PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A Miocene pyrgodesmid millipede (Polydesmida: Pyrgodesmidae) from Mexico
items: The association of fracture risk in atrial fibrillation patients and long-term anticoagulant therapy category: a systematic review and meta-analysis
items: Changes in precipitation amounts and extremes across Xinjiang (northwest China) and their connection to climate indices
items: Acoustic cues to individuality in wild male adult African savannah elephants (Loxodonta africana)
items: ACPT gene is inactivated in mammalian lineages that lack enamel or teeth
items: Chemical composition of Luffa aegyptiaca Mill., Agave durangensis Gentry and Pennisetum sp.
items: Prebiotic supplementation effect on Escherichia coli and Salmonella species associated with experimentally induced intestinal coccidiosis in rabbits
items: Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes
items: Pseudomonas chlororaphis PA23 metabolites protect against protozoan grazing by the predator Acanthamoeba castellanii
items: Estimating the average daily rainfall in Thailand using confidence intervals for the common mean of several delta-lognormal distributions

A Miocene pyrgodesmid millipede (Polydesmida: Pyrgodesmidae) from Mexico
type: item
type: AcademicArticle
description: A new fossil species of pyrgodesmid millipede (Polydesmida: Pyrgodesmidae) placed in the genus Myrmecodesmus Silvestri, 1910 is described. The type materials are two amber inclusions, male and female specimens that come from Miocene strata in Chiapas, Mexico. Myrmecodesmus antiquus sp. nov. has collum with 10 dorsal tubercles; without porosteles or ozopores; legs of the rings 2–9 with a short projection on the prefemur in both the female and male. Myrmecodesmus antiquus sp. nov is the first fossil record of the genus Myrmecodesmus. This is a New World taxon that belongs to the pantropical family Pyrgodesmidae. Thus, Myrmecodesmus antiquus sp. nov expands the range of the genus to the Miocene tropics in Middle America.
format: application/pdf
format: text/html
creator: Francisco Riquelme
creator: Miguel Hernández-Patricio
creator: Michelle Álvarez-Rodríguez
subject: Biodiversity
subject: Entomology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10574
publisher: PeerJ Inc.
rights: © 2021 Riquelme et al.
abstract: A new fossil species of pyrgodesmid millipede (Polydesmida: Pyrgodesmidae) placed in the genus Myrmecodesmus Silvestri, 1910 is described. The type materials are two amber inclusions, male and female specimens that come from Miocene strata in Chiapas, Mexico. Myrmecodesmus antiquus sp. nov. has collum with 10 dorsal tubercles; without porosteles or ozopores; legs of the rings 2–9 with a short projection on the prefemur in both the female and male. Myrmecodesmus antiquus sp. nov is the first fossil record of the genus Myrmecodesmus. This is a New World taxon that belongs to the pantropical family Pyrgodesmidae. Thus, Myrmecodesmus antiquus sp. nov expands the range of the genus to the Miocene tropics in Middle America.
bibliographic citation: Riquelme et al. (2021) A Miocene pyrgodesmid millipede (Polydesmida: Pyrgodesmidae) from Mexico. PeerJ 9:e10574 https://doi.org/10.7717/peerj.10574
date submitted: 2020-09-29
date accepted: 2020-11-24
issued: 2021-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Riquelme
  given name: Francisco
author list: Agent
  family name: Hernández-Patricio
  given name: Miguel
author list: Agent
  family name: Álvarez-Rodríguez
  given name: Michelle
doi: 10.7717/peerj.10574
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-25
copyright: © 2021 Riquelme et al.
attribution name: Riquelme et al.

