PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: 5-Methylindole kills various bacterial pathogens and potentiates aminoglycoside against methicillin-resistant Staphylococcus aureus
items: The emergence of spiraling tracheary element bundles in incompatible grafts
items: The below-ground carbon and nitrogen cycling patterns of different mycorrhizal forests on the eastern Qinghai-Tibetan Plateau
items: A novel virtual reality application for autonomous assessment of cervical range of motion: development and reliability study
items: The effects of rumen-protected tryptophan (RPT) on production performance and relevant hormones of dairy cows
items: High temperature mortality of Wolbachia impacts the sex ratio of the parasitoid Ooencyrtus mirus (Hymenoptera: Encyrtidae)
items: PTC2 region genotypes counteract Biomphalaria glabrata population differences between M-line and BS90 in resistance to infection by Schistosoma mansoni
items: Screening of potential key ferroptosis-related genes in sepsis
items: Moonlighting proteins in medically relevant fungi
items: Effects of establishing cultivated grassland on soil organic carbon fractions in a degraded alpine meadow on the Tibetan Plateau

5-Methylindole kills various bacterial pathogens and potentiates aminoglycoside against methicillin-resistant Staphylococcus aureus
type: item
type: AcademicArticle
description: Antibiotic resistance of bacterial pathogens has become a severe threat to human health. To counteract antibiotic resistance, it is of significance to discover new antibiotics and also improve the efficacy of existing antibiotics. Here we show that 5-methylindole, a derivative of the interspecies signaling molecule indole, is able to directly kill various Gram-positive pathogens (e.g., Staphylococcus aureus and Enterococcus faecalis) and also Gram-negative ones (e.g., Escherichia coli and Pseudomonas aeruginosa), with 2-methylindole being less potent. Particularly, 5-methylindole can kill methicillin-resistant S. aureus, multidrug-resistant Klebsiella pneumoniae, Mycobacterium tuberculosis, and antibiotic-tolerant S. aureus persisters. Furthermore, 5-methylindole significantly potentiates aminoglycoside antibiotics, but not fluoroquinolones, killing of S. aureus. In addition, 5-iodoindole also potentiates aminoglycosides. Our findings open a new avenue to develop indole derivatives like 5-methylindole as antibacterial agents or adjuvants of aminoglycoside.
format: application/pdf
format: text/html
creator: Zhongyan Li
creator: Fengqi Sun
creator: Xinmiao Fu
creator: Yajuan Chen
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
description: doi:10.7717/peerj.14010
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Antibiotic resistance of bacterial pathogens has become a severe threat to human health. To counteract antibiotic resistance, it is of significance to discover new antibiotics and also improve the efficacy of existing antibiotics. Here we show that 5-methylindole, a derivative of the interspecies signaling molecule indole, is able to directly kill various Gram-positive pathogens (e.g., Staphylococcus aureus and Enterococcus faecalis) and also Gram-negative ones (e.g., Escherichia coli and Pseudomonas aeruginosa), with 2-methylindole being less potent. Particularly, 5-methylindole can kill methicillin-resistant S. aureus, multidrug-resistant Klebsiella pneumoniae, Mycobacterium tuberculosis, and antibiotic-tolerant S. aureus persisters. Furthermore, 5-methylindole significantly potentiates aminoglycoside antibiotics, but not fluoroquinolones, killing of S. aureus. In addition, 5-iodoindole also potentiates aminoglycosides. Our findings open a new avenue to develop indole derivatives like 5-methylindole as antibacterial agents or adjuvants of aminoglycoside.
bibliographic citation: Li et al. (2022) 5-Methylindole kills various bacterial pathogens and potentiates aminoglycoside against methicillin-resistant Staphylococcus aureus. PeerJ 10:e14010 https://doi.org/10.7717/peerj.14010
date submitted: 2022-05-27
date accepted: 2022-08-15
issued: 2022-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhongyan
author list: Agent
  family name: Sun
  given name: Fengqi
author list: Agent
  family name: Fu
  given name: Xinmiao
author list: Agent
  family name: Chen
  given name: Yajuan
doi: 10.7717/peerj.14010
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-14
copyright: © 2022 Li et al.
attribution name: Li et al.

The emergence of spiraling tracheary element bundles in incompatible grafts
type: item
type: AcademicArticle
description: In distantly-related plant grafting, incompatibility often occurs between scion and rootstock, resulting in growth stagnation, and eventually graft failure. In this study, we found that an emergent structure, or the spiraling tracheary element (TE) bundles consisting of TE masses occurring at the graft interface, was extensively present in the highly incompatible interfamilial graft of Brassica napus/Portulaca oleracea (Bn/Po) and Nicotiana benthamiana/Portulaca oleracea (Nb/Po). This special structure mostly appeared in the local area near the grafting union, and the frequency and quantity of the spiraling tracheary element bundles were much higher in the scion than in the rootstock. Nevertheless, only a small portion of Arabidopsis thaliana/Portulaca oleracea (At/Po) interfamilial grafts showed a less spiraled TEs at the grafting union (usually a circular TE), which is consistent with its growth performance. This study consolidated that spiraling TE bundles were an important indicator for graft incompatibility. The possible reason for the formation of spiraling TE bundles in interfamilial grafts was discussed.
