PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis
items: Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe
items: Study on the cultivation of seedlings using buds of potato (Solanum tuberosum L.)
items: Genome-wide identification of the trehalose-6-phosphate synthase gene family in sweet orange (Citrus sinensis) and expression analysis in response to phytohormones and abiotic stresses
items: A retrospective study of real-world effectiveness and safety of rivaroxaban in patients with non-valvular atrial fibrillation and venous thromboembolism in Saudi Arabia

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.

Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis
type: item
type: AcademicArticle
description: Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.
format: application/pdf
format: text/html
creator: Peilun Li
creator: Wei Liu
creator: Wanqiao Lu
creator: Jilong Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.13585
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.
bibliographic citation: Li et al. (2022) Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis. PeerJ 10:e13585 https://doi.org/10.7717/peerj.13585
date submitted: 2021-12-06
date accepted: 2022-05-23
issued: 2022-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Peilun
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Lu
  given name: Wanqiao
author list: Agent
  family name: Wang
  given name: Jilong
doi: 10.7717/peerj.13585
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-12
copyright: © 2022 Li et al.
attribution name: Li et al.

Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe
type: item
type: AcademicArticle
description: Thinning in forest management primarily reduces the density of trees and alters the patchiness and spatial complexity of environmental factors and individual interactions between plant recruits. At fine spatial scales, little is known about the relative weight of ecological processes affecting tree regeneration before and after thinning events. Here we studied the density and aggregation of tree recruits in fully-mapped plots located in mixed forests in Northern Iberian Peninsula (Southern Europe) for over four years, which comprises one year before and three years after a thinning event. We applied spatial point-pattern analyses to examine (a) the aggregation of recruits, and their association with trees and (b) the relative effect of both environmental (i.e., the patchiness of the local environment) and density-dependent factors (i.e., the aggregation of trees and/or recruits) to predict the density, aggregation, and survival of recruits. We found, in thinning plots, that recruits were less dense, their aggregation pattern was more heterogeneous, were distributed randomly in respect of trees and their survival was almost unaffected by the tree proximity. By contrast, recruits in control plots were denser, were only aggregated at distances lower than 1.0 m, were closer to trees, and such closer distance to trees affected negatively in their survival. Independently of the treatment, the aggregation of recruits was chiefly determined by the density-dependent factors at less than 1.0 m and environmental factors at distances beyond that proximity. Overall, our results suggest that thinning affected the aggregation of recruits at two spatial scales: (a) by favoring the tree-recruit and recruit-recruit facilitation at less than 1.0 m and (b) by modifying spatial heterogeneity of the environment at distances beyond that proximity.
format: application/pdf
format: text/html
creator: Javier Rodríguez-Pérez
creator: Bosco Imbert
creator: Javier Peralta
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.13892
publisher: PeerJ Inc.
rights: © 2022 Rodríguez-Pérez et al.
abstract: Thinning in forest management primarily reduces the density of trees and alters the patchiness and spatial complexity of environmental factors and individual interactions between plant recruits. At fine spatial scales, little is known about the relative weight of ecological processes affecting tree regeneration before and after thinning events. Here we studied the density and aggregation of tree recruits in fully-mapped plots located in mixed forests in Northern Iberian Peninsula (Southern Europe) for over four years, which comprises one year before and three years after a thinning event. We applied spatial point-pattern analyses to examine (a) the aggregation of recruits, and their association with trees and (b) the relative effect of both environmental (i.e., the patchiness of the local environment) and density-dependent factors (i.e., the aggregation of trees and/or recruits) to predict the density, aggregation, and survival of recruits. We found, in thinning plots, that recruits were less dense, their aggregation pattern was more heterogeneous, were distributed randomly in respect of trees and their survival was almost unaffected by the tree proximity. By contrast, recruits in control plots were denser, were only aggregated at distances lower than 1.0 m, were closer to trees, and such closer distance to trees affected negatively in their survival. Independently of the treatment, the aggregation of recruits was chiefly determined by the density-dependent factors at less than 1.0 m and environmental factors at distances beyond that proximity. Overall, our results suggest that thinning affected the aggregation of recruits at two spatial scales: (a) by favoring the tree-recruit and recruit-recruit facilitation at less than 1.0 m and (b) by modifying spatial heterogeneity of the environment at distances beyond that proximity.
bibliographic citation: Rodríguez-Pérez et al. (2022) Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe. PeerJ 10:e13892 https://doi.org/10.7717/peerj.13892
date submitted: 2022-01-20
date accepted: 2022-07-22
issued: 2022-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Pérez
  given name: Javier
author list: Agent
  family name: Imbert
  given name: Bosco
author list: Agent
  family name: Peralta
  given name: Javier
doi: 10.7717/peerj.13892
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-12
copyright: ©2022 Rodríguez-Pérez et al.
attribution name: Rodríguez-Pérez et al.

