PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Quantitative analysis of vegetation restoration and potential driving factors in a typical subalpine region of the Eastern Tibet Plateau
items: Predicting crown width using nonlinear mixed-effects models accounting for competition in multi-species secondary forests
items: Skeletal variation in bird domestication: limb proportions and sternum in chicken, with comparisons to mallard ducks and Muscovy ducks
items: Lipids associated with plant-bacteria interaction identified using a metabolomics approach in an Arabidopsis thaliana model
items: Winter diet of Burrowing Owls in the Llano La Soledad, Galeana, Nuevo León, México
items: Polyphenolic extract from Punica granatum peel causes cytoskeleton-related damage on Giardia lamblia trophozoites in vitro
items: Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
items: Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica
items: Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies
items: Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)

Quantitative analysis of vegetation restoration and potential driving factors in a typical subalpine region of the Eastern Tibet Plateau
type: item
type: AcademicArticle
description: Vegetation restoration is an essential approach to re-establish the ecological balance in subalpine areas. Changes in vegetation cover represent, to some extent, vegetation growth trends and are the consequence of a complex of different natural factors and human activities. Microtopography influences vegetation growth by affecting the amount of heat and moisture reaching the ground, a role that is more pronounced in subalpine areas. However, little research is concerned with the characteristics and dynamics of vegetation restoration in different microtopography types. The respective importance of the factors driving vegetation changes in subalpine areas is also not clear yet. We used linear regression and the Hurst exponent to analyze the trends in vegetation restoration and sustainability in different microtopography types since 2000, based on Fractional Vegetation Cover (FVC) and identified potential driving factors of vegetation change and their importance by using Geographical Detector. The results show that: (1) The FVC in the region under study has shown an up-trend since 2000, and the rate of increase is 0.26/year (P = 0.028). It would be going from improvement to degradation, continuous decrease or continuous significant decrease in 47.48% of the region, in the future. (2) The mean FVC is in the following order: lower slope (cool), lower slope, lower slope (warm), valley, upper slope (warm), upper slope, valley (narrow), upper slope (cool), cliff, mountain/divide, peak/ridge (warm), peak/ridge, peak/ridge (cool). The lower slope is the microtopographic type with the best vegetation cover, and ridge peak is the most difficult to be afforested. (3) The main factors affecting vegetation restoration in subalpine areas are aspect, microtopographic type, and soil taxonomy great groups. The interaction between multiple factors has a much stronger effect on vegetation cover than single factors, with the effect of temperatures and aspects having the most significant …
format: application/pdf
format: text/html
creator: Yu Feng
creator: Juan Wang
creator: Qin Zhou
creator: Maoyang Bai
creator: Peihao Peng
creator: Dan Zhao
creator: Zengyan Guan
creator: Xian’an Liu
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13358
publisher: PeerJ Inc.
rights: © 2022 Feng et al.
abstract: Vegetation restoration is an essential approach to re-establish the ecological balance in subalpine areas. Changes in vegetation cover represent, to some extent, vegetation growth trends and are the consequence of a complex of different natural factors and human activities. Microtopography influences vegetation growth by affecting the amount of heat and moisture reaching the ground, a role that is more pronounced in subalpine areas. However, little research is concerned with the characteristics and dynamics of vegetation restoration in different microtopography types. The respective importance of the factors driving vegetation changes in subalpine areas is also not clear yet. We used linear regression and the Hurst exponent to analyze the trends in vegetation restoration and sustainability in different microtopography types since 2000, based on Fractional Vegetation Cover (FVC) and identified potential driving factors of vegetation change and their importance by using Geographical Detector. The results show that: (1) The FVC in the region under study has shown an up-trend since 2000, and the rate of increase is 0.26/year (P = 0.028). It would be going from improvement to degradation, continuous decrease or continuous significant decrease in 47.48% of the region, in the future. (2) The mean FVC is in the following order: lower slope (cool), lower slope, lower slope (warm), valley, upper slope (warm), upper slope, valley (narrow), upper slope (cool), cliff, mountain/divide, peak/ridge (warm), peak/ridge, peak/ridge (cool). The lower slope is the microtopographic type with the best vegetation cover, and ridge peak is the most difficult to be afforested. (3) The main factors affecting vegetation restoration in subalpine areas are aspect, microtopographic type, and soil taxonomy great groups. The interaction between multiple factors has a much stronger effect on vegetation cover than single factors, with the effect of temperatures and aspects having the most significant …
bibliographic citation: Feng et al. (2022) Quantitative analysis of vegetation restoration and potential driving factors in a typical subalpine region of the Eastern Tibet Plateau. PeerJ 10:e13358 https://doi.org/10.7717/peerj.13358
date submitted: 2021-11-26
date accepted: 2022-04-08
issued: 2022-04-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Yu
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Zhou
  given name: Qin
author list: Agent
  family name: Bai
  given name: Maoyang
author list: Agent
  family name: Peng
  given name: Peihao
author list: Agent
  family name: Zhao
  given name: Dan
author list: Agent
  family name: Guan
  given name: Zengyan
author list: Agent
  family name: Liu
  given name: Xian’an
doi: 10.7717/peerj.13358
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-28
copyright: ©2022 Feng et al.