format: application/pdf
format: text/html
creator: Huiyan Wu
creator: Zhuying Deng
creator: Xue Wang
creator: Dacheng Liang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.14020
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: In distantly-related plant grafting, incompatibility often occurs between scion and rootstock, resulting in growth stagnation, and eventually graft failure. In this study, we found that an emergent structure, or the spiraling tracheary element (TE) bundles consisting of TE masses occurring at the graft interface, was extensively present in the highly incompatible interfamilial graft of Brassica napus/Portulaca oleracea (Bn/Po) and Nicotiana benthamiana/Portulaca oleracea (Nb/Po). This special structure mostly appeared in the local area near the grafting union, and the frequency and quantity of the spiraling tracheary element bundles were much higher in the scion than in the rootstock. Nevertheless, only a small portion of Arabidopsis thaliana/Portulaca oleracea (At/Po) interfamilial grafts showed a less spiraled TEs at the grafting union (usually a circular TE), which is consistent with its growth performance. This study consolidated that spiraling TE bundles were an important indicator for graft incompatibility. The possible reason for the formation of spiraling TE bundles in interfamilial grafts was discussed.
bibliographic citation: Wu et al. (2022) The emergence of spiraling tracheary element bundles in incompatible grafts. PeerJ 10:e14020 https://doi.org/10.7717/peerj.14020
date submitted: 2022-05-16
date accepted: 2022-08-16
issued: 2022-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Huiyan
author list: Agent
  family name: Deng
  given name: Zhuying
author list: Agent
  family name: Wang
  given name: Xue
author list: Agent
  family name: Liang
  given name: Dacheng
doi: 10.7717/peerj.14020
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-14
copyright: ©2022 Wu et al.
attribution name: Wu et al.

The below-ground carbon and nitrogen cycling patterns of different mycorrhizal forests on the eastern Qinghai-Tibetan Plateau
type: item
type: AcademicArticle
description: Mycorrhizal fungi can form symbiotic associations with tree species, which not only play an important role in plant survival and growth, but also in soil carbon (C) and nitrogen (N) cycling. However, the understanding of differences in soil C and N cycling patterns among forests with different mycorrhizal types is still incomplete. In order to determine the similarities and differences of soil C and N cycling patterns in different mycorrhizal forest types, three primary forests dominated by ectomycorrhizal (EcM), arbuscular mycorrhizal (AM) and ericoid mycorrhizal (ErM) trees respectively were studied on the eastern Qinghai-Tibetan Plateau. Indicators associated with soil C and N cycling, including leaf litter quality, soil C and N contents, soil C and N fluxes, and soil microbial biomass C and N contents were measured in each mycorrhizal type forest. The results showed that leaf litter quality was significantly lower with high C:N ratio and lignin: N ratio in ErM forest than that in AM and EcM forests. Soil CO2 flux (508.25 ± 65.51 mg m−2 h−1) in AM forest was significantly higher than that in EcM forest (387.18 ± 56.19 mg m−2 h−1) and ErM forest (177.87 ± 58.40 mg m−2 h−1). Furthermore, soil inorganic N content was higher in the AM forest than that in EcM and ErM forests. Soil net N mineralization rate (−0.02 ± 0.03 mg kg−1 d−1) was lower in ErM forest than that in EcM and AM forests. We speculated that AM and EcM forests were relatively characterized by rapid soil C cycling comparing to ErM forest. The soil N cycling in EcM and ErM forests were lower, implying they were ‘organic’ N nutrition patterns, and the pattern in ErM forest was more obvious.
format: application/pdf
format: text/html
creator: Miaomiao Zhang
creator: Shun Liu
creator: Miao Chen
creator: Jian Chen
creator: Xiangwen Cao
creator: Gexi Xu
creator: Hongshuang Xing
creator: Feifan Li
creator: Zuomin Shi
subject: Ecology
subject: Soil Science
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.14028
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Mycorrhizal fungi can form symbiotic associations with tree species, which not only play an important role in plant survival and growth, but also in soil carbon (C) and nitrogen (N) cycling. However, the understanding of differences in soil C and N cycling patterns among forests with different mycorrhizal types is still incomplete. In order to determine the similarities and differences of soil C and N cycling patterns in different mycorrhizal forest types, three primary forests dominated by ectomycorrhizal (EcM), arbuscular mycorrhizal (AM) and ericoid mycorrhizal (ErM) trees respectively were studied on the eastern Qinghai-Tibetan Plateau. Indicators associated with soil C and N cycling, including leaf litter quality, soil C and N contents, soil C and N fluxes, and soil microbial biomass C and N contents were measured in each mycorrhizal type forest. The results showed that leaf litter quality was significantly lower with high C:N ratio and lignin: N ratio in ErM forest than that in AM and EcM forests. Soil CO2 flux (508.25 ± 65.51 mg m−2 h−1) in AM forest was significantly higher than that in EcM forest (387.18 ± 56.19 mg m−2 h−1) and ErM forest (177.87 ± 58.40 mg m−2 h−1). Furthermore, soil inorganic N content was higher in the AM forest than that in EcM and ErM forests. Soil net N mineralization rate (−0.02 ± 0.03 mg kg−1 d−1) was lower in ErM forest than that in EcM and AM forests. We speculated that AM and EcM forests were relatively characterized by rapid soil C cycling comparing to ErM forest. The soil N cycling in EcM and ErM forests were lower, implying they were ‘organic’ N nutrition patterns, and the pattern in ErM forest was more obvious.