Study on the cultivation of seedlings using buds of potato (Solanum tuberosum L.)
type: item
type: AcademicArticle
description: Background Potato, a vegetable crop grown worldwide, has many uses, a short growth period, a large market demand and high economic benefits. The loss of potato seediness due to traditional potato growing methods is becoming increasingly evident, and research on new ways of growing potatoes is particularly important. Bud planting technology has the advantages of more reproduction, faster growth, and simplified maintenance of crop plants under cultivation. Methods In this study, a bud planting method was adopted for the cultivation of potato seedlings. Specifically, we assessed different types of treatments for the production of high-quality buds and seedlings of potato. A total of four disease-free potato varieties (Fujin, Youjin, Zhongshu 4, and Feiwuruita) were selected, potato buds with three different lengths (3 cm, 5 cm, and 7 cm) were considered the T1, T2, and T3 treatments, and terminal buds, middle buds, and tail buds were used as the T4, T5, and T6 treatments. A nutrient pot experiment was performed following a randomized complete block design (RCBD) with three replicates and a natural control (CK) treatment. Cultivation was performed with the common horticultural practices of weeding and hoeing applied as needed. The photosynthetic indices, physiological indices, growth indices and quality of potato seedlings and quality of potato buds were measured at two-week intervals, and yield indices were measured when the final crop was harvested 14 weeks after planting. Results and Conclusions Cultivation of seedlings from potato buds of different lengths increased the reproduction coefficient and reduced the number of seed potatoes needed for cultivation. All morphological, physiological, and yield indices showed positive trends. A potato bud length of 7 cm was optimal for raising seedlings. Moreover, buds located at the terminal of the potato yielded seedlings with the best quality. In conclusion, we recommend that our proven bud planting technique be adopted at …
format: application/pdf
format: text/html
creator: Chaonan Wang
creator: Chong Du
creator: Zhongmin Yang
creator: Huilin Wang
creator: Leijuan Shang
creator: Lili Liu
creator: Zhiyi Yang
creator: Shuyao Song
creator: Sikandar Amanullah
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.13804
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Potato, a vegetable crop grown worldwide, has many uses, a short growth period, a large market demand and high economic benefits. The loss of potato seediness due to traditional potato growing methods is becoming increasingly evident, and research on new ways of growing potatoes is particularly important. Bud planting technology has the advantages of more reproduction, faster growth, and simplified maintenance of crop plants under cultivation. Methods In this study, a bud planting method was adopted for the cultivation of potato seedlings. Specifically, we assessed different types of treatments for the production of high-quality buds and seedlings of potato. A total of four disease-free potato varieties (Fujin, Youjin, Zhongshu 4, and Feiwuruita) were selected, potato buds with three different lengths (3 cm, 5 cm, and 7 cm) were considered the T1, T2, and T3 treatments, and terminal buds, middle buds, and tail buds were used as the T4, T5, and T6 treatments. A nutrient pot experiment was performed following a randomized complete block design (RCBD) with three replicates and a natural control (CK) treatment. Cultivation was performed with the common horticultural practices of weeding and hoeing applied as needed. The photosynthetic indices, physiological indices, growth indices and quality of potato seedlings and quality of potato buds were measured at two-week intervals, and yield indices were measured when the final crop was harvested 14 weeks after planting. Results and Conclusions Cultivation of seedlings from potato buds of different lengths increased the reproduction coefficient and reduced the number of seed potatoes needed for cultivation. All morphological, physiological, and yield indices showed positive trends. A potato bud length of 7 cm was optimal for raising seedlings. Moreover, buds located at the terminal of the potato yielded seedlings with the best quality. In conclusion, we recommend that our proven bud planting technique be adopted at …
bibliographic citation: Wang et al. (2022) Study on the cultivation of seedlings using buds of potato (Solanum tuberosum L.). PeerJ 10:e13804 https://doi.org/10.7717/peerj.13804
date submitted: 2021-12-27
date accepted: 2022-07-07
issued: 2022-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chaonan
author list: Agent
  family name: Du
  given name: Chong
author list: Agent
  family name: Yang
  given name: Zhongmin
author list: Agent
  family name: Wang
  given name: Huilin
author list: Agent
  family name: Shang
  given name: Leijuan
author list: Agent
  family name: Liu
  given name: Lili
author list: Agent
  family name: Yang
  given name: Zhiyi
author list: Agent
  family name: Song
