PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Blood glucose, insulin and glycogen profiles in Sprague-Dawley rats co-infected with Plasmodium berghei ANKA and Trichinella zimbabwensis
items: Screening of ferroptosis-related genes in sepsis-induced liver failure and analysis of immune correlation
items: LncRNA/miRNA/mRNA ceRNA network analysis in spinal cord injury rat with physical exercise therapy
items: Algae from Aiptasia egesta are robust representations of Symbiodiniaceae in the free-living state
items: Baseline scenarios of heat-related ambulance transportations under climate change in Tokyo, Japan
items: Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity
items: Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
items: Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region)
items: Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings
items: Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity

Blood glucose, insulin and glycogen profiles in Sprague-Dawley rats co-infected with Plasmodium berghei ANKA and Trichinella zimbabwensis
type: item
type: AcademicArticle
description: Background Plasmodium falciparum and tissue dwelling helminth parasites are endemic in sub-Saharan Africa (SSA). The geographical overlap in co-infection is a common phenomenon. However, there is continued paucity of information on how the co-infection influence the blood glucose and insulin profiles in the infected host. Animal models are ideal to elucidate effects of co-infection on disease outcomes and hence, blood glucose, insulin and glycogen profiles were assessed in Sprague-Dawley rats co-infected with P. berghei ANKA (Pb) and Trichinella zimbabwensis (Tz), a tissue-dwelling nematode. Methods One-hundred-and-sixty-eight male Sprague-Dawley rats (weight range 90–150 g) were randomly divided into four separate experimental groups: Control (n = 42), Pb-infected (n = 42), Tz-infected (n = 42) and Pb- + Tz-infected group (n = 42). Measurement of Pb parasitaemia was done daily throughout the experimental study period for the Pb and the Pb + Tz group. Blood glucose was recorded every third day in all experimental groups throughout the experimental study period. Liver and skeletal muscle samples were harvested, snap frozen for determination of glycogen concentration. Results Results showed that Tz mono-infection and Tz + Pb co-infection did not have blood glucose lowering effect in the host as expected. This points to other possible mechanisms through which tissue-dwelling parasites up-regulate the glucose store without decreasing the blood glucose concentration as exhibited by the absence of hypoglycaemia in Tz + Pb co-infection group. Hypoinsulinemia and an increase in liver glycogen content was observed in Tz mono-infection and Tz + Pb co-infection groups of which the triggering mechanism remains unclear. Conclusions To get more insights into how glucose, insulin and glycogen profiles are affected during plasmodium-helminths co-infections, further studies are recommended where other tissue-dwelling helminths such as Taenia taeniformis which has strobilocercus as t…
format: application/pdf
format: text/html
creator: Pretty Murambiwa
creator: Achasih Quinta Nkemzi
creator: Samson Mukaratirwa
subject: Biochemistry
subject: Parasitology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.13713
publisher: PeerJ Inc.
rights: © 2022 Murambiwa et al.
abstract: Background Plasmodium falciparum and tissue dwelling helminth parasites are endemic in sub-Saharan Africa (SSA). The geographical overlap in co-infection is a common phenomenon. However, there is continued paucity of information on how the co-infection influence the blood glucose and insulin profiles in the infected host. Animal models are ideal to elucidate effects of co-infection on disease outcomes and hence, blood glucose, insulin and glycogen profiles were assessed in Sprague-Dawley rats co-infected with P. berghei ANKA (Pb) and Trichinella zimbabwensis (Tz), a tissue-dwelling nematode. Methods One-hundred-and-sixty-eight male Sprague-Dawley rats (weight range 90–150 g) were randomly divided into four separate experimental groups: Control (n = 42), Pb-infected (n = 42), Tz-infected (n = 42) and Pb- + Tz-infected group (n = 42). Measurement of Pb parasitaemia was done daily throughout the experimental study period for the Pb and the Pb + Tz group. Blood glucose was recorded every third day in all experimental groups throughout the experimental study period. Liver and skeletal muscle samples were harvested, snap frozen for determination of glycogen concentration. Results Results showed that Tz mono-infection and Tz + Pb co-infection did not have blood glucose lowering effect in the host as expected. This points to other possible mechanisms through which tissue-dwelling parasites up-regulate the glucose store without decreasing the blood glucose concentration as exhibited by the absence of hypoglycaemia in Tz + Pb co-infection group. Hypoinsulinemia and an increase in liver glycogen content was observed in Tz mono-infection and Tz + Pb co-infection groups of which the triggering mechanism remains unclear. Conclusions To get more insights into how glucose, insulin and glycogen profiles are affected during plasmodium-helminths co-infections, further studies are recommended where other tissue-dwelling helminths such as Taenia taeniformis which has strobilocercus as t…
bibliographic citation: Murambiwa et al. (2022) Blood glucose, insulin and glycogen profiles in Sprague-Dawley rats co-infected with Plasmodium berghei ANKA and Trichinella zimbabwensis. PeerJ 10:e13713 https://doi.org/10.7717/peerj.13713
date submitted: 2022-03-02
date accepted: 2022-06-21
issued: 2022-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murambiwa
  given name: Pretty
author list: Agent
  family name: Nkemzi
  given name: Achasih Quinta
author list: Agent
  family name: Mukaratirwa
  given name: Samson
doi: 10.7717/peerj.13713
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-29
copyright: ©2022 Murambiwa et al.