bibliographic citation: Zhang et al. (2022) The below-ground carbon and nitrogen cycling patterns of different mycorrhizal forests on the eastern Qinghai-Tibetan Plateau. PeerJ 10:e14028 https://doi.org/10.7717/peerj.14028
date submitted: 2022-04-21
date accepted: 2022-08-16
issued: 2022-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Miaomiao
author list: Agent
  family name: Liu
  given name: Shun
author list: Agent
  family name: Chen
  given name: Miao
author list: Agent
  family name: Chen
  given name: Jian
author list: Agent
  family name: Cao
  given name: Xiangwen
author list: Agent
  family name: Xu
  given name: Gexi
author list: Agent
  family name: Xing
  given name: Hongshuang
author list: Agent
  family name: Li
  given name: Feifan
author list: Agent
  family name: Shi
  given name: Zuomin
doi: 10.7717/peerj.14028
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-14
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

A novel virtual reality application for autonomous assessment of cervical range of motion: development and reliability study
type: item
type: AcademicArticle
description: Background Neck pain, one of the most common musculoskeletal diseases, affects 222 million people worldwide. The cervical range of motion (CROM) is a tool used to assess the neck’s state across three movement axes: flexo-extension, rotation, and lateral flexion. People with neck pain often have a reduced CROM, and they feel pain at the end-range and/or accompany neck movements with compensatory trunk movements. Virtual reality (VR) setups can track the movement of the head and other body parts in order to create the sensation of immersion in the virtual environment. Using this tracking position information, a CROM assessment can be performed using a VR setup that may be carried out autonomously from the user’s home. The objectives of this study were to develop a VR experience that could be used to perform a CROM assessment, and to evaluate the intra-rater and inter-rater reliability of the CROM measures guided by this VR experience. To the best of our knowledge, a study of this type has not been carried out before. Materials & Methods A total of 30 asymptomatic adults were assessed using a VR device (HTC Vive Pro Eye™). Two raters provided support with the VR setup, and the participants were guided by the VR experience as they performed the movements. Each rater tested each subject twice, in random order. In addition to a head-mounted display (HMD), a tracker located on the subject’s back was used to measure trunk compensatory movements. The CROM was estimated using only the HMD position and this measurement was corrected using the tracker data. The mean and standard deviation were calculated to characterize the CROM. To evaluate the reliability, the interclass correlation coefficients (ICC) were calculated for intra-rater and inter-rater analysis. The standard error of measurement and minimum detectable change were also calculated. The usability of the VR system was measured using the Spanish version of the System Usability Scale. Results The mean CROM values in ea…
format: application/pdf
format: text/html
creator: Jose Angel Santos-Paz
creator: Álvaro Sánchez-Picot
creator: Ana Rojo
creator: Aitor Martín-Pintado-Zugasti
creator: Abraham Otero
creator: Rodrigo Garcia-Carmona
subject: Anatomy and Physiology
subject: Orthopedics
subject: Human-Computer Interaction
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.14031
publisher: PeerJ Inc.
rights: © 2022 Santos-Paz et al.
abstract: Background Neck pain, one of the most common musculoskeletal diseases, affects 222 million people worldwide. The cervical range of motion (CROM) is a tool used to assess the neck’s state across three movement axes: flexo-extension, rotation, and lateral flexion. People with neck pain often have a reduced CROM, and they feel pain at the end-range and/or accompany neck movements with compensatory trunk movements. Virtual reality (VR) setups can track the movement of the head and other body parts in order to create the sensation of immersion in the virtual environment. Using this tracking position information, a CROM assessment can be performed using a VR setup that may be carried out autonomously from the user’s home. The objectives of this study were to develop a VR experience that could be used to perform a CROM assessment, and to evaluate the intra-rater and inter-rater reliability of the CROM measures guided by this VR experience. To the best of our knowledge, a study of this type has not been carried out before. Materials & Methods A total of 30 asymptomatic adults were assessed using a VR device (HTC Vive Pro Eye™). Two raters provided support with the VR setup, and the participants were guided by the VR experience as they performed the movements. Each rater tested each subject twice, in random order. In addition to a head-mounted display (HMD), a tracker located on the subject’s back was used to measure trunk compensatory movements. The CROM was estimated using only the HMD position and this measurement was corrected using the tracker data. The mean and standard deviation were calculated to characterize the CROM. To evaluate the reliability, the interclass correlation coefficients (ICC) were calculated for intra-rater and inter-rater analysis. The standard error of measurement and minimum detectable change were also calculated. The usability of the VR system was measured using the Spanish version of the System Usability Scale. Results The mean CROM values in ea…
bibliographic citation: Santos-Paz et al. (2022) A novel virtual reality application for autonomous assessment of cervical range of motion: development and reliability study. PeerJ 10:e14031 https://doi.org/10.7717/peerj.14031
date submitted: 2022-04-19
date accepted: 2022-08-17
issued: 2022-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos-Paz
  given name: Jose Angel
author list: Agent
  family name: Sánchez-Picot
  given name: Álvaro
author list: Agent
  family name: Rojo
  given name: Ana
author list: Agent
  family name: Martín-Pintado-Zugasti
  given name: Aitor
author list: Agent
  family name: Otero
  given name: Abraham
author list: Agent
  family name: Garcia-Carmona
  given name: Rodrigo
doi: 10.7717/peerj.14031
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-14
copyright: ©2022 Santos-Paz et al.
attribution name: Santos-Paz et al.