  given name: Shuyao
author list: Agent
  family name: Amanullah
  given name: Sikandar
doi: 10.7717/peerj.13804
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-09
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Genome-wide identification of the trehalose-6-phosphate synthase gene family in sweet orange (Citrus sinensis) and expression analysis in response to phytohormones and abiotic stresses
type: item
type: AcademicArticle
description: Background Trehalose-6-phosphate synthase (TPS) is an essential enzyme for synthesizing trehalose and is a significant regulator of plant development and stress response. Sweet orange (Citrus sinensis) is an economically important fruit tree crop and a common transgenic material. At present, little information is available about the TPS gene family in sweet orange. Methods The TPS gene family were identified from sweet orange genome by bioinformatics analysis. Additionally, the expression of CisTPS genes was analyzed under phytohormones and abiotic stresses by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). Results Here, eight TPS genes were identified and were found to be randomly distributed in five sweet orange chromosomes. TPS and trehalose-6-phosphate phosphatase (TPP) domains were observed in all CisTPS proteins. The phylogenetic tree showed that CisTPS genes were divided into two subfamilies, and genes in each subfamily had conserved intron structures and motif compositions. The cis-acting elements of CisTPS genes suggested their roles in phytohormone and stress responses. All CisTPS genes were ubiquitously expressed in roots, leaves, and stems, and six members were highly expressed in roots. Expression profiles showed that CisTPS genes exhibited tissue specificity and were differentially expressed in response to phytohormones and abiotic stresses. This study lays a foundation for revealing the functions of the TPS gene family in trehalose regulation in sweet orange, and provides a valuable reference for this gene family in other plants.
format: application/pdf
format: text/html
creator: Kehong Liu
creator: Yan Zhou
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13934
publisher: PeerJ Inc.
rights: © 2022 Liu and Zhou
abstract: Background Trehalose-6-phosphate synthase (TPS) is an essential enzyme for synthesizing trehalose and is a significant regulator of plant development and stress response. Sweet orange (Citrus sinensis) is an economically important fruit tree crop and a common transgenic material. At present, little information is available about the TPS gene family in sweet orange. Methods The TPS gene family were identified from sweet orange genome by bioinformatics analysis. Additionally, the expression of CisTPS genes was analyzed under phytohormones and abiotic stresses by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). Results Here, eight TPS genes were identified and were found to be randomly distributed in five sweet orange chromosomes. TPS and trehalose-6-phosphate phosphatase (TPP) domains were observed in all CisTPS proteins. The phylogenetic tree showed that CisTPS genes were divided into two subfamilies, and genes in each subfamily had conserved intron structures and motif compositions. The cis-acting elements of CisTPS genes suggested their roles in phytohormone and stress responses. All CisTPS genes were ubiquitously expressed in roots, leaves, and stems, and six members were highly expressed in roots. Expression profiles showed that CisTPS genes exhibited tissue specificity and were differentially expressed in response to phytohormones and abiotic stresses. This study lays a foundation for revealing the functions of the TPS gene family in trehalose regulation in sweet orange, and provides a valuable reference for this gene family in other plants.
bibliographic citation: Liu et al. (2022) Genome-wide identification of the trehalose-6-phosphate synthase gene family in sweet orange (Citrus sinensis) and expression analysis in response to phytohormones and abiotic stresses. PeerJ 10:e13934 https://doi.org/10.7717/peerj.13934
date submitted: 2022-05-11
date accepted: 2022-08-01
issued: 2022-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Kehong
author list: Agent
  family name: Zhou
  given name: Yan
doi: 10.7717/peerj.13934
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-09
copyright: ©2022 Liu and Zhou
attribution name: Liu and Zhou

A retrospective study of real-world effectiveness and safety of rivaroxaban in patients with non-valvular atrial fibrillation and venous thromboembolism in Saudi Arabia
type: item
type: AcademicArticle
