glycerol cysteine (Pam3CSK4 or P3C4), a TLR2 agonist, as an adjuvant in the vaccination against C. gattii infection. Methods and Results C57BL/6 mice were immunized with 2 × 107 inactivated yeasts of C. gattii via intranasal route on day 1, 14 and 28 (Immunized group). Immunization was associated with 1µg or 10µg of adjuvant P3C4 (Immunized+P3C4-1µg or Immunized+P3C4-10 µg), followed by C. gattii infection on day 42 after the immunization protocol. Immunized+P3C4-1 µg group had reduced levels of IgG1, IgG2a and IgA and no significant difference in the IgG and IgM anti-GXM antibody titer was detected, compared to the Immunized group. High levels of IL-17 and IL-1β in lung tissue of mice from the Immunized+P3C4-1µg group did not promote a predominance of Th17 cells, in contrast, the frequency of TLR2+ cells was increased in immunized mice that received 1 µg of P3C4. The reduction in the relative expression of T-bet and high levels of Foxp3 detected in the lungs of the Immunized+P3C4-1µg group suggest a prevalence of regulatory T cells in the tissue, which did not contribute to the control of C. gattii infectio…
bibliographic citation: de Campos et al. (2023) Adjuvant Pam3CSk4 does not improve the immunization against Cryptococcus gattii infection in C57BL/6 mice. PeerJ 11:e14778 https://doi.org/10.7717/peerj.14778
date submitted: 2022-08-08
date accepted: 2023-01-03
issued: 2023-01-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Campos
  given name: Gabriela Yamazaki
author list: Agent
  family name: Oliveira-Brito
  given name: Patrícia Kellen Martins
author list: Agent
  family name: Guimarães
  given name: Júlia Garcia
author list: Agent
  family name: da Costa
  given name: Letícia Serafim
author list: Agent
  family name: Lazo Chica
  given name: Javier Emílio
author list: Agent
  family name: da Silva
  given name: Thiago Aparecido
doi: 10.7717/peerj.14778
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-31
copyright: ©2023 de Campos et al.
attribution name: de Campos et al.

Bidirectional effect of vitamin D on brown adipogenesis of C3H10T1/2 fibroblast-like cells
type: item
type: AcademicArticle
description: Background Brown adipose tissue (BAT) dissipates caloric energy as heat and plays a role in glucose and lipid metabolism. Therefore, augmentation and activation of BAT are the focus of new treatment strategies against obesity, a primary risk factor of metabolic syndrome. The vitamin D system plays a crucial role in mineral homeostasis, bone metabolism, and cell proliferation and differentiation. In this study, we investigated the effects of vitamin D3 [1,25(OH)2D3] on brown adipocyte differentiation. Methods The mouse fibroblast-like cell line C3H10T1/2 was differentiated into brown adipocytes in the presence of 1,25(OH)2D3. The effect of 1,25(OH)2D3 on brown adipocyte differentiation was assessed by measuring lipid accumulation, the expression of related genes, and cytotoxicity. The viability of C3H10T1/2 cells was measured using the Cell Counting Kit-8 assay. Gene expression was investigated using quantitative reverse transcription-polymerase chain reaction. Protein expression was estimated using western blotting. Results 1,25(OH)2D3 inhibited adipocyte differentiation and exerted a cytotoxic effect at 1 nM. However, in the physiological concentration range (50–250 pM), 1,25(OH)2D3 promoted uncoupling protein 1 (UCP1) expression in C3H10T1/2 cells. This effect was not observed when 1,25(OH)2D3 was added 48 h after the initiation of differentiation, suggesting that the vitamin D system acts in the early phase of the differentiation program. We showed that 1,25(OH)2D3 increased the expression of two key regulators of brown adipogenesis, PR domain containing 16 (Prdm16) and peroxisome proliferator-activated receptor γ coactivator-1α (Pgc1α). Furthermore, 1,25(OH)2D3 increased Ucp1 expression in 3T3-L1 beige adipogenesis in a dose-dependent manner. Conclusion These data indicate the potential of vitamin D and its analogs as therapeutics for the treatment of obesity and related metabolic diseases.
format: application/pdf
format: text/html
creator: Takako Mukai
creator: Tatsuya Kusudo
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.14785
publisher: PeerJ Inc.