The association of fracture risk in atrial fibrillation patients and long-term anticoagulant therapy category: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective Our study aimed to assess the risk of all fractures and hip fractures in patients with atrial fibrillation (AF) who took non-vitamin K antagonist oral anticoagulants (NOACs) compared to warfarin. Methods We searched PubMed, Embase, and Cochrane Library and Clinical Trials.gov Website. Reviewed related researches up to January 31, 2020, to identify studies with more than 12 months of follow-up data. The protocol for this systematic review and meta-analysis has been registered in the International Prospective Register of Systematic Reviews (PROSPERO Number: CRD42020156893). Results We included five RCT studies, and five observational studies that contained a total of 326,846 patients in our meta-analysis. Our meta-analysis showed that patients taken NOACs had no significant all fracture risk (RR = 0.91, 95% CI [0.81–1.01]) and hip fracture risk (RR = 0.92, 95% CI [0.82–1.03]) compared with those taken warfarin. Subanalysis showed that the risk of all fractures and hip fractures treated by NOACs were significant lower compared with warfarin in observational studies compared with RCT studies. Also, a subanalysis across the duration of anticoagulation showed the NOACs users have lower all fracture risk than warfarin users when the duration of anticoagulation ≤2 years (RR = 0.89, 95% CI [0.80–0.99]). Further analysis, significant lower all fracture risk in the rivaroxaban therapy (RR = 0.81; 95% CI [0.76–0.86]) compared with warfarin but no statistical significance in hip fracture. There were no significant difference of all fracture risk and hip fracture risk in dabigatran, apixaban, and edoxaban therapy compared with warfarin. Conclusion The meta-analysis demonstrated that NOACs associated with a significantly lower all fracture risk compared with warfarin when the duration of anticoagulation more than 2 years. Rivaroxaban users had lower risk of all fracture than warfarin users in AF patients. But there was no evidence to verify apixaban, edoxaban, and dabiga…
format: application/pdf
format: text/html
creator: Jun Chen
creator: Lingchun Lyu
creator: Jiayi Shen
creator: Chunlai Zeng
creator: Cheng Chen
creator: Tiemin Wei
subject: Cardiology
subject: Drugs and Devices
subject: Pathology
description: doi:10.7717/peerj.10683
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Objective Our study aimed to assess the risk of all fractures and hip fractures in patients with atrial fibrillation (AF) who took non-vitamin K antagonist oral anticoagulants (NOACs) compared to warfarin. Methods We searched PubMed, Embase, and Cochrane Library and Clinical Trials.gov Website. Reviewed related researches up to January 31, 2020, to identify studies with more than 12 months of follow-up data. The protocol for this systematic review and meta-analysis has been registered in the International Prospective Register of Systematic Reviews (PROSPERO Number: CRD42020156893). Results We included five RCT studies, and five observational studies that contained a total of 326,846 patients in our meta-analysis. Our meta-analysis showed that patients taken NOACs had no significant all fracture risk (RR = 0.91, 95% CI [0.81–1.01]) and hip fracture risk (RR = 0.92, 95% CI [0.82–1.03]) compared with those taken warfarin. Subanalysis showed that the risk of all fractures and hip fractures treated by NOACs were significant lower compared with warfarin in observational studies compared with RCT studies. Also, a subanalysis across the duration of anticoagulation showed the NOACs users have lower all fracture risk than warfarin users when the duration of anticoagulation ≤2 years (RR = 0.89, 95% CI [0.80–0.99]). Further analysis, significant lower all fracture risk in the rivaroxaban therapy (RR = 0.81; 95% CI [0.76–0.86]) compared with warfarin but no statistical significance in hip fracture. There were no significant difference of all fracture risk and hip fracture risk in dabigatran, apixaban, and edoxaban therapy compared with warfarin. Conclusion The meta-analysis demonstrated that NOACs associated with a significantly lower all fracture risk compared with warfarin when the duration of anticoagulation more than 2 years. Rivaroxaban users had lower risk of all fracture than warfarin users in AF patients. But there was no evidence to verify apixaban, edoxaban, and dabiga…
bibliographic citation: Chen et al. (2021) The association of fracture risk in atrial fibrillation patients and long-term anticoagulant therapy category: a systematic review and meta-analysis. PeerJ 9:e10683 https://doi.org/10.7717/peerj.10683
date submitted: 2020-06-24
date accepted: 2020-12-09
issued: 2021-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Lyu
  given name: Lingchun
author list: Agent
  family name: Shen
  given name: Jiayi
author list: Agent
  family name: Zeng
  given name: Chunlai
author list: Agent
  family name: Chen
  given name: Cheng
author list: Agent
  family name: Wei
  given name: Tiemin
doi: 10.7717/peerj.10683
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-25
copyright: ©2021 Chen et al.
attribution name: Chen et al.

Changes in precipitation amounts and extremes across Xinjiang (northwest China) and their connection to climate indices
type: item
type: AcademicArticle
description: Xinjiang is a major part of China’s arid region and its water resource is extremely scarcity. The change in precipitation amounts and extremes is of significant importance for the reliable management of regional water resources in this region. Thus, this study explored the spatiotemporal changes in extreme precipitation using the Mann–Kendall (M–K) trend analysis, mutation test, and probability distribution functions, based on the observed daily precipitation data from 89 weather stations in Xinjiang, China during 1961–2018. We also examined the correlations between extreme precipitation and climate indices using the cross-wavelet analysis. The results indicated that the climate in Xinjiang is becoming wetter and the intensity and frequency of extreme precipitation has begun to strengthen, with these trends being more obvious after the 1990s. Extreme precipitation trends displayed spatial heterogeneity in Xinjiang. Extreme precipitation was mainly concentrated in mountainous areas, northern Xinjiang, and western Xinjiang. The significant increasing trend of extreme precipitation was also concentrated in the Tianshan Mountains and in northern Xinjiang. In addition, the climate indices, North Atlantic Oscillation, Atlantic Multidecadal Oscillation, Multivariate ENSO Index and Indian Ocean Dipole Index had obvious relationships with extreme precipitation in Xinjiang. The relationships between the extreme precipitation and climate indices were not clearly positive or negative, with many correlations advanced or delayed in phase. At the same time, extreme precipitation displayed periodic changes, with a frequency of approximately 1–3 or 4–7 years. These periodic changes were more obvious after the 1990s; however, the exact mechanisms involved in this require further study.