attribution name: Murambiwa et al.

Screening of ferroptosis-related genes in sepsis-induced liver failure and analysis of immune correlation
type: item
type: AcademicArticle
description: Purpose Sepsis-induced liver failure is a kind of liver injury with a high mortality, and ferroptosis plays a key role in this disease. Our research aims to screen ferroptosis-related genes in sepsis-induced liver failure as targeted therapy for patients with liver failure. Methods Using the limma software, we analyzed the differentially expressed genes (DEGs) in the GSE60088 dataset downloaded from the Gene Expression Omnibus (GEO) database. Clusterprofiler was applied for enrichment analysis of DEGs enrichment function. Then, the ferroptosis-related genes of the mice in the FerrDb database were crossed with DEGs. Sepsis mice model were prepared by cecal ligation and perforation (CLP). ALT and AST in the serum of mice were measured using detection kit. The pathological changes of the liver tissues in mice were observed by hematoxylin-eosin (H & E) staining. We detected the apoptosis of mice liver tissues using TUNEL. The expression of Hmox1, Epas1, Sirt1, Slc3a2, Jun, Plin2 and Zfp36 were detected by qRT-PCR. Results DEGs analysis showed 136 up-regulated and 45 down-regulated DEGs. Meanwhile, we found that the up-regulated DEGs were enriched in pathways including the cytokine biosynthesis process while the down-regulated DEGs were enriched in pathways such as organic hydroxy compound metabolic process. In this study, seven genes (Hmox1, Epas1, Sirt1, Slc3a2, Jun, Plin2 and Zfp36) were obtained through the intersection of FerrDb database and DEGs. However, immune infiltration analysis revealed that ferroptosis-related genes may promote the development of liver failure through B cells and natural killer (NK) cells. Finally, it was confirmed by the construction of septic liver failure mice model that ferroptosis-related genes of Hmox1, Slc3a2, Jun and Zfp36 were significantly correlated with liver failure and were highly expressed. Conclusion The identification of ferroptosis-related genes Hmox1, Slc3a2, Jun and Zfp36 in the present study contribute to our understandi…
format: application/pdf
format: text/html
creator: Qingli Chen
creator: Luxiang Liu
creator: Shuangling Ni
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.13757
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Purpose Sepsis-induced liver failure is a kind of liver injury with a high mortality, and ferroptosis plays a key role in this disease. Our research aims to screen ferroptosis-related genes in sepsis-induced liver failure as targeted therapy for patients with liver failure. Methods Using the limma software, we analyzed the differentially expressed genes (DEGs) in the GSE60088 dataset downloaded from the Gene Expression Omnibus (GEO) database. Clusterprofiler was applied for enrichment analysis of DEGs enrichment function. Then, the ferroptosis-related genes of the mice in the FerrDb database were crossed with DEGs. Sepsis mice model were prepared by cecal ligation and perforation (CLP). ALT and AST in the serum of mice were measured using detection kit. The pathological changes of the liver tissues in mice were observed by hematoxylin-eosin (H & E) staining. We detected the apoptosis of mice liver tissues using TUNEL. The expression of Hmox1, Epas1, Sirt1, Slc3a2, Jun, Plin2 and Zfp36 were detected by qRT-PCR. Results DEGs analysis showed 136 up-regulated and 45 down-regulated DEGs. Meanwhile, we found that the up-regulated DEGs were enriched in pathways including the cytokine biosynthesis process while the down-regulated DEGs were enriched in pathways such as organic hydroxy compound metabolic process. In this study, seven genes (Hmox1, Epas1, Sirt1, Slc3a2, Jun, Plin2 and Zfp36) were obtained through the intersection of FerrDb database and DEGs. However, immune infiltration analysis revealed that ferroptosis-related genes may promote the development of liver failure through B cells and natural killer (NK) cells. Finally, it was confirmed by the construction of septic liver failure mice model that ferroptosis-related genes of Hmox1, Slc3a2, Jun and Zfp36 were significantly correlated with liver failure and were highly expressed. Conclusion The identification of ferroptosis-related genes Hmox1, Slc3a2, Jun and Zfp36 in the present study contribute to our understandi…