rights: © 2023 Mukai and Kusudo
abstract: Background Brown adipose tissue (BAT) dissipates caloric energy as heat and plays a role in glucose and lipid metabolism. Therefore, augmentation and activation of BAT are the focus of new treatment strategies against obesity, a primary risk factor of metabolic syndrome. The vitamin D system plays a crucial role in mineral homeostasis, bone metabolism, and cell proliferation and differentiation. In this study, we investigated the effects of vitamin D3 [1,25(OH)2D3] on brown adipocyte differentiation. Methods The mouse fibroblast-like cell line C3H10T1/2 was differentiated into brown adipocytes in the presence of 1,25(OH)2D3. The effect of 1,25(OH)2D3 on brown adipocyte differentiation was assessed by measuring lipid accumulation, the expression of related genes, and cytotoxicity. The viability of C3H10T1/2 cells was measured using the Cell Counting Kit-8 assay. Gene expression was investigated using quantitative reverse transcription-polymerase chain reaction. Protein expression was estimated using western blotting. Results 1,25(OH)2D3 inhibited adipocyte differentiation and exerted a cytotoxic effect at 1 nM. However, in the physiological concentration range (50–250 pM), 1,25(OH)2D3 promoted uncoupling protein 1 (UCP1) expression in C3H10T1/2 cells. This effect was not observed when 1,25(OH)2D3 was added 48 h after the initiation of differentiation, suggesting that the vitamin D system acts in the early phase of the differentiation program. We showed that 1,25(OH)2D3 increased the expression of two key regulators of brown adipogenesis, PR domain containing 16 (Prdm16) and peroxisome proliferator-activated receptor γ coactivator-1α (Pgc1α). Furthermore, 1,25(OH)2D3 increased Ucp1 expression in 3T3-L1 beige adipogenesis in a dose-dependent manner. Conclusion These data indicate the potential of vitamin D and its analogs as therapeutics for the treatment of obesity and related metabolic diseases.
bibliographic citation: Mukai et al. (2023) Bidirectional effect of vitamin D on brown adipogenesis of C3H10T1/2 fibroblast-like cells. PeerJ 11:e14785 https://doi.org/10.7717/peerj.14785
date submitted: 2021-11-26
date accepted: 2023-01-03
issued: 2023-01-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mukai
  given name: Takako
author list: Agent
  family name: Kusudo
  given name: Tatsuya
doi: 10.7717/peerj.14785
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-31
copyright: ©2023 Mukai and Kusudo
attribution name: Mukai and Kusudo

Hereditary etiology of non-syndromic sensorineural hearing loss in the Republic of North Ossetia–Alania
type: item
type: AcademicArticle
description: More than 50% of congenital hearing loss is hereditary, in which the majority form is non-syndromic. In this study we estimate the most prevalent pathogenic genetic changes in an Ossetian cohort of patients. This is useful for local public health officials to promote genetic counseling of affected families with regard to high allele frequencies of prevalent pathogenic variants and assortative mating in the community of people with hearing loss. In this study, genetic heterogeneity of hereditary non-syndromic sensorineural hearing loss (NSNHL) in a cohort of 109 patients and an assessment of the frequency of two GJB2 gene pathogenic variants in a cohort of 349 healthy individuals from the populations of the Republic of North Ossetia–Alania (RNO–Alania) were assessed. The molecular genetic cause of NSNHL in the GJB2 gene in RNO–Alania was confirmed in ~30% of the cases, including ~27% in Ossetians. In Russian patients, the most frequent variant is GJB2:c.35delG (~83%). The GJB2:c.358_360delGAG variant was found to be the most frequent among Ossetians (~54%). Two genetic variants in GJB2, c.35delG and c.358_360delGAG, accounted for 91% of GJB2 pathogenic alleles in the Ossetian patients. A search for large genome rearrangements revealed etiological cause in two Ossetian patients, a deletion at the POU3F4 gene locus associated with X-linked hearing loss (type DFNX2). In another Ossetian patient, a biallelic pathogenic variant in the MYO15A gene caused hearing loss type DFNB3 was identified, and in one Russian family a heterozygous MYH14 gene variant associated with dominant NSNHL was found. Thus, the informative value of the diagnosis was ~37% among all patients with NSNHL from RNO–Alania and ~32% among the Ossetians. These estimates correspond to the literature data on the fraction of recessive genetic forms of hearing loss within the affected population. The importance of this study consists not only in the estimation of the most prevalent pathogenic genetic changes i…
format: application/pdf
format: text/html
creator: Nika Petrova
creator: Inna Tebieva
creator: Vitaly Kadyshev
creator: Zalina Getoeva
creator: Natalia Balinova
creator: Andrey Marakhonov
creator: Tatyana Vasilyeva
creator: Evgeny Ginter
creator: Sergey Kutsev
creator: Rena Zinchenko
subject: Epidemiology
subject: Otorhinolaryngology
subject: Medical Genetics
description: doi:10.7717/peerj.14514
publisher: PeerJ Inc.
rights: © 2023 Petrova et al.