format: application/pdf
format: text/html
creator: Wenfeng Hu
creator: Junqiang Yao
creator: Qing He
creator: Jing Chen
subject: Statistics
subject: Natural Resource Management
subject: Ecohydrology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10792
publisher: PeerJ Inc.
rights: © 2021 Hu et al.
abstract: Xinjiang is a major part of China’s arid region and its water resource is extremely scarcity. The change in precipitation amounts and extremes is of significant importance for the reliable management of regional water resources in this region. Thus, this study explored the spatiotemporal changes in extreme precipitation using the Mann–Kendall (M–K) trend analysis, mutation test, and probability distribution functions, based on the observed daily precipitation data from 89 weather stations in Xinjiang, China during 1961–2018. We also examined the correlations between extreme precipitation and climate indices using the cross-wavelet analysis. The results indicated that the climate in Xinjiang is becoming wetter and the intensity and frequency of extreme precipitation has begun to strengthen, with these trends being more obvious after the 1990s. Extreme precipitation trends displayed spatial heterogeneity in Xinjiang. Extreme precipitation was mainly concentrated in mountainous areas, northern Xinjiang, and western Xinjiang. The significant increasing trend of extreme precipitation was also concentrated in the Tianshan Mountains and in northern Xinjiang. In addition, the climate indices, North Atlantic Oscillation, Atlantic Multidecadal Oscillation, Multivariate ENSO Index and Indian Ocean Dipole Index had obvious relationships with extreme precipitation in Xinjiang. The relationships between the extreme precipitation and climate indices were not clearly positive or negative, with many correlations advanced or delayed in phase. At the same time, extreme precipitation displayed periodic changes, with a frequency of approximately 1–3 or 4–7 years. These periodic changes were more obvious after the 1990s; however, the exact mechanisms involved in this require further study.
bibliographic citation: Hu et al. (2021) Changes in precipitation amounts and extremes across Xinjiang (northwest China) and their connection to climate indices. PeerJ 9:e10792 https://doi.org/10.7717/peerj.10792
date submitted: 2020-05-20
date accepted: 2020-12-28
issued: 2021-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Wenfeng
author list: Agent
  family name: Yao
  given name: Junqiang
author list: Agent
  family name: He
  given name: Qing
author list: Agent
  family name: Chen
  given name: Jing
doi: 10.7717/peerj.10792
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-25
copyright: © 2021 Hu et al.
attribution name: Hu et al.

Acoustic cues to individuality in wild male adult African savannah elephants (Loxodonta africana)
type: item
type: AcademicArticle
description: The ability to recognize conspecifics plays a pivotal role in animal communication systems. It is especially important for establishing and maintaining associations among individuals of social, long-lived species, such as elephants. While research on female elephant sociality and communication is prevalent, until recently male elephants have been considered far less social than females. This resulted in a dearth of information about their communication and recognition abilities. With new knowledge about the intricacies of the male elephant social structure come questions regarding the communication basis that allows for social bonds to be established and maintained. By analyzing the acoustic parameters of social rumbles recorded over 1.5 years from wild, mature, male African savanna elephants (Loxodonta africana) we expand current knowledge about the information encoded within these vocalizations and their potential to facilitate individual recognition. We showed that social rumbles are individually distinct and stable over time and therefore provide an acoustic basis for individual recognition. Furthermore, our results revealed that different frequency parameters contribute to individual differences of these vocalizations.
format: application/pdf
format: text/html
creator: Kaja Wierucka
creator: Michelle D. Henley
creator: Hannah S. Mumby
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.10736
publisher: PeerJ Inc.
rights: © 2021 Wierucka et al.
abstract: The ability to recognize conspecifics plays a pivotal role in animal communication systems. It is especially important for establishing and maintaining associations among individuals of social, long-lived species, such as elephants. While research on female elephant sociality and communication is prevalent, until recently male elephants have been considered far less social than females. This resulted in a dearth of information about their communication and recognition abilities. With new knowledge about the intricacies of the male elephant social structure come questions regarding the communication basis that allows for social bonds to be established and maintained. By analyzing the acoustic parameters of social rumbles recorded over 1.5 years from wild, mature, male African savanna elephants (Loxodonta africana) we expand current knowledge about the information encoded within these vocalizations and their potential to facilitate individual recognition. We showed that social rumbles are individually distinct and stable over time and therefore provide an acoustic basis for individual recognition. Furthermore, our results revealed that different frequency parameters contribute to individual differences of these vocalizations.
bibliographic citation: Wierucka et al. (2021) Acoustic cues to individuality in wild male adult African savannah elephants (Loxodonta africana). PeerJ 9:e10736 https://doi.org/10.7717/peerj.10736
date submitted: 2020-08-25
date accepted: 2020-12-18
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wierucka
  given name: Kaja
author list: Agent
  family name: Henley
  given name: Michelle D.
author list: Agent
  family name: Mumby
  given name: Hannah S.
doi: 10.7717/peerj.10736
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: © 2021 Wierucka et al.
attribution name: Wierucka et al.