bibliographic citation: Chen et al. (2022) Screening of ferroptosis-related genes in sepsis-induced liver failure and analysis of immune correlation. PeerJ 10:e13757 https://doi.org/10.7717/peerj.13757
date submitted: 2022-02-08
date accepted: 2022-06-29
issued: 2022-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qingli
author list: Agent
  family name: Liu
  given name: Luxiang
author list: Agent
  family name: Ni
  given name: Shuangling
doi: 10.7717/peerj.13757
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-29
copyright: ©2022 Chen et al.
attribution name: Chen et al.

LncRNA/miRNA/mRNA ceRNA network analysis in spinal cord injury rat with physical exercise therapy
type: item
type: AcademicArticle
description: Noncoding RNAs have been implicated in the pathophysiology of spinal cord injury (SCI), including cell death, glial scar formation, axonal collapse and demyelination, and inflammation. The evidence suggests that exercise therapy is just as effective as medical treatment in SCI. However, studies of competing endogenous RNA (ceRNA)-mediated regulation mechanisms in the therapy of SCI with exercise are rare. The focus of this research was to investigate the effect of exercise therapy on the expression levels of long noncoding RNA (lncRNA), microRNA (miRNA), and mRNA in rats with SCI. The RNA-seq technology has been used to examine the differentially expressed circRNAs (DECs), lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between SCI and exercise therapy rats. The ceRNA network was established using interactions between miRNAs and mRNAs, as well as between miRNAs and lncRNAs/circRNAs. The Database for Annotation, Visualization, and Integrated Discovery was used to anticipate the underlying functions of mRNAs. Our current study identified 76 DELs, 33 DEMs, and 30 DEGs between groups of SCI rats and exercise therapy rats. Subsequently, these newly discovered ceRNA interaction axes could be important targets for the exercise treatment of SCI.
format: application/pdf
format: text/html
creator: Jiahuan Wu
creator: Xiangzhe Li
creator: Qinghua Wang
creator: Sheng Wang
creator: Wenhua He
creator: Qinfeng Wu
creator: Chuanming Dong
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Neuroscience
subject: Sports Medicine
description: doi:10.7717/peerj.13783
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Noncoding RNAs have been implicated in the pathophysiology of spinal cord injury (SCI), including cell death, glial scar formation, axonal collapse and demyelination, and inflammation. The evidence suggests that exercise therapy is just as effective as medical treatment in SCI. However, studies of competing endogenous RNA (ceRNA)-mediated regulation mechanisms in the therapy of SCI with exercise are rare. The focus of this research was to investigate the effect of exercise therapy on the expression levels of long noncoding RNA (lncRNA), microRNA (miRNA), and mRNA in rats with SCI. The RNA-seq technology has been used to examine the differentially expressed circRNAs (DECs), lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between SCI and exercise therapy rats. The ceRNA network was established using interactions between miRNAs and mRNAs, as well as between miRNAs and lncRNAs/circRNAs. The Database for Annotation, Visualization, and Integrated Discovery was used to anticipate the underlying functions of mRNAs. Our current study identified 76 DELs, 33 DEMs, and 30 DEGs between groups of SCI rats and exercise therapy rats. Subsequently, these newly discovered ceRNA interaction axes could be important targets for the exercise treatment of SCI.