The effects of rumen-protected tryptophan (RPT) on production performance and relevant hormones of dairy cows
type: item
type: AcademicArticle
description: Tryptophan is an essential amino acid that cannot be synthesized in mammals. Therefore, the dietary supply of tryptophan is critical for the health and production performance (e.g., milk) of mammals. In the present study, 36 lactating Holstein cows were used, of which 24 cows were in the rumen-protected tryptophan (RPT) feeding groups with different doses at 14 g/d and 28 g/d, respectively and 12 cows were in the control group. This approach could avoid dietary tryptophan being degraded by the rumen microorganisms and improve its bioavailability for cows. The results showed that RPT increased milk protein percentage, milk protein yield, milk solid non-fat (SNF), and milk yield. In response to RPT treatment, the levels of melatonin (MT), prolactin (PRL), and insulin-like growth factor-1 (IGF-1) were significantly increased in the serum of cows compared to the controls. RPT feeding improved nutrient utilization efficiency and lactation performance of dairy cows, which enhanced the quality of milk.
format: application/pdf
format: text/html
creator: Hui Ma
creator: Songyang Yao
creator: Libing Bai
creator: Sarvvl Bai
creator: Guoshi Liu
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.13831
publisher: PeerJ Inc.
rights: © 2022 Ma et al.
abstract: Tryptophan is an essential amino acid that cannot be synthesized in mammals. Therefore, the dietary supply of tryptophan is critical for the health and production performance (e.g., milk) of mammals. In the present study, 36 lactating Holstein cows were used, of which 24 cows were in the rumen-protected tryptophan (RPT) feeding groups with different doses at 14 g/d and 28 g/d, respectively and 12 cows were in the control group. This approach could avoid dietary tryptophan being degraded by the rumen microorganisms and improve its bioavailability for cows. The results showed that RPT increased milk protein percentage, milk protein yield, milk solid non-fat (SNF), and milk yield. In response to RPT treatment, the levels of melatonin (MT), prolactin (PRL), and insulin-like growth factor-1 (IGF-1) were significantly increased in the serum of cows compared to the controls. RPT feeding improved nutrient utilization efficiency and lactation performance of dairy cows, which enhanced the quality of milk.
bibliographic citation: Ma et al. (2022) The effects of rumen-protected tryptophan (RPT) on production performance and relevant hormones of dairy cows. PeerJ 10:e13831 https://doi.org/10.7717/peerj.13831
date submitted: 2022-03-09
date accepted: 2022-07-11
issued: 2022-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Hui
author list: Agent
  family name: Yao
  given name: Songyang
author list: Agent
  family name: Bai
  given name: Libing
author list: Agent
  family name: Bai
  given name: Sarvvl
author list: Agent
  family name: Liu
  given name: Guoshi
doi: 10.7717/peerj.13831
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-13
copyright: ©2022 Ma et al.
attribution name: Ma et al.

High temperature mortality of Wolbachia impacts the sex ratio of the parasitoid Ooencyrtus mirus (Hymenoptera: Encyrtidae)
type: item
type: AcademicArticle
description: Background Wolbachia bacteria are estimated to occur in more than half of all insect species. In Hymenoptera, Wolbachia often manipulates its host’s reproduction to its own advantage. Wolbachia is likely the reason that males are rare in the uniparental Ooencyrtus mirus Triapitsyn & Power (Hymenoptera: Encyrtidae). The likelihood of producing male offspring can be increased by giving mothers a continuous supply of Bagrada hilaris (Burmeister) (Heteroptera: Pentatomidae) host eggs to parasitize for 2–3 weeks, by feeding the parents antibiotics, or by rearing parent wasps at high temperatures; all variables that have been shown to correlate with depleting Wolbachia titers in other organisms. The purpose of the current study was to determine whether thelytoky in O. mirus is due to Wolbachia, and if so, at what time in development the sex change occurs. We also wished to determine if Wolbachia removal results in the production of intersexes, as in some other hymenopterans. Finally, mating behavior was observed to see if and where it breaks down as a result of the species becoming thelytokous. Methods Females were collected from parental lines of O. mirus reared at 26, 30, 31, 32, 33, 34, and 36 °C. The offspring of these females were reared at 26 °C, and their sex-ratio was determined. In a subsequent experiment, the parental generation was switched between 26 °C and 36 °C during development to narrow down the critical period at which changes occurred that subsequently affected the sex-ratio of their offspring. Results The sex ratio was male biased in the offspring of O. mirus parents reared at 34 °C and 36 °C (high temperatures), even if the offspring themselves were reared at 26 °C. The constant temperature at which the percentage of males started to increase after two generations was 31 °C (10% males), rising to 39% males at 33 °C, and 100% males at 34 °C and 36 °C. Lasting more than 2 days, the critical period for the change toward a male biased sex ratio was during…
format: application/pdf
format: text/html
creator: Nancy R. Power
creator: Paul F. Rugman-Jones
creator: Richard Stouthamer
creator: Fatemeh Ganjisaffar
creator: Thomas M. Perring
subject: Developmental Biology
subject: Ecology
subject: Entomology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.13912
publisher: PeerJ Inc.