ACPT gene is inactivated in mammalian lineages that lack enamel or teeth
type: item
type: AcademicArticle
description: Loss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth/enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and/or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT playing a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals. The results shows that variant ORF-disrupting mutations were detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN/dS values on transitional branches were used to estimate ACPT inactivation records. In the case of aardvark, inactivation of ACPT was estimated at ~23.60–28.32 Ma, which is earlier than oldest aardvark fossil record (Orycteropus minutus, ~19 Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18–11.30 Ma) is later than oldest fossil record, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth/enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.
format: application/pdf
format: text/html
creator: Yuan Mu
creator: Xin Huang
creator: Rui Liu
creator: Yulin Gai
creator: Na Liang
creator: Daiqing Yin
creator: Lei Shan
creator: Shixia Xu
creator: Guang Yang
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.10219
publisher: PeerJ Inc.
rights: © 2021 Mu et al.
abstract: Loss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth/enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and/or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT playing a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals. The results shows that variant ORF-disrupting mutations were detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN/dS values on transitional branches were used to estimate ACPT inactivation records. In the case of aardvark, inactivation of ACPT was estimated at ~23.60–28.32 Ma, which is earlier than oldest aardvark fossil record (Orycteropus minutus, ~19 Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18–11.30 Ma) is later than oldest fossil record, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth/enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.
bibliographic citation: Mu et al. (2021) ACPT gene is inactivated in mammalian lineages that lack enamel or teeth. PeerJ 9:e10219 https://doi.org/10.7717/peerj.10219
date submitted: 2020-04-06
date accepted: 2020-09-29
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mu
  given name: Yuan
author list: Agent
  family name: Huang
  given name: Xin
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Gai
  given name: Yulin
author list: Agent
  family name: Liang
  given name: Na
author list: Agent
  family name: Yin
  given name: Daiqing
author list: Agent
  family name: Shan
  given name: Lei
author list: Agent
  family name: Xu
  given name: Shixia
author list: Agent
  family name: Yang
  given name: Guang
doi: 10.7717/peerj.10219
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: © 2021 Mu et al.
attribution name: Mu et al.

Chemical composition of Luffa aegyptiaca Mill., Agave durangensis Gentry and Pennisetum sp.
type: item
type: AcademicArticle
description: The particleboard industry faces problems of wood shortage, which has led to the use of non-wood lignocellulosic materials. Furthermore, there is also interest in looking for materials that improve their physical and mechanical properties. The species Luffa aegyptiaca Mill. (fruit), Agave durangensis Gentry (bagasse) and Pennisetum sp. (plant, leaves and stem) could be used in the elaboration of wood-based particleboards. The aim of this study is to determine the feasibility of using these materials to produce particleboards in accordance with their chemical composition. Five materials were studied, A. durangensis (bagasse), L. aegyptiaca (fruit) and Pennisetum sp. (whole plant, leaves and stem). Extractives, holocellulose, Runkel lignin and ash content was determined. The pH of the fibers was also measured and a microanalysis of the ash was performed. ANOVA and Kruskal-Wallis tests were carried out, in addition Tukey and Dunn tests for group comparison were performed. Pennisetum sp. leaves presented the highest total extractives and ash content, while L. aegyptiaca fruit and A. durangensis bagasse had the highest both content of holocellulose and Runkel lignin respectively. The lowest pH was presented by the L. aegyptiaca fruit, while the highest was from the Pennisetum sp. stem. The element with the greatest presence in the five materials was potassium, except in A. durangensis bagasse showing calcium. L. aegyptiaca fruit has better characteristics to be used in particleboards with greater mechanical resistance because of its higher holocellulose content. However, Pennisetum sp. (plant, leaves and stem) could be used to make particleboards with high resistance to water absorption.
format: application/pdf
format: text/html
creator: Oswaldo Moreno-Anguiano
creator: Artemio Carrillo-Parra
creator: José G. Rutiaga-Quiñones
creator: Christian Wehenkel
creator: Marín Pompa-García
creator: Francisco Márquez-Montesino
creator: Luis F. Pintor-Ibarra
subject: Plant Science
subject: Natural Resource Management
subject: Biogeochemistry
subject: Forestry
subject: Green Chemistry
description: doi:10.7717/peerj.10626
publisher: PeerJ Inc.
rights: © 2021 Moreno-Anguiano et al.