bibliographic citation: Wu et al. (2022) LncRNA/miRNA/mRNA ceRNA network analysis in spinal cord injury rat with physical exercise therapy. PeerJ 10:e13783 https://doi.org/10.7717/peerj.13783
date submitted: 2022-03-30
date accepted: 2022-07-05
issued: 2022-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Jiahuan
author list: Agent
  family name: Li
  given name: Xiangzhe
author list: Agent
  family name: Wang
  given name: Qinghua
author list: Agent
  family name: Wang
  given name: Sheng
author list: Agent
  family name: He
  given name: Wenhua
author list: Agent
  family name: Wu
  given name: Qinfeng
author list: Agent
  family name: Dong
  given name: Chuanming
doi: 10.7717/peerj.13783
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-29
copyright: ©2022 Wu et al.
attribution name: Wu et al.

Algae from Aiptasia egesta are robust representations of Symbiodiniaceae in the free-living state
type: item
type: AcademicArticle
description: Many cnidarians rely on their dinoflagellate partners from the family Symbiodiniaceae for their ecological success. Symbiotic species of Symbiodiniaceae have two distinct life stages: inside the host, in hospite, and outside the host, ex hospite. Several aspects of cnidarian-algal symbiosis can be understood by comparing these two life stages. Most commonly, algae in culture are used in comparative studies to represent the ex hospite life stage, however, nutrition becomes a confounding variable for this comparison because algal culture media is nutrient rich, while algae in hospite are sampled from hosts maintained in oligotrophic seawater. In contrast to cultured algae, expelled algae may be a more robust representation of the ex hospite state, as the host and expelled algae are in the same seawater environment, removing differences in culture media as a confounding variable. Here, we studied the physiology of algae released from the sea anemone Exaiptasia diaphana (commonly called Aiptasia), a model system for the study of coral-algal symbiosis. In Aiptasia, algae are released in distinct pellets, referred to as egesta, and we explored its potential as an experimental system to represent Symbiodiniaceae in the ex hospite state. Observation under confocal and differential interference contrast microscopy revealed that egesta contained discharged nematocysts, host tissue, and were populated by a diversity of microbes, including protists and cyanobacteria. Further experiments revealed that egesta were released at night. In addition, algae in egesta had a higher mitotic index than algae in hospite, were photosynthetically viable for at least 48 hrs after expulsion, and could competently establish symbiosis with aposymbiotic Aiptasia. We then studied the gene expression of nutrient-related genes and studied their expression using qPCR. From the genes tested, we found that algae from egesta closely mirrored gene expression profiles of algae in hospite and were dissimila…
format: application/pdf
format: text/html
creator: Shumpei Maruyama
creator: Julia R. Unsworth
creator: Valeri Sawiccy
creator: Virginia M. Weis
subject: Cell Biology
subject: Marine Biology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.13796
publisher: PeerJ Inc.
rights: © 2022 Maruyama et al.
abstract: Many cnidarians rely on their dinoflagellate partners from the family Symbiodiniaceae for their ecological success. Symbiotic species of Symbiodiniaceae have two distinct life stages: inside the host, in hospite, and outside the host, ex hospite. Several aspects of cnidarian-algal symbiosis can be understood by comparing these two life stages. Most commonly, algae in culture are used in comparative studies to represent the ex hospite life stage, however, nutrition becomes a confounding variable for this comparison because algal culture media is nutrient rich, while algae in hospite are sampled from hosts maintained in oligotrophic seawater. In contrast to cultured algae, expelled algae may be a more robust representation of the ex hospite state, as the host and expelled algae are in the same seawater environment, removing differences in culture media as a confounding variable. Here, we studied the physiology of algae released from the sea anemone Exaiptasia diaphana (commonly called Aiptasia), a model system for the study of coral-algal symbiosis. In Aiptasia, algae are released in distinct pellets, referred to as egesta, and we explored its potential as an experimental system to represent Symbiodiniaceae in the ex hospite state. Observation under confocal and differential interference contrast microscopy revealed that egesta contained discharged nematocysts, host tissue, and were populated by a diversity of microbes, including protists and cyanobacteria. Further experiments revealed that egesta were released at night. In addition, algae in egesta had a higher mitotic index than algae in hospite, were photosynthetically viable for at least 48 hrs after expulsion, and could competently establish symbiosis with aposymbiotic Aiptasia. We then studied the gene expression of nutrient-related genes and studied their expression using qPCR. From the genes tested, we found that algae from egesta closely mirrored gene expression profiles of algae in hospite and were dissimila…
bibliographic citation: Maruyama et al. (2022) Algae from Aiptasia egesta are robust representations of Symbiodiniaceae in the free-living state. PeerJ 10:e13796 https://doi.org/10.7717/peerj.13796
date submitted: 2022-04-21
date accepted: 2022-07-06
issued: 2022-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maruyama
  given name: Shumpei
author list: Agent
  family name: Unsworth
  given name: Julia R.