rights: © 2022 Power et al.
abstract: Background Wolbachia bacteria are estimated to occur in more than half of all insect species. In Hymenoptera, Wolbachia often manipulates its host’s reproduction to its own advantage. Wolbachia is likely the reason that males are rare in the uniparental Ooencyrtus mirus Triapitsyn & Power (Hymenoptera: Encyrtidae). The likelihood of producing male offspring can be increased by giving mothers a continuous supply of Bagrada hilaris (Burmeister) (Heteroptera: Pentatomidae) host eggs to parasitize for 2–3 weeks, by feeding the parents antibiotics, or by rearing parent wasps at high temperatures; all variables that have been shown to correlate with depleting Wolbachia titers in other organisms. The purpose of the current study was to determine whether thelytoky in O. mirus is due to Wolbachia, and if so, at what time in development the sex change occurs. We also wished to determine if Wolbachia removal results in the production of intersexes, as in some other hymenopterans. Finally, mating behavior was observed to see if and where it breaks down as a result of the species becoming thelytokous. Methods Females were collected from parental lines of O. mirus reared at 26, 30, 31, 32, 33, 34, and 36 °C. The offspring of these females were reared at 26 °C, and their sex-ratio was determined. In a subsequent experiment, the parental generation was switched between 26 °C and 36 °C during development to narrow down the critical period at which changes occurred that subsequently affected the sex-ratio of their offspring. Results The sex ratio was male biased in the offspring of O. mirus parents reared at 34 °C and 36 °C (high temperatures), even if the offspring themselves were reared at 26 °C. The constant temperature at which the percentage of males started to increase after two generations was 31 °C (10% males), rising to 39% males at 33 °C, and 100% males at 34 °C and 36 °C. Lasting more than 2 days, the critical period for the change toward a male biased sex ratio was during…
bibliographic citation: Power et al. (2022) High temperature mortality of Wolbachia impacts the sex ratio of the parasitoid Ooencyrtus mirus (Hymenoptera: Encyrtidae). PeerJ 10:e13912 https://doi.org/10.7717/peerj.13912
date submitted: 2021-09-01
date accepted: 2022-07-27
issued: 2022-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Power
  given name: Nancy R.
author list: Agent
  family name: Rugman-Jones
  given name: Paul F.
author list: Agent
  family name: Stouthamer
  given name: Richard
author list: Agent
  family name: Ganjisaffar
  given name: Fatemeh
author list: Agent
  family name: Perring
  given name: Thomas M.
doi: 10.7717/peerj.13912
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-13
copyright: ©2022 Power et al.
attribution name: Power et al.

PTC2 region genotypes counteract Biomphalaria glabrata population differences between M-line and BS90 in resistance to infection by Schistosoma mansoni
type: item
type: AcademicArticle
description: Background Biomphalaria glabrata is a snail intermediate host for Schistosoma mansoni, a trematode responsible for human schistosomiasis. BS90 is one of the most well studied strains of B. glabrata owing to its high resistance to infection by most strains of S. mansoni. An F2 mapping study from 1999 identified two RAPD markers that associated with what appeared to be single-locus, dominant resistance by the BS90 population relative to the susceptible M-line population. One marker cannot be mapped, but the other, OPM-04, maps to within 5 Mb of PTC2, a region we recently showed has a very large effect on resistance within another snail population challenged by the same strain of parasite (PR1). Here we tested the hypothesis that the PTC2 region contains the causal gene/s that explain the iconic resistance of BS90 snails. Methods We used marker-assisted backcrossing to drive the BS90 version of the PTC2 region (+/−~1 Mb on either side) into an M-line (susceptible strain) genetic background, and the M-line version into a BS90 genetic background. We challenged the offspring with PR1-strain schistosomes and tested for effects of allelic variation in the PTC2 region in a common genetic background. Results Relative to M-line haplotypes, the BS90 haplotype actually confers enhanced susceptibility. So we reject our original hypothesis. One possible explanation for our result was that the causal gene linked to OPM-04 is near, but not in the PTC2 block that we introgressed into each line. So we used an F2 cross to independently test the effects of the PTC2 and OPM-04 regions in a randomized genetic background. We confirmed that the BS90 haplotype confers increased susceptibility, and we see a similar, although non-significant effect at OPM-04. We discuss possible reasons why our results differed so dramatically from those of the 1999 study. We also present Pacbio assemblies of the PTC2 and flanking region in BS90 and M-line, compare with previously published PTC2 haplotypes, an…
format: application/pdf
format: text/html
creator: Michael S. Blouin
creator: Stephanie R. Bollmann
creator: Jacob A. Tennessen
subject: Genetics
subject: Genomics
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.13971
publisher: PeerJ Inc.