abstract: The particleboard industry faces problems of wood shortage, which has led to the use of non-wood lignocellulosic materials. Furthermore, there is also interest in looking for materials that improve their physical and mechanical properties. The species Luffa aegyptiaca Mill. (fruit), Agave durangensis Gentry (bagasse) and Pennisetum sp. (plant, leaves and stem) could be used in the elaboration of wood-based particleboards. The aim of this study is to determine the feasibility of using these materials to produce particleboards in accordance with their chemical composition. Five materials were studied, A. durangensis (bagasse), L. aegyptiaca (fruit) and Pennisetum sp. (whole plant, leaves and stem). Extractives, holocellulose, Runkel lignin and ash content was determined. The pH of the fibers was also measured and a microanalysis of the ash was performed. ANOVA and Kruskal-Wallis tests were carried out, in addition Tukey and Dunn tests for group comparison were performed. Pennisetum sp. leaves presented the highest total extractives and ash content, while L. aegyptiaca fruit and A. durangensis bagasse had the highest both content of holocellulose and Runkel lignin respectively. The lowest pH was presented by the L. aegyptiaca fruit, while the highest was from the Pennisetum sp. stem. The element with the greatest presence in the five materials was potassium, except in A. durangensis bagasse showing calcium. L. aegyptiaca fruit has better characteristics to be used in particleboards with greater mechanical resistance because of its higher holocellulose content. However, Pennisetum sp. (plant, leaves and stem) could be used to make particleboards with high resistance to water absorption.
bibliographic citation: Moreno-Anguiano et al. (2021) Chemical composition of Luffa aegyptiaca Mill., Agave durangensis Gentry and Pennisetum sp.. PeerJ 9:e10626 https://doi.org/10.7717/peerj.10626
date submitted: 2020-07-16
date accepted: 2020-11-30
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-Anguiano
  given name: Oswaldo
author list: Agent
  family name: Carrillo-Parra
  given name: Artemio
author list: Agent
  family name: Rutiaga-Quiñones
  given name: José G.
author list: Agent
  family name: Wehenkel
  given name: Christian
author list: Agent
  family name: Pompa-García
  given name: Marín
author list: Agent
  family name: Márquez-Montesino
  given name: Francisco
author list: Agent
  family name: Pintor-Ibarra
  given name: Luis F.
doi: 10.7717/peerj.10626
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: © 2021 Moreno-Anguiano et al.
attribution name: Moreno-Anguiano et al.

Prebiotic supplementation effect on Escherichia coli and Salmonella species associated with experimentally induced intestinal coccidiosis in rabbits
type: item
type: AcademicArticle
description: Background Coccidian infection may enhance the proliferation of gut Enterobacteriaceae. Bacterial infections in rabbits can negatively affect the body condition and cause high mortality, especially at young ages. Therefore, the effect of prebiotic supplementation on the presence of Escherichia coli and Salmonella species in rabbits experimentally infected with intestinal coccidiosis was investigated. Methods Thirty male rabbits aged 35–40 days were divided into three equal groups. These groups were; prebiotic supplemented (PS), positive control (PC), and negative control (NC) groups. The prebiotic group was supplemented with 2 g/L of Bio-Mos® until the end of the experiment. At day ten post prebiotic supplementation; the PS and PC groups were inoculated orally with 5.0 × 104 sporulated oocysts of mixed species of rabbit Eimeria. The daily fecal examination was carried out from the day 4 post-infection (PI) until the day 8 PI. At day 5 and day 8 PI, 5 rabbits from each group (PS, PC, and NC) were humanely slaughtered and parts of intestinal tissue were collected for microbiological analysis. Results There was a significant decrease (P≤ 0.05) in the oocyst count in the PS group (25.12 × 104 ± 10.36) when compared with the PC group (43.43 × 104 ± 11.52) and this decrease was continued till the end of the experiment. Eleven E. coli isolates were detected in the collected samples with an overall prevalence of 24.4%. The highest prevalence of E. coli was in the PC group (13.33%) while the lowest one was in the PS group (4.44%). Meanwhile, four Salmonella serovars were isolated with an overall prevalence of 8.89%. The NC group showed one serovar (2.22%) and PC revealed three serovars (6.67%) while the prebiotic supplemented group didn’t show any salmonella isolate. Of E. coli isolates, five isolates (O78, O125, O152, O115 and O168) showed high resistance to florfenicol and neomycin (100%). Also, of salmonella serovars, thee serovars (Salmonella entrica subsp. enterica sero…
format: application/pdf
format: text/html
creator: Shawky M. Aboelhadid
creator: Shaymaa Hashem
creator: El-Sayed Abdel-Kafy
creator: Lilian N. Mahrous
creator: Eman M. Farghly
creator: Abdel-Azeem S. Abdel-Baki
creator: Saleh Al-Quraishy
creator: Asmaa A. Kamel
subject: Microbiology
subject: Parasitology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10714
publisher: PeerJ Inc.