author list: Agent
  family name: Sawiccy
  given name: Valeri
author list: Agent
  family name: Weis
  given name: Virginia M.
doi: 10.7717/peerj.13796
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-29
copyright: ©2022 Maruyama et al.
attribution name: Maruyama et al.

Baseline scenarios of heat-related ambulance transportations under climate change in Tokyo, Japan
type: item
type: AcademicArticle
description: Background Predictive scenarios of heatstroke over the long-term future have yet to be formulated. The purpose of the present study was to generate baseline scenarios of heat-related ambulance transportations using climate change scenario datasets in Tokyo, Japan. Methods Data on the number of heat-related ambulance transportations in Tokyo from 2015 to 2019 were examined, and the relationship between the risk of heat-related ambulance transportations and the daily maximum wet-bulb globe temperature (WBGT) was modeled using three simple dose–response models. To quantify the risk of heatstroke, future climatological variables were then retrieved to compute the WBGT up to the year 2100 from climate change scenarios (i.e., RCP2.6, RCP4.5, and RCP8.5) using two scenario models. The predicted risk of heat-related ambulance transportations was embedded onto the future age-specific projected population. Results The proportion of the number of days with a WBGT above 28°C is predicted to increase every five years by 0.16% for RCP2.6, 0.31% for RCP4.5, and 0.68% for RCP8.5. In 2100, compared with 2000, the number of heat-related ambulance transportations is predicted to be more than three times greater among people aged 0–64 years and six times greater among people aged 65 years or older. The variance of the heatstroke risk becomes greater as the WBGT increases. Conclusions The increased risk of heatstroke for the long-term future was demonstrated using a simple statistical approach. Even with the RCP2.6 scenario, with the mildest impact of global warming, the risk of heatstroke is expected to increase. The future course of heatstroke predicted by our approach acts as a baseline for future studies.
format: application/pdf
format: text/html
creator: Marie Fujimoto
creator: Hiroshi Nishiura
subject: Emergency and Critical Care
subject: Public Health
subject: Environmental Health
subject: Healthcare Services
description: doi:10.7717/peerj.13838
publisher: PeerJ Inc.
rights: © 2022 Fujimoto and Nishiura
abstract: Background Predictive scenarios of heatstroke over the long-term future have yet to be formulated. The purpose of the present study was to generate baseline scenarios of heat-related ambulance transportations using climate change scenario datasets in Tokyo, Japan. Methods Data on the number of heat-related ambulance transportations in Tokyo from 2015 to 2019 were examined, and the relationship between the risk of heat-related ambulance transportations and the daily maximum wet-bulb globe temperature (WBGT) was modeled using three simple dose–response models. To quantify the risk of heatstroke, future climatological variables were then retrieved to compute the WBGT up to the year 2100 from climate change scenarios (i.e., RCP2.6, RCP4.5, and RCP8.5) using two scenario models. The predicted risk of heat-related ambulance transportations was embedded onto the future age-specific projected population. Results The proportion of the number of days with a WBGT above 28°C is predicted to increase every five years by 0.16% for RCP2.6, 0.31% for RCP4.5, and 0.68% for RCP8.5. In 2100, compared with 2000, the number of heat-related ambulance transportations is predicted to be more than three times greater among people aged 0–64 years and six times greater among people aged 65 years or older. The variance of the heatstroke risk becomes greater as the WBGT increases. Conclusions The increased risk of heatstroke for the long-term future was demonstrated using a simple statistical approach. Even with the RCP2.6 scenario, with the mildest impact of global warming, the risk of heatstroke is expected to increase. The future course of heatstroke predicted by our approach acts as a baseline for future studies.