rights: © 2022 Blouin et al.
abstract: Background Biomphalaria glabrata is a snail intermediate host for Schistosoma mansoni, a trematode responsible for human schistosomiasis. BS90 is one of the most well studied strains of B. glabrata owing to its high resistance to infection by most strains of S. mansoni. An F2 mapping study from 1999 identified two RAPD markers that associated with what appeared to be single-locus, dominant resistance by the BS90 population relative to the susceptible M-line population. One marker cannot be mapped, but the other, OPM-04, maps to within 5 Mb of PTC2, a region we recently showed has a very large effect on resistance within another snail population challenged by the same strain of parasite (PR1). Here we tested the hypothesis that the PTC2 region contains the causal gene/s that explain the iconic resistance of BS90 snails. Methods We used marker-assisted backcrossing to drive the BS90 version of the PTC2 region (+/−~1 Mb on either side) into an M-line (susceptible strain) genetic background, and the M-line version into a BS90 genetic background. We challenged the offspring with PR1-strain schistosomes and tested for effects of allelic variation in the PTC2 region in a common genetic background. Results Relative to M-line haplotypes, the BS90 haplotype actually confers enhanced susceptibility. So we reject our original hypothesis. One possible explanation for our result was that the causal gene linked to OPM-04 is near, but not in the PTC2 block that we introgressed into each line. So we used an F2 cross to independently test the effects of the PTC2 and OPM-04 regions in a randomized genetic background. We confirmed that the BS90 haplotype confers increased susceptibility, and we see a similar, although non-significant effect at OPM-04. We discuss possible reasons why our results differed so dramatically from those of the 1999 study. We also present Pacbio assemblies of the PTC2 and flanking region in BS90 and M-line, compare with previously published PTC2 haplotypes, an…
bibliographic citation: Blouin et al. (2022) PTC2 region genotypes counteract Biomphalaria glabrata population differences between M-line and BS90 in resistance to infection by Schistosoma mansoni. PeerJ 10:e13971 https://doi.org/10.7717/peerj.13971
date submitted: 2022-06-10
date accepted: 2022-08-09
issued: 2022-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blouin
  given name: Michael S.
author list: Agent
  family name: Bollmann
  given name: Stephanie R.
author list: Agent
  family name: Tennessen
  given name: Jacob A.
doi: 10.7717/peerj.13971
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-13
copyright: © 2022 Blouin et al.
attribution name: Blouin et al.

Screening of potential key ferroptosis-related genes in sepsis
type: item
type: AcademicArticle
description: Background Sepsis leads to multiple organ dysfunction caused by a dysregulated host response to infection with a high incidence and mortality. The effect of ferroptosis on the development of sepsis remains unclear. In this study, we aimed to identify the key ferroptosis-related genes involved in sepsis and further explore the potential biological functions of these ferroptosis-related genes in sepsis using bioinformatics analysis. Methods The GSE13904 (from children) and GSE28750 (from adults) datasets were downloaded from the Gene Expression Omnibus (GEO). The ferroptosis-related genes were obtained from the FerrDb database. The ferroptosis-related differentially expressed genes (DEGs) were screened by the limma R package. The DAVID online database or clusterProfiler R package was used for the functional enrichment analysis. Then, the STRING database was used to predict the interactions of proteins, and the CytoHubba plugin of Cytoscape was used to confirm key clustering modules. Then, the miRNAs and lncRNAs associated with the key clustering modules were predicted by miRWalk 2.0 and LncBase v.2 respectively. Finally, we generated a cecal ligation and puncture (CLP) polymicrobial sepsis model in C57 male mice and examined the expression of the mRNAs and noncoding RNAs of interest in peripheral blood leukocytes by PCR during the acute inflammation phase. Results In total, 34 ferroptosis-related DEGs were identified in both adult and pediatric septic patients. These ferroptosis-related DEGs were mainly enriched in inflammatory pathways. Then, a significant clustering module containing eight genes was identified. Among them, the following five genes were closely associated with the MAPK signaling pathway: MAPK14, MAPK8, DUSP1, MAP3K5 and MAPK1. Then, crucial miRNAs and lncRNAs associated with biomarker MAPK-related genes were also identified. In particular, let-7b-5p and NEAT1 were selected as noncoding RNAs of interest because of their correlation with ferroptosis in…
format: application/pdf
format: text/html
creator: Shunan Cui
creator: Kun Niu
creator: Yining Xie
creator: Shuo Li
creator: Wenzhi Zhu
creator: Ling Yu
creator: Hongyu Tan
subject: Bioinformatics
subject: Molecular Biology
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Medical Genetics
description: doi:10.7717/peerj.13983
publisher: PeerJ Inc.
rights: © 2022 Cui et al.