rights: © 2021 Aboelhadid et al.
abstract: Background Coccidian infection may enhance the proliferation of gut Enterobacteriaceae. Bacterial infections in rabbits can negatively affect the body condition and cause high mortality, especially at young ages. Therefore, the effect of prebiotic supplementation on the presence of Escherichia coli and Salmonella species in rabbits experimentally infected with intestinal coccidiosis was investigated. Methods Thirty male rabbits aged 35–40 days were divided into three equal groups. These groups were; prebiotic supplemented (PS), positive control (PC), and negative control (NC) groups. The prebiotic group was supplemented with 2 g/L of Bio-Mos® until the end of the experiment. At day ten post prebiotic supplementation; the PS and PC groups were inoculated orally with 5.0 × 104 sporulated oocysts of mixed species of rabbit Eimeria. The daily fecal examination was carried out from the day 4 post-infection (PI) until the day 8 PI. At day 5 and day 8 PI, 5 rabbits from each group (PS, PC, and NC) were humanely slaughtered and parts of intestinal tissue were collected for microbiological analysis. Results There was a significant decrease (P≤ 0.05) in the oocyst count in the PS group (25.12 × 104 ± 10.36) when compared with the PC group (43.43 × 104 ± 11.52) and this decrease was continued till the end of the experiment. Eleven E. coli isolates were detected in the collected samples with an overall prevalence of 24.4%. The highest prevalence of E. coli was in the PC group (13.33%) while the lowest one was in the PS group (4.44%). Meanwhile, four Salmonella serovars were isolated with an overall prevalence of 8.89%. The NC group showed one serovar (2.22%) and PC revealed three serovars (6.67%) while the prebiotic supplemented group didn’t show any salmonella isolate. Of E. coli isolates, five isolates (O78, O125, O152, O115 and O168) showed high resistance to florfenicol and neomycin (100%). Also, of salmonella serovars, thee serovars (Salmonella entrica subsp. enterica sero…
bibliographic citation: Aboelhadid et al. (2021) Prebiotic supplementation effect on Escherichia coli and Salmonella species associated with experimentally induced intestinal coccidiosis in rabbits. PeerJ 9:e10714 https://doi.org/10.7717/peerj.10714
date submitted: 2020-07-27
date accepted: 2020-12-15
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aboelhadid
  given name: Shawky M.
author list: Agent
  family name: Hashem
  given name: Shaymaa
author list: Agent
  family name: Abdel-Kafy
  given name: El-Sayed
author list: Agent
  family name: Mahrous
  given name: Lilian N.
author list: Agent
  family name: Farghly
  given name: Eman M.
author list: Agent
  family name: Abdel-Baki
  given name: Abdel-Azeem S.
author list: Agent
  family name: Al-Quraishy
  given name: Saleh
author list: Agent
  family name: Kamel
  given name: Asmaa A.
doi: 10.7717/peerj.10714
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: ©2021 Aboelhadid et al.
attribution name: Aboelhadid et al.

Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes
type: item
type: AcademicArticle
description: Background Melatonin is a hormone substance that exists in various living organisms. Since it was discovered in the pineal gland of cattle in 1956, the function of melatonin in animals has been roughly clarified. Nevertheless, in plants, the research on melatonin is still insufficient. Hulless barley (Hordeum vulgare L. var. nudum hook. f.) is a crop that originates from cultivated barley in the east, usually grown on the Qinghai-Tibet Plateau, becoming the most important food crop in this area. Although the genome and transcriptome research of highland barley has gradually increased recently years, there are still many problems about how hulless barley adapts to the cold climate of the Qinghai-Tibet Plateau. Methods In this study, we set three temperature conditions 25°C, 15°C, 5°C hulless barley seedlings, and at the same time soaked the hulless barley seeds with a 1 µM melatonin solution for 12 hours before the hulless barley seeds germinated. Afterwards, the growth and physiological indicators of hulless barley seedlings under different treatment conditions were determined. Meanwhile, the qRT-PCR method was used to determine the transcription level of the hulless barley circadian clock genes under different treatment conditions under continuous light conditions. Results The results showed the possible mechanism by which melatonin pretreatment can promote the growth of hulless barley under cold stress conditions by studying the effect of melatonin on the rhythm of the circadian clock system and some physiological indicators. The results revealed that the application of 1 µM melatonin could alleviate the growth inhibition of hulless barley seedlings caused by cold stress. In addition, exogenous melatonin could also restore the circadian rhythmic oscillation of circadian clock genes, such as HvCCA1 and HvTOC1, whose circadian rhythmic phenotypes were lost due to environmental cold stress. Additionally, the results confirmed that exogenous melatonin even reduced the…
format: application/pdf
format: text/html
creator: Tianliang Chang
creator: Yi Zhao
creator: Hongyan He
creator: Qianqian Xi
creator: Jiayi Fu
creator: Yuwei Zhao
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10740
publisher: PeerJ Inc.