bibliographic citation: Fujimoto et al. (2022) Baseline scenarios of heat-related ambulance transportations under climate change in Tokyo, Japan. PeerJ 10:e13838 https://doi.org/10.7717/peerj.13838
date submitted: 2022-05-10
date accepted: 2022-07-13
issued: 2022-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fujimoto
  given name: Marie
author list: Agent
  family name: Nishiura
  given name: Hiroshi
doi: 10.7717/peerj.13838
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-29
copyright: ©2022 Fujimoto and Nishiura
attribution name: Fujimoto and Nishiura

Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity
type: item
type: AcademicArticle
description: Background The Sultanate of Oman is country a low TB-incidence, with less than seven cases per 105 population detected in 2020. Recent years have witnessed a persistence in TB cases, with sustained incidence rate among expatriates and limited reduction among Omanis. This pattern suggests transmission from the migrant population. The present study examined the genetic profile and drug resistance-conferring mutations in Mycobacterium tuberculosis collected from Omanis and expatriates to recognise possible causes of disease transmission. Methods We examined M. tuberculosis cultured positive samples, collected from Omanis (n = 1,344) and expatriates (n = 1,203) between 2009 and 2018. These isolates had a known in vitro susceptibility profile to first line anti-TB, Streptomycin (SM), Isoniazid (INH), Rifampicin (RIF), Ethambutol (EMB) and Pyrazinamide (PZA). The diversity of the isolates was assessed by spacer oligo-typing (spoligotyping). Drug resistance-conferring mutations resulted from full-length sequence of nine genes (katG, inhA, ahpc, rpoB, rpsL, rrs, embB, embC, pncA) and their phenotypic relationship were analysed. Results In total, 341/2192 (13.4%), M. tuberculosis strains showed resistance to any drug, comprising mono-resistance (MR) (242, 71%), poly-resistance (PR) (40, 11.7%) and multi-drug resistance (MDR) (59, 17.3%). The overall rate of resistance among Omanis and expatriates was similar; however, MDR and PZAR were significantly higher among Omanis, while INHR was greater among expatriates. Mutations rpsL K43R and rpoB S450L were linked to Streptomycin (SMR) and Rifampicin resistance (RIFR) respectively. Whereas, katG S315T and inhA –C15T/G–17T were associated with Isoniazid resistance (INHR). The resistance patterns (mono-resistant, poly-resistant and MDR) and drug resistance-conferring mutations were found in different spoligo-lineages. rpsL K43R, katG S315T and rpoB S450L mutations were significantly higher in Beijing strains. Conclusions Diverse drug…
format: application/pdf
format: text/html
creator: Sara Al Mahrouqi
creator: Amal Gadalla
creator: Saleh Al Azri
creator: Salama Al-Hamidhi
creator: Amina Al-Jardani
creator: Abdullah Balkhair
creator: Amira Al-fahdi
creator: Laila Al Balushi
creator: Samiya Al Zadjali
creator: Asmahan Mohammed Nasser Al Marhoubi
creator: Hamza A. Babiker
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.13645
publisher: PeerJ Inc.
rights: © 2022 Al Mahrouqi et al.
abstract: Background The Sultanate of Oman is country a low TB-incidence, with less than seven cases per 105 population detected in 2020. Recent years have witnessed a persistence in TB cases, with sustained incidence rate among expatriates and limited reduction among Omanis. This pattern suggests transmission from the migrant population. The present study examined the genetic profile and drug resistance-conferring mutations in Mycobacterium tuberculosis collected from Omanis and expatriates to recognise possible causes of disease transmission. Methods We examined M. tuberculosis cultured positive samples, collected from Omanis (n = 1,344) and expatriates (n = 1,203) between 2009 and 2018. These isolates had a known in vitro susceptibility profile to first line anti-TB, Streptomycin (SM), Isoniazid (INH), Rifampicin (RIF), Ethambutol (EMB) and Pyrazinamide (PZA). The diversity of the isolates was assessed by spacer oligo-typing (spoligotyping). Drug resistance-conferring mutations resulted from full-length sequence of nine genes (katG, inhA, ahpc, rpoB, rpsL, rrs, embB, embC, pncA) and their phenotypic relationship were analysed. Results In total, 341/2192 (13.4%), M. tuberculosis strains showed resistance to any drug, comprising mono-resistance (MR) (242, 71%), poly-resistance (PR) (40, 11.7%) and multi-drug resistance (MDR) (59, 17.3%). The overall rate of resistance among Omanis and expatriates was similar; however, MDR and PZAR were significantly higher among Omanis, while INHR was greater among expatriates. Mutations rpsL K43R and rpoB S450L were linked to Streptomycin (SMR) and Rifampicin resistance (RIFR) respectively. Whereas, katG S315T and inhA –C15T/G–17T were associated with Isoniazid resistance (INHR). The resistance patterns (mono-resistant, poly-resistant and MDR) and drug resistance-conferring mutations were found in different spoligo-lineages. rpsL K43R, katG S315T and rpoB S450L mutations were significantly higher in Beijing strains. Conclusions Diverse drug…
bibliographic citation: Al Mahrouqi et al. (2022) Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity. PeerJ 10:e13645 https://doi.org/10.7717/peerj.13645