abstract: Background Sepsis leads to multiple organ dysfunction caused by a dysregulated host response to infection with a high incidence and mortality. The effect of ferroptosis on the development of sepsis remains unclear. In this study, we aimed to identify the key ferroptosis-related genes involved in sepsis and further explore the potential biological functions of these ferroptosis-related genes in sepsis using bioinformatics analysis. Methods The GSE13904 (from children) and GSE28750 (from adults) datasets were downloaded from the Gene Expression Omnibus (GEO). The ferroptosis-related genes were obtained from the FerrDb database. The ferroptosis-related differentially expressed genes (DEGs) were screened by the limma R package. The DAVID online database or clusterProfiler R package was used for the functional enrichment analysis. Then, the STRING database was used to predict the interactions of proteins, and the CytoHubba plugin of Cytoscape was used to confirm key clustering modules. Then, the miRNAs and lncRNAs associated with the key clustering modules were predicted by miRWalk 2.0 and LncBase v.2 respectively. Finally, we generated a cecal ligation and puncture (CLP) polymicrobial sepsis model in C57 male mice and examined the expression of the mRNAs and noncoding RNAs of interest in peripheral blood leukocytes by PCR during the acute inflammation phase. Results In total, 34 ferroptosis-related DEGs were identified in both adult and pediatric septic patients. These ferroptosis-related DEGs were mainly enriched in inflammatory pathways. Then, a significant clustering module containing eight genes was identified. Among them, the following five genes were closely associated with the MAPK signaling pathway: MAPK14, MAPK8, DUSP1, MAP3K5 and MAPK1. Then, crucial miRNAs and lncRNAs associated with biomarker MAPK-related genes were also identified. In particular, let-7b-5p and NEAT1 were selected as noncoding RNAs of interest because of their correlation with ferroptosis in…
bibliographic citation: Cui et al. (2022) Screening of potential key ferroptosis-related genes in sepsis. PeerJ 10:e13983 https://doi.org/10.7717/peerj.13983
date submitted: 2022-05-17
date accepted: 2022-08-10
issued: 2022-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Shunan
author list: Agent
  family name: Niu
  given name: Kun
author list: Agent
  family name: Xie
  given name: Yining
author list: Agent
  family name: Li
  given name: Shuo
author list: Agent
  family name: Zhu
  given name: Wenzhi
author list: Agent
  family name: Yu
  given name: Ling
author list: Agent
  family name: Tan
  given name: Hongyu
doi: 10.7717/peerj.13983
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-13
copyright: © 2022 Cui et al.
attribution name: Cui et al.

Moonlighting proteins in medically relevant fungi
type: item
type: AcademicArticle
description: Moonlighting proteins represent an intriguing area of cell biology, due to their ability to perform two or more unrelated functions in one or many cellular compartments. These proteins have been described in all kingdoms of life and are usually constitutively expressed and conserved proteins with housekeeping functions. Although widely studied in pathogenic bacteria, the information about these proteins in pathogenic fungi is scarce, but there are some reports of their functions in the etiological agents of the main human mycoses, such as Candida spp., Paracoccidioides brasiliensis, Histoplasma capsulatum, Aspergillus fumigatus, Cryptococcus neoformans, and Sporothrix schenckii. In these fungi, most of the described moonlighting proteins are metabolic enzymes, such as enolase and glyceraldehyde-3-phosphate dehydrogenase; chaperones, transcription factors, and redox response proteins, such as peroxiredoxin and catalase, which moonlight at the cell surface and perform virulence-related processes, contributing to immune evasion, adhesions, invasion, and dissemination to host cells and tissues. All moonlighting proteins and their functions described in this review highlight the limited information about this biological aspect in pathogenic fungi, representing this a relevant opportunity area that will contribute to expanding our current knowledge of these organisms’ pathogenesis.
format: application/pdf
format: text/html
creator: Verania J. Arvizu-Rubio
creator: Laura C. García-Carnero
creator: Héctor Manuel Mora-Montes
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.14001
publisher: PeerJ Inc.
rights: © 2022 Arvizu-Rubio et al.
abstract: Moonlighting proteins represent an intriguing area of cell biology, due to their ability to perform two or more unrelated functions in one or many cellular compartments. These proteins have been described in all kingdoms of life and are usually constitutively expressed and conserved proteins with housekeeping functions. Although widely studied in pathogenic bacteria, the information about these proteins in pathogenic fungi is scarce, but there are some reports of their functions in the etiological agents of the main human mycoses, such as Candida spp., Paracoccidioides brasiliensis, Histoplasma capsulatum, Aspergillus fumigatus, Cryptococcus neoformans, and Sporothrix schenckii. In these fungi, most of the described moonlighting proteins are metabolic enzymes, such as enolase and glyceraldehyde-3-phosphate dehydrogenase; chaperones, transcription factors, and redox response proteins, such as peroxiredoxin and catalase, which moonlight at the cell surface and perform virulence-related processes, contributing to immune evasion, adhesions, invasion, and dissemination to host cells and tissues. All moonlighting proteins and their functions described in this review highlight the limited information about this biological aspect in pathogenic fungi, representing this a relevant opportunity area that will contribute to expanding our current knowledge of these organisms’ pathogenesis.
bibliographic citation: Arvizu-Rubio et al. (2022) Moonlighting proteins in medically relevant fungi. PeerJ 10:e14001 https://doi.org/10.7717/peerj.14001
date submitted: 2022-07-11
date accepted: 2022-08-13
issued: 2022-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arvizu-Rubio
  given name: Verania J.
author list: Agent
  family name: García-Carnero
  given name: Laura C.
author list: Agent
  family name: Mora-Montes
  given name: Héctor Manuel
doi: 10.7717/peerj.14001
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-13
copyright: © 2022 Arvizu-Rubio et al.
attribution name: Arvizu-Rubio et al.