attribution name: Feng et al.

Predicting crown width using nonlinear mixed-effects models accounting for competition in multi-species secondary forests
type: item
type: AcademicArticle
description: Crown width (CW) is an important tree variable and is often used as a covariate predictor in forest growth models. The precise measurement and prediction of CW is therefore critical for forest management. In this study, we introduced tree species as a random effect to develop nonlinear mixed-effects CW models for individual trees in multi-species secondary forests, accounting for the effects of competition. We identified a simple power function for the basic CW model. In addition to diameter at breast height (DBH), other significant predictor variables including height to crown base (HCB), tree height (TH), and competition indices (CI) were selected for the mixed-effects CW model. The sum of relative DBH (SRD) was identified the optimal distance-independent CI and as a covariate predictor for spatially non-explicit CW models, whereas the sum of the Hegyi index for fixed number competitors (SHGN) was the optimal distance-dependent CI for spatially explicit CW models, with significant linear correlation (R2 = 0.943, P < 0.001). Both spatially non-explicit and spatially explicit mixed-effects CW models were developed for studied secondary forests. We found that these models can describe more than 50% of the variation in CW without significant residual trends. Spatially explicit models exhibited a significantly larger effect on CW than spatially non-explicit ones; however, spatially explicit models are computationally complex and difficult and can be replaced by corresponding spatially non-explicit models due to the small differences in the fit statistics. The models we present may be useful for forestry inventory practices and have the potential to aid the evaluation and management of secondary forests in the region.
format: application/pdf
format: text/html
creator: Rui Hou
creator: Zongzheng Chai
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.13105
publisher: PeerJ Inc.
rights: © 2022 Hou and Chai
abstract: Crown width (CW) is an important tree variable and is often used as a covariate predictor in forest growth models. The precise measurement and prediction of CW is therefore critical for forest management. In this study, we introduced tree species as a random effect to develop nonlinear mixed-effects CW models for individual trees in multi-species secondary forests, accounting for the effects of competition. We identified a simple power function for the basic CW model. In addition to diameter at breast height (DBH), other significant predictor variables including height to crown base (HCB), tree height (TH), and competition indices (CI) were selected for the mixed-effects CW model. The sum of relative DBH (SRD) was identified the optimal distance-independent CI and as a covariate predictor for spatially non-explicit CW models, whereas the sum of the Hegyi index for fixed number competitors (SHGN) was the optimal distance-dependent CI for spatially explicit CW models, with significant linear correlation (R2 = 0.943, P < 0.001). Both spatially non-explicit and spatially explicit mixed-effects CW models were developed for studied secondary forests. We found that these models can describe more than 50% of the variation in CW without significant residual trends. Spatially explicit models exhibited a significantly larger effect on CW than spatially non-explicit ones; however, spatially explicit models are computationally complex and difficult and can be replaced by corresponding spatially non-explicit models due to the small differences in the fit statistics. The models we present may be useful for forestry inventory practices and have the potential to aid the evaluation and management of secondary forests in the region.