rights: © 2021 Chang et al.
abstract: Background Melatonin is a hormone substance that exists in various living organisms. Since it was discovered in the pineal gland of cattle in 1956, the function of melatonin in animals has been roughly clarified. Nevertheless, in plants, the research on melatonin is still insufficient. Hulless barley (Hordeum vulgare L. var. nudum hook. f.) is a crop that originates from cultivated barley in the east, usually grown on the Qinghai-Tibet Plateau, becoming the most important food crop in this area. Although the genome and transcriptome research of highland barley has gradually increased recently years, there are still many problems about how hulless barley adapts to the cold climate of the Qinghai-Tibet Plateau. Methods In this study, we set three temperature conditions 25°C, 15°C, 5°C hulless barley seedlings, and at the same time soaked the hulless barley seeds with a 1 µM melatonin solution for 12 hours before the hulless barley seeds germinated. Afterwards, the growth and physiological indicators of hulless barley seedlings under different treatment conditions were determined. Meanwhile, the qRT-PCR method was used to determine the transcription level of the hulless barley circadian clock genes under different treatment conditions under continuous light conditions. Results The results showed the possible mechanism by which melatonin pretreatment can promote the growth of hulless barley under cold stress conditions by studying the effect of melatonin on the rhythm of the circadian clock system and some physiological indicators. The results revealed that the application of 1 µM melatonin could alleviate the growth inhibition of hulless barley seedlings caused by cold stress. In addition, exogenous melatonin could also restore the circadian rhythmic oscillation of circadian clock genes, such as HvCCA1 and HvTOC1, whose circadian rhythmic phenotypes were lost due to environmental cold stress. Additionally, the results confirmed that exogenous melatonin even reduced the…
bibliographic citation: Chang et al. (2021) Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes. PeerJ 9:e10740 https://doi.org/10.7717/peerj.10740
date submitted: 2020-08-18
date accepted: 2020-12-18
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Tianliang
author list: Agent
  family name: Zhao
  given name: Yi
author list: Agent
  family name: He
  given name: Hongyan
author list: Agent
  family name: Xi
  given name: Qianqian
author list: Agent
  family name: Fu
  given name: Jiayi
author list: Agent
  family name: Zhao
  given name: Yuwei
doi: 10.7717/peerj.10740
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: ©2021 Chang et al.
attribution name: Chang et al.

Pseudomonas chlororaphis PA23 metabolites protect against protozoan grazing by the predator Acanthamoeba castellanii
type: item
type: AcademicArticle
description: Background Pseudomonas chlororaphis strain PA23 is a biocontrol agent that is able to protect canola against the pathogenic fungus Sclerotinia sclerotiorum. This bacterium secretes a number of metabolites that contribute to fungal antagonism, including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN) and degradative enzymes. In order to be successful, a biocontrol agent must be able to persist in the environment and avoid the threat of grazing predators. The focus of the current study was to investigate whether PA23 is able to resist grazing by the protozoan predator Acanthamoeba castellanii (Ac) and to define the role of bacterial metabolites in the PA23-Ac interaction. Methods Ac was co-cultured with PA23 WT and a panel of derivative strains for a period of 15 days, and bacteria and amoebae were enumerated on days 1, 5, 10 and 15. Ac was subsequently incubated in the presence of purified PRN, PHZ, and KCN and viability was assessed at 24, 48 and 72 h. Chemotactic assays were conducted to assess whether PA23 compounds exhibit repellent or attractant properties towards Ac. Finally, PA23 grown in the presence and absence of amoebae was subject to phenotypic characterization and gene expression analyses. Results PRN, PHZ and HCN were found to contribute to PA23 toxicity towards Ac trophozoites, either by killing or inducing cyst formation. This is the first report of PHZ-mediated toxicity towards amoebae. In chemotaxis assays, amoebae preferentially migrated towards regulatory mutants devoid of extracellular metabolite production as well as a PRN mutant, indicating this antibiotic has repellent properties. Co-culturing of bacteria with amoebae led to elevated expression of the PA23 phzI/phzR quorum-sensing (QS) genes and phzA and prnA, which are under QS control. PHZ and PRN levels were similarly increased in Ac co-cultures, suggesting that PA23 can respond to predator cues and upregulate expression of toxins accordingly. Conclusions PA23 compounds includin…
format: application/pdf
format: text/html
creator: Akrm Ghergab
creator: Carrie Selin
creator: Jennifer Tanner
creator: Ann Karen Brassinga
creator: Teresa Dekievit
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10756
publisher: PeerJ Inc.
rights: © 2021 Ghergab et al.