abstract: More than 50% of congenital hearing loss is hereditary, in which the majority form is non-syndromic. In this study we estimate the most prevalent pathogenic genetic changes in an Ossetian cohort of patients. This is useful for local public health officials to promote genetic counseling of affected families with regard to high allele frequencies of prevalent pathogenic variants and assortative mating in the community of people with hearing loss. In this study, genetic heterogeneity of hereditary non-syndromic sensorineural hearing loss (NSNHL) in a cohort of 109 patients and an assessment of the frequency of two GJB2 gene pathogenic variants in a cohort of 349 healthy individuals from the populations of the Republic of North Ossetia–Alania (RNO–Alania) were assessed. The molecular genetic cause of NSNHL in the GJB2 gene in RNO–Alania was confirmed in ~30% of the cases, including ~27% in Ossetians. In Russian patients, the most frequent variant is GJB2:c.35delG (~83%). The GJB2:c.358_360delGAG variant was found to be the most frequent among Ossetians (~54%). Two genetic variants in GJB2, c.35delG and c.358_360delGAG, accounted for 91% of GJB2 pathogenic alleles in the Ossetian patients. A search for large genome rearrangements revealed etiological cause in two Ossetian patients, a deletion at the POU3F4 gene locus associated with X-linked hearing loss (type DFNX2). In another Ossetian patient, a biallelic pathogenic variant in the MYO15A gene caused hearing loss type DFNB3 was identified, and in one Russian family a heterozygous MYH14 gene variant associated with dominant NSNHL was found. Thus, the informative value of the diagnosis was ~37% among all patients with NSNHL from RNO–Alania and ~32% among the Ossetians. These estimates correspond to the literature data on the fraction of recessive genetic forms of hearing loss within the affected population. The importance of this study consists not only in the estimation of the most prevalent pathogenic genetic changes i…
bibliographic citation: Petrova et al. (2023) Hereditary etiology of non-syndromic sensorineural hearing loss in the Republic of North Ossetia–Alania. PeerJ 11:e14514 https://doi.org/10.7717/peerj.14514
date submitted: 2022-07-13
date accepted: 2022-11-14
issued: 2023-01-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petrova
  given name: Nika
author list: Agent
  family name: Tebieva
  given name: Inna
author list: Agent
  family name: Kadyshev
  given name: Vitaly
author list: Agent
  family name: Getoeva
  given name: Zalina
author list: Agent
  family name: Balinova
  given name: Natalia
author list: Agent
  family name: Marakhonov
  given name: Andrey
author list: Agent
  family name: Vasilyeva
  given name: Tatyana
author list: Agent
  family name: Ginter
  given name: Evgeny
author list: Agent
  family name: Kutsev
  given name: Sergey
author list: Agent
  family name: Zinchenko
  given name: Rena
doi: 10.7717/peerj.14514
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-30
copyright: © 2023 Petrova et al.
attribution name: Petrova et al.

Alien species revises systematic status: integrative species delimitation of two similar taxa of Symbrenthia Hübner, [1819] (Lepidoptera, Nymphalidae)
type: item
type: AcademicArticle
description: Introduction of organisms to new range may impose detrimental effects on local organisms, especially when closely related species are involved. Species delimitation employing an integrative taxonomy approach may provide a quick assessment for the species status between taxa of interest, and to infer ecological competition and/or introgression that may be associated with the introduction. A nymphalid butterfly, Symbrenthia lilaea lunica, was recently introduced to Taiwan, where a closely related local taxon, S. l. formosanus, can be found. We employed multiple species delimitation methods to study the species status between the two taxa, and the results revealed that they can be recognized as two distinct species, revised to S. l. lilaea (syn. nov.) and S. formosanus (stat. rev.) respectively. We further performed a niche modeling approach to investigate the ecological interaction between the two species. The taxonomic status of the two taxa, now elevated to species, has been revised and conservation facing rapid expansion of the introduced species discussed.
format: application/pdf
format: text/html
creator: Yu-Feng Hsu
creator: Zong-Yu Shen
creator: Hang-Chi Huang
creator: Chih-Wei Huang
creator: Chen-Chih Lu
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.14644
publisher: PeerJ Inc.
rights: © 2023 Hsu et al.
abstract: Introduction of organisms to new range may impose detrimental effects on local organisms, especially when closely related species are involved. Species delimitation employing an integrative taxonomy approach may provide a quick assessment for the species status between taxa of interest, and to infer ecological competition and/or introgression that may be associated with the introduction. A nymphalid butterfly, Symbrenthia lilaea lunica, was recently introduced to Taiwan, where a closely related local taxon, S. l. formosanus, can be found. We employed multiple species delimitation methods to study the species status between the two taxa, and the results revealed that they can be recognized as two distinct species, revised to S. l. lilaea (syn. nov.) and S. formosanus (stat. rev.) respectively. We further performed a niche modeling approach to investigate the ecological interaction between the two species. The taxonomic status of the two taxa, now elevated to species, has been revised and conservation facing rapid expansion of the introduced species discussed.
bibliographic citation: Hsu et al. (2023) Alien species revises systematic status: integrative species delimitation of two similar taxa of Symbrenthia Hübner, [1819] (Lepidoptera, Nymphalidae). PeerJ 11:e14644 https://doi.org/10.7717/peerj.14644
date submitted: 2022-09-14
date accepted: 2022-12-06
issued: 2023-01-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hsu
  given name: Yu-Feng
author list: Agent
  family name: Shen
  given name: Zong-Yu
author list: Agent
  family name: Huang
  given name: Hang-Chi
author list: Agent
  family name: Huang
  given name: Chih-Wei
author list: Agent
  family name: Lu
  given name: Chen-Chih
doi: 10.7717/peerj.14644
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-30
copyright: ©2023 Hsu et al.
attribution name: Hsu et al.

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