bibliographic citation: Hou et al. (2022) Predicting crown width using nonlinear mixed-effects models accounting for competition in multi-species secondary forests. PeerJ 10:e13105 https://doi.org/10.7717/peerj.13105
date submitted: 2021-05-13
date accepted: 2022-02-22
issued: 2022-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Rui
author list: Agent
  family name: Chai
  given name: Zongzheng
doi: 10.7717/peerj.13105
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: ©2022 Hou and Chai
attribution name: Hou and Chai

Skeletal variation in bird domestication: limb proportions and sternum in chicken, with comparisons to mallard ducks and Muscovy ducks
type: item
type: AcademicArticle
description: Background Domestication, including selective breeding, can lead to morphological changes of biomechanical relevance. In birds, limb proportions and sternum characteristics are of great importance and have been studied in the past for their relation with flight, terrestrial locomotion and animal welfare. In this work we studied the effects of domestication and breed formation in limb proportions and sternum characteristics in chicken (Gallus gallus), mallard ducks (Anas plathyrhynchos) and Muscovy ducks (Cairina moschata). Methods First, we quantified the proportional length of three long bones of the forelimb (humerus, radius, and carpometacarpus) and the hind limb (femur, tibiotarsus, and tarsometatarsus) in domestic chickens, mallard ducks, and Muscovy ducks and their wild counterparts. For this, we took linear measurements of these bones and compared their proportions in the wild vs. the domestic group in each species. In chicken, these comparisons could also be conducted among different breeds. We then evaluated the proportional differences in the context of static and ontogenetic allometry. Further, we compared discrete sternum characteristics in red jungle fowl and chicken breeds. In total, we examined limb bones of 287 specimens and keel bones of 63 specimens. Results We found a lack of significant change in the proportions of limb bones of chicken and Muscovy duck due to domestication, but significant differences in the case of mallard ducks. Variation of evolvability, allometric scaling, and heterochrony may serve to describe some of the patterns of change we report. Flight capacity loss in mallard ducks resulting from domestication may have a relation with the difference in limb proportions. The lack of variation in proportions that could distinguish domestic from wild forms of chicken and Muscovy ducks may reflect no selection for flight capacity during the domestication process in these groups. In chicken, some of the differences identified in the trait…
format: application/pdf
format: text/html
creator: Carlos Manuel Herrera-Castillo
creator: Madeleine Geiger
creator: Daniel Núñez-León
creator: Hiroshi Nagashima
creator: Sabine Gebhardt-Henrich
creator: Michael Toscano
creator: Marcelo R. Sanchez-Villagra
subject: Developmental Biology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.13229
publisher: PeerJ Inc.
rights: © 2022 Herrera-Castillo et al.
abstract: Background Domestication, including selective breeding, can lead to morphological changes of biomechanical relevance. In birds, limb proportions and sternum characteristics are of great importance and have been studied in the past for their relation with flight, terrestrial locomotion and animal welfare. In this work we studied the effects of domestication and breed formation in limb proportions and sternum characteristics in chicken (Gallus gallus), mallard ducks (Anas plathyrhynchos) and Muscovy ducks (Cairina moschata). Methods First, we quantified the proportional length of three long bones of the forelimb (humerus, radius, and carpometacarpus) and the hind limb (femur, tibiotarsus, and tarsometatarsus) in domestic chickens, mallard ducks, and Muscovy ducks and their wild counterparts. For this, we took linear measurements of these bones and compared their proportions in the wild vs. the domestic group in each species. In chicken, these comparisons could also be conducted among different breeds. We then evaluated the proportional differences in the context of static and ontogenetic allometry. Further, we compared discrete sternum characteristics in red jungle fowl and chicken breeds. In total, we examined limb bones of 287 specimens and keel bones of 63 specimens. Results We found a lack of significant change in the proportions of limb bones of chicken and Muscovy duck due to domestication, but significant differences in the case of mallard ducks. Variation of evolvability, allometric scaling, and heterochrony may serve to describe some of the patterns of change we report. Flight capacity loss in mallard ducks resulting from domestication may have a relation with the difference in limb proportions. The lack of variation in proportions that could distinguish domestic from wild forms of chicken and Muscovy ducks may reflect no selection for flight capacity during the domestication process in these groups. In chicken, some of the differences identified in the trait…
bibliographic citation: Herrera-Castillo et al. (2022) Skeletal variation in bird domestication: limb proportions and sternum in chicken, with comparisons to mallard ducks and Muscovy ducks. PeerJ 10:e13229 https://doi.org/10.7717/peerj.13229
date submitted: 2021-03-05
date accepted: 2022-03-16
issued: 2022-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Herrera-Castillo
  given name: Carlos Manuel
author list: Agent
  family name: Geiger
  given name: Madeleine
author list: Agent
  family name: Núñez-León
  given name: Daniel
author list: Agent
  family name: Nagashima
  given name: Hiroshi
author list: Agent
  family name: Gebhardt-Henrich
  given name: Sabine
author list: Agent
  family name: Toscano
  given name: Michael
author list: Agent
  family name: Sanchez-Villagra
  given name: Marcelo R.