description: Background Real-world evidence on factor Xa inhibitor (rivaroxaban) prescribing patterns, safety, and efficacy in patients with non-valvular atrial fibrillation (NVAF) and venous thromboembolism (VTE) is rare. Herein, we sought to examine the above outcomes in the largest academic center in the Kingdom of Saudi Arabia (KSA). Methods This is a retrospective observational study designed to examine the prescribing pattern, safety and real-world effectiveness of the factor Xa inhibitor rivaroxaban in patients with NVAF and VTE. Data on rivaroxaban prescriptions were collected and analyzed. Bleeding outcomes were defined as per the International Society on Thrombosis and Hemostasis (ISTH) definition. Results A total of 2,316 patients taking rivaroxaban recruited through several departments of King Saud University Medical City (KSUMC). The mean age was 61 years (±17.8) with 55% above the age of 60 and 58% were females. Deep vein thrombosis and pulmonary embolism (VTE) was the most prevalent reason for prescribing rivaroxaban, followed by NVAF. A total daily dosage of 15 mg was given to 23% of the patients. The incidence rate of recurrent thrombosis and recurrent stroke was 0.2%. Furthermore, rivaroxaban had a 0.04 percent incidence rate of myocardial infarction. Half of the patients with recurrent thrombosis and stroke were taking 15 mg per day. The incidence rate of major bleeding was 1.1%. More over half of the patients who experienced significant bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score (>2 score), 48 percent of patients who experienced significant bleeding had a high risk of bleeding. Non-major bleeding occurred in 0.6% of cases. Similarly, 40% of patients with non-major bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score, just 6.6% of these individuals had a high risk of bleeding. 93.4% of the patients, on the other hand, were at intermediate risk. Conclusion The prescrip…
format: application/pdf
format: text/html
creator: Hind M. Alosaimi
creator: Saeed Alqahtani
creator: Bander Balkhi
creator: Mishari Alqahtani
creator: Faisal Alzamil
creator: Abdulaziz Alhossan
creator: Fatmah S. Alqahtany
creator: Abdullah A. Alharbi
creator: Nawaf Abdullah Alqahtani
creator: Hanan Albackr
creator: Ghada Elgohary
creator: Farjah H. Algahtani
subject: Cardiology
subject: Drugs and Devices
subject: Hematology
description: doi:10.7717/peerj.13974
publisher: PeerJ Inc.
rights: © 2022 Alosaimi et al.
abstract: Background Real-world evidence on factor Xa inhibitor (rivaroxaban) prescribing patterns, safety, and efficacy in patients with non-valvular atrial fibrillation (NVAF) and venous thromboembolism (VTE) is rare. Herein, we sought to examine the above outcomes in the largest academic center in the Kingdom of Saudi Arabia (KSA). Methods This is a retrospective observational study designed to examine the prescribing pattern, safety and real-world effectiveness of the factor Xa inhibitor rivaroxaban in patients with NVAF and VTE. Data on rivaroxaban prescriptions were collected and analyzed. Bleeding outcomes were defined as per the International Society on Thrombosis and Hemostasis (ISTH) definition. Results A total of 2,316 patients taking rivaroxaban recruited through several departments of King Saud University Medical City (KSUMC). The mean age was 61 years (±17.8) with 55% above the age of 60 and 58% were females. Deep vein thrombosis and pulmonary embolism (VTE) was the most prevalent reason for prescribing rivaroxaban, followed by NVAF. A total daily dosage of 15 mg was given to 23% of the patients. The incidence rate of recurrent thrombosis and recurrent stroke was 0.2%. Furthermore, rivaroxaban had a 0.04 percent incidence rate of myocardial infarction. Half of the patients with recurrent thrombosis and stroke were taking 15 mg per day. The incidence rate of major bleeding was 1.1%. More over half of the patients who experienced significant bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score (>2 score), 48 percent of patients who experienced significant bleeding had a high risk of bleeding. Non-major bleeding occurred in 0.6% of cases. Similarly, 40% of patients with non-major bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score, just 6.6% of these individuals had a high risk of bleeding. 93.4% of the patients, on the other hand, were at intermediate risk. Conclusion The prescrip…
bibliographic citation: Alosaimi et al. (2022) A retrospective study of real-world effectiveness and safety of rivaroxaban in patients with non-valvular atrial fibrillation and venous thromboembolism in Saudi Arabia. PeerJ 10:e13974 https://doi.org/10.7717/peerj.13974
date submitted: 2022-02-28
date accepted: 2022-08-09
issued: 2022-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alosaimi
  given name: Hind M.
author list: Agent
  family name: Alqahtani
  given name: Saeed
author list: Agent
  family name: Balkhi
  given name: Bander
author list: Agent
  family name: Alqahtani
  given name: Mishari
author list: Agent
  family name: Alzamil
  given name: Faisal
author list: Agent
  family name: Alhossan
  given name: Abdulaziz
author list: Agent
  family name: Alqahtany
  given name: Fatmah S.
author list: Agent
  family name: Alharbi
  given name: Abdullah A.
author list: Agent
  family name: Alqahtani
  given name: Nawaf Abdullah
author list: Agent
  family name: Albackr
  given name: Hanan
author list: Agent
  family name: Elgohary
  given name: Ghada
author list: Agent
  family name: Algahtani
  given name: Farjah H.
doi: 10.7717/peerj.13974
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-09
copyright: © 2022 Alosaimi et al.
attribution name: Alosaimi et al.

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