date submitted: 2022-03-04
date accepted: 2022-06-07
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Mahrouqi
  given name: Sara
author list: Agent
  family name: Gadalla
  given name: Amal
author list: Agent
  family name: Al Azri
  given name: Saleh
author list: Agent
  family name: Al-Hamidhi
  given name: Salama
author list: Agent
  family name: Al-Jardani
  given name: Amina
author list: Agent
  family name: Balkhair
  given name: Abdullah
author list: Agent
  family name: Al-fahdi
  given name: Amira
author list: Agent
  family name: Al Balushi
  given name: Laila
author list: Agent
  family name: Al Zadjali
  given name: Samiya
author list: Agent
  family name: Al Marhoubi
  given name: Asmahan Mohammed Nasser
author list: Agent
  family name: Babiker
  given name: Hamza A.
doi: 10.7717/peerj.13645
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Al Mahrouqi et al.
attribution name: Al Mahrouqi et al.

Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
type: item
type: AcademicArticle
description: Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-SerAGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-SerAGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
format: application/pdf
format: text/html
creator: Shao’e Sun
creator: Ning Xiao
creator: Zhongli Sha
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13730
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-SerAGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-SerAGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
bibliographic citation: Sun et al. (2022) Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 10:e13730 https://doi.org/10.7717/peerj.13730
date submitted: 2022-04-22
date accepted: 2022-06-23
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Shao’e
author list: Agent
  family name: Xiao
  given name: Ning
author list: Agent
  family name: Sha
  given name: Zhongli
doi: 10.7717/peerj.13730
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Sun et al.
attribution name: Sun et al.

Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region)
type: item
type: AcademicArticle
description: In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than…
format: application/pdf
format: text/html
creator: Tineke Kraaij
creator: Samukelisiwe T. Msweli
creator: Alastair J. Potts
subject: Ecology
subject: Plant Science
subject: Biosphere Interactions
subject: Natural Resource Management
description: doi:10.7717/peerj.13765
publisher: PeerJ Inc.
rights: © 2022 Kraaij et al.
abstract: In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than…
bibliographic citation: Kraaij et al. (2022) Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region). PeerJ 10:e13765 https://doi.org/10.7717/peerj.13765
date submitted: 2022-03-16
date accepted: 2022-06-30
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kraaij
  given name: Tineke
author list: Agent
  family name: Msweli
  given name: Samukelisiwe T.
author list: Agent
  family name: Potts
  given name: Alastair J.
doi: 10.7717/peerj.13765
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: © 2022 Kraaij et al.
attribution name: Kraaij et al.

Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings
type: item
type: AcademicArticle
description: Elymus sibiricus is a highly valuable perennial forage that is widely planted in the Qinghai-Tibet Plateau (QTP) region. However, E. sibiricus artificial grasslands have a short utilization lifespan, and reach the highest yield in the 2nd and 3rd year of plantation, then rapidly drop its productivity. We hypothesized that autotoxicity is one of the mechanisms for the reduction of the productivity. To test this hypothesis, we prepared the water extract from rhizosphere soils of E. sibiricus planted for 3, 4, 5, and 8 years and examined the effects of the extract concentrations at 0.05, 0.1, 0.2, and 0.5 g/mL on seed germination, seedling growth, physiological characteristics and phytohormones in the aboveground and roots of E. sibiricus. The results showed that the soil extract concentration, planting years, and their interaction had significant influences on the most of these indices. The soil extract inhibited the seed germination and growth of seedlings, and the inhibitory effects appeared to be stronger at the 0.5 g/mL rhizosphere soil extract for 5 and 8 years. The superoxide dismultase and peroxide activities, the free proline concentration, soluble sugar concentration were altered. The malondialdehyde concentration was, in general, increased, especially in 8 years soil extract. The indole acetic acid and gibberellic acids concentrations were lowered, while the abscisic acid concentration varied. These changes were depending on the extract concentration and the years of planting, without clear patterns in some of them in response to the extract concentration and planting years. In summary, autotoxicity can be a contributor to the retardation of the growth and development of artificial E. sibiricus grasslands. The inhibitory effects could be attribute to impaired antioxidant capacity and disturbance of osmortic-regulatory substances and plant hormones, and are more profound on the root than on the aboveground part of the seedlings.