Effects of establishing cultivated grassland on soil organic carbon fractions in a degraded alpine meadow on the Tibetan Plateau
type: item
type: AcademicArticle
description: Background The degradation of alpine meadows has induced substantial losses of soil organic carbon (SOC) on the Tibetan Plateau. A commonly-used method for rehabilitating degraded alpine meadows in this region is establishing cultivated grasslands through sowing seed mixtures, but its impact on the biochemical stability of SOC has remained inadequately explored. Methods In this study, a total of 20 composited 0-20 cm soil samples were collected from a heavily degraded alpine meadow (DM) and three adjacent cultivated grasslands established for 3 years (CG3), 12 years (CG12), and 17 years (CG17) on the eastern Tibetan Plateau, and the SOC pool was separated into labile C pool I (LOC I), labile C pool II (LOC II), and recalcitrant C pool (ROC) in order to investigate changes in contents of SOC fractions that have different biochemical stabilities after the establishment of cultivated grassland. Results Although the establishment of cultivated grasslands led to increases in soil total organic C content, the increase was only significant in samples with 17 years of cultivation. We found that the contents of the three SOC fractions were higher at CG3 and CG12 compared with those in the DM, and the differences were only significant for soil LOC II. By comparison, 17 years of cultivation led to significant increases in all of the SOC fraction contents. The results implied that different cultivation years had distinct impacts on SOC fractions in cultivated grasslands, and longer cultivation years contributed to accumulated soil ROC. The recalcitrance index of SOC in the DM was higher than that at CG3 and CG12, but lower than that at CG17. This was possibly due to the generally low litter quality of cultivated grasslands, which led to a slow release of complex compounds to soils. Moreover, it was observed that soil C:N ratio was a potential indicator of SOC biochemical stability because of their close correlation. Conclusions Our findings suggest that the long-term establishm…
format: application/pdf
format: text/html
creator: Xiang Liu
creator: Xiaotao Huang
creator: Wenping Qin
creator: Xiaoan Li
creator: Zhiwen Ma
creator: Hongxiao Shi
creator: Lanhai Li
creator: Changzhong Li
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.14012
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Background The degradation of alpine meadows has induced substantial losses of soil organic carbon (SOC) on the Tibetan Plateau. A commonly-used method for rehabilitating degraded alpine meadows in this region is establishing cultivated grasslands through sowing seed mixtures, but its impact on the biochemical stability of SOC has remained inadequately explored. Methods In this study, a total of 20 composited 0-20 cm soil samples were collected from a heavily degraded alpine meadow (DM) and three adjacent cultivated grasslands established for 3 years (CG3), 12 years (CG12), and 17 years (CG17) on the eastern Tibetan Plateau, and the SOC pool was separated into labile C pool I (LOC I), labile C pool II (LOC II), and recalcitrant C pool (ROC) in order to investigate changes in contents of SOC fractions that have different biochemical stabilities after the establishment of cultivated grassland. Results Although the establishment of cultivated grasslands led to increases in soil total organic C content, the increase was only significant in samples with 17 years of cultivation. We found that the contents of the three SOC fractions were higher at CG3 and CG12 compared with those in the DM, and the differences were only significant for soil LOC II. By comparison, 17 years of cultivation led to significant increases in all of the SOC fraction contents. The results implied that different cultivation years had distinct impacts on SOC fractions in cultivated grasslands, and longer cultivation years contributed to accumulated soil ROC. The recalcitrance index of SOC in the DM was higher than that at CG3 and CG12, but lower than that at CG17. This was possibly due to the generally low litter quality of cultivated grasslands, which led to a slow release of complex compounds to soils. Moreover, it was observed that soil C:N ratio was a potential indicator of SOC biochemical stability because of their close correlation. Conclusions Our findings suggest that the long-term establishm…
bibliographic citation: Liu et al. (2022) Effects of establishing cultivated grassland on soil organic carbon fractions in a degraded alpine meadow on the Tibetan Plateau. PeerJ 10:e14012 https://doi.org/10.7717/peerj.14012
date submitted: 2022-04-26
date accepted: 2022-08-15
issued: 2022-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiang
author list: Agent
  family name: Huang
  given name: Xiaotao
author list: Agent
  family name: Qin
  given name: Wenping
author list: Agent
  family name: Li
  given name: Xiaoan
author list: Agent
  family name: Ma
  given name: Zhiwen
author list: Agent
  family name: Shi
  given name: Hongxiao
author list: Agent
  family name: Li
  given name: Lanhai
author list: Agent
  family name: Li
  given name: Changzhong
doi: 10.7717/peerj.14012
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-13
copyright: ©2022 Liu et al.
attribution name: Liu et al.

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