abstract: Background Pseudomonas chlororaphis strain PA23 is a biocontrol agent that is able to protect canola against the pathogenic fungus Sclerotinia sclerotiorum. This bacterium secretes a number of metabolites that contribute to fungal antagonism, including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN) and degradative enzymes. In order to be successful, a biocontrol agent must be able to persist in the environment and avoid the threat of grazing predators. The focus of the current study was to investigate whether PA23 is able to resist grazing by the protozoan predator Acanthamoeba castellanii (Ac) and to define the role of bacterial metabolites in the PA23-Ac interaction. Methods Ac was co-cultured with PA23 WT and a panel of derivative strains for a period of 15 days, and bacteria and amoebae were enumerated on days 1, 5, 10 and 15. Ac was subsequently incubated in the presence of purified PRN, PHZ, and KCN and viability was assessed at 24, 48 and 72 h. Chemotactic assays were conducted to assess whether PA23 compounds exhibit repellent or attractant properties towards Ac. Finally, PA23 grown in the presence and absence of amoebae was subject to phenotypic characterization and gene expression analyses. Results PRN, PHZ and HCN were found to contribute to PA23 toxicity towards Ac trophozoites, either by killing or inducing cyst formation. This is the first report of PHZ-mediated toxicity towards amoebae. In chemotaxis assays, amoebae preferentially migrated towards regulatory mutants devoid of extracellular metabolite production as well as a PRN mutant, indicating this antibiotic has repellent properties. Co-culturing of bacteria with amoebae led to elevated expression of the PA23 phzI/phzR quorum-sensing (QS) genes and phzA and prnA, which are under QS control. PHZ and PRN levels were similarly increased in Ac co-cultures, suggesting that PA23 can respond to predator cues and upregulate expression of toxins accordingly. Conclusions PA23 compounds includin…
bibliographic citation: Ghergab et al. (2021) Pseudomonas chlororaphis PA23 metabolites protect against protozoan grazing by the predator Acanthamoeba castellanii. PeerJ 9:e10756 https://doi.org/10.7717/peerj.10756
date submitted: 2020-10-21
date accepted: 2020-12-21
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghergab
  given name: Akrm
author list: Agent
  family name: Selin
  given name: Carrie
author list: Agent
  family name: Tanner
  given name: Jennifer
author list: Agent
  family name: Brassinga
  given name: Ann Karen
author list: Agent
  family name: Dekievit
  given name: Teresa
doi: 10.7717/peerj.10756
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: ©2021 Ghergab et al.
attribution name: Ghergab et al.

Estimating the average daily rainfall in Thailand using confidence intervals for the common mean of several delta-lognormal distributions
type: item
type: AcademicArticle
description: The daily average natural rainfall amounts in the five regions of Thailand can be estimated using the confidence intervals for the common mean of several delta-lognormal distributions based on the fiducial generalized confidence interval (FGCI), large sample (LS), method of variance estimates recovery (MOVER), parametric bootstrap (PB), and highest posterior density intervals based on Jeffreys’ rule (HPD-JR) and normal-gamma-beta (HPD-NGB) priors. Monte Carlo simulation was conducted to assess the performance in terms of the coverage probability and average length of the proposed methods. The numerical results indicate that MOVER and PB provided better performances than the other methods in a variety of situations, even when the sample case was large. The efficacies of the proposed methods were illustrated by applying them to real rainfall datasets from the five regions of Thailand.
format: application/pdf
format: text/html
creator: Patcharee Maneerat
creator: Sa-Aat Niwitpong
subject: Agricultural Science
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Ecohydrology
description: doi:10.7717/peerj.10758
publisher: PeerJ Inc.
rights: © 2021 Maneerat and Niwitpong
abstract: The daily average natural rainfall amounts in the five regions of Thailand can be estimated using the confidence intervals for the common mean of several delta-lognormal distributions based on the fiducial generalized confidence interval (FGCI), large sample (LS), method of variance estimates recovery (MOVER), parametric bootstrap (PB), and highest posterior density intervals based on Jeffreys’ rule (HPD-JR) and normal-gamma-beta (HPD-NGB) priors. Monte Carlo simulation was conducted to assess the performance in terms of the coverage probability and average length of the proposed methods. The numerical results indicate that MOVER and PB provided better performances than the other methods in a variety of situations, even when the sample case was large. The efficacies of the proposed methods were illustrated by applying them to real rainfall datasets from the five regions of Thailand.
bibliographic citation: Maneerat et al. (2021) Estimating the average daily rainfall in Thailand using confidence intervals for the common mean of several delta-lognormal distributions. PeerJ 9:e10758 https://doi.org/10.7717/peerj.10758
date submitted: 2020-08-11
date accepted: 2020-12-21
issued: 2021-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maneerat
  given name: Patcharee
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
doi: 10.7717/peerj.10758
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-22
copyright: ©2021 Maneerat and Niwitpong
attribution name: Maneerat and Niwitpong

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