format: application/pdf
format: text/html
creator: Hang Yang
creator: Jinglong Su
creator: Juan Qi
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13768
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Elymus sibiricus is a highly valuable perennial forage that is widely planted in the Qinghai-Tibet Plateau (QTP) region. However, E. sibiricus artificial grasslands have a short utilization lifespan, and reach the highest yield in the 2nd and 3rd year of plantation, then rapidly drop its productivity. We hypothesized that autotoxicity is one of the mechanisms for the reduction of the productivity. To test this hypothesis, we prepared the water extract from rhizosphere soils of E. sibiricus planted for 3, 4, 5, and 8 years and examined the effects of the extract concentrations at 0.05, 0.1, 0.2, and 0.5 g/mL on seed germination, seedling growth, physiological characteristics and phytohormones in the aboveground and roots of E. sibiricus. The results showed that the soil extract concentration, planting years, and their interaction had significant influences on the most of these indices. The soil extract inhibited the seed germination and growth of seedlings, and the inhibitory effects appeared to be stronger at the 0.5 g/mL rhizosphere soil extract for 5 and 8 years. The superoxide dismultase and peroxide activities, the free proline concentration, soluble sugar concentration were altered. The malondialdehyde concentration was, in general, increased, especially in 8 years soil extract. The indole acetic acid and gibberellic acids concentrations were lowered, while the abscisic acid concentration varied. These changes were depending on the extract concentration and the years of planting, without clear patterns in some of them in response to the extract concentration and planting years. In summary, autotoxicity can be a contributor to the retardation of the growth and development of artificial E. sibiricus grasslands. The inhibitory effects could be attribute to impaired antioxidant capacity and disturbance of osmortic-regulatory substances and plant hormones, and are more profound on the root than on the aboveground part of the seedlings.
bibliographic citation: Yang et al. (2022) Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings. PeerJ 10:e13768 https://doi.org/10.7717/peerj.13768
date submitted: 2022-04-12
date accepted: 2022-07-01
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Hang
author list: Agent
  family name: Su
  given name: Jinglong
author list: Agent
  family name: Qi
  given name: Juan
doi: 10.7717/peerj.13768
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity
type: item
type: AcademicArticle
description: Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut.
format: application/pdf
format: text/html
creator: Yi Han
creator: Qiqi Dong
creator: Kezhao Zhang
creator: Dejian Sha
creator: Chunji Jiang
creator: Xu Yang
creator: Xibo Liu
creator: He Zhang
creator: Xiaoguang Wang
creator: Feng Guo
creator: Zheng Zhang
creator: Shubo Wan
creator: Xinhua Zhao
creator: Haiqiu Yu
subject: Ecology
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13777
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut.
bibliographic citation: Han et al. (2022) Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity. PeerJ 10:e13777 https://doi.org/10.7717/peerj.13777
date submitted: 2022-04-05
date accepted: 2022-07-01
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Yi
author list: Agent
  family name: Dong
  given name: Qiqi
author list: Agent
  family name: Zhang
  given name: Kezhao
author list: Agent
  family name: Sha
  given name: Dejian
author list: Agent
  family name: Jiang
  given name: Chunji
author list: Agent
  family name: Yang
  given name: Xu
author list: Agent
  family name: Liu
  given name: Xibo
author list: Agent
  family name: Zhang
  given name: He
author list: Agent
  family name: Wang
  given name: Xiaoguang
author list: Agent
  family name: Guo
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Zheng
author list: Agent
  family name: Wan
  given name: Shubo
author list: Agent
  family name: Zhao
  given name: Xinhua
author list: Agent
  family name: Yu
  given name: Haiqiu
doi: 10.7717/peerj.13777
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Han et al.
attribution name: Han et al.

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