doi: 10.7717/peerj.13229
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: ©2022 Herrera-Castillo et al.
attribution name: Herrera-Castillo et al.

Lipids associated with plant-bacteria interaction identified using a metabolomics approach in an Arabidopsis thaliana model
type: item
type: AcademicArticle
description: Background Systemic acquired resistance (SAR) protects plants against a wide variety of pathogens. In recent decades, numerous studies have focused on the induction of SAR, but its molecular mechanisms remain largely unknown. Methods We used a metabolomics approach based on ultra-high-performance liquid chromatographic (UPLC) and mass spectrometric (MS) techniques to identify SAR-related lipid metabolites in an Arabidopsis thaliana model. Multiple statistical analyses were used to identify the differentially regulated metabolites. Results Numerous lipids were implicated as potential factors in both plant basal resistance and SAR; these include species of phosphatidic acid (PA), monogalactosyldiacylglycerol (MGDG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and triacylglycerol (TG). Conclusions Our findings indicate that lipids accumulated in both local and systemic leaves, while other lipids only accumulated in local leaves or in systemic leaves. PA (16:0_18:2), PE (34:5) and PE (16:0_18:2) had higher levels in both local leaves inoculated with Psm ES4326 or Psm avrRpm1 and systemic leaves of the plants locally infected with Psm avrRpm1 or Psm ES4326. PC (32:5) had high levels in leaves inoculated with Psm ES4326. Other differentially regulated metabolites, including PA (18:2_18:2), PA (16:0_18:3), PA (18:3_18:2), PE (16:0_18:3), PE (16:1_16:1), PE (34:4) and TGs showed higher levels in systemic leaves of the plants locally infected with Psm avrRpm1 or Psm ES4326. These findings will help direct future studies on the molecular mechanisms of SAR.
format: application/pdf
format: text/html
creator: Jian-Bo Song
creator: Rui-Ke Huang
creator: Miao-Jie Guo
creator: Qian Zhou
creator: Rui Guo
creator: Shu-Yuan Zhang
creator: Jing-Wen Yao
creator: Ya-Ni Bai
creator: Xuan Huang
subject: Cell Biology
subject: Plant Science
subject: Immunology
description: doi:10.7717/peerj.13293
publisher: PeerJ Inc.
rights: © 2022 Song et al.
abstract: Background Systemic acquired resistance (SAR) protects plants against a wide variety of pathogens. In recent decades, numerous studies have focused on the induction of SAR, but its molecular mechanisms remain largely unknown. Methods We used a metabolomics approach based on ultra-high-performance liquid chromatographic (UPLC) and mass spectrometric (MS) techniques to identify SAR-related lipid metabolites in an Arabidopsis thaliana model. Multiple statistical analyses were used to identify the differentially regulated metabolites. Results Numerous lipids were implicated as potential factors in both plant basal resistance and SAR; these include species of phosphatidic acid (PA), monogalactosyldiacylglycerol (MGDG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and triacylglycerol (TG). Conclusions Our findings indicate that lipids accumulated in both local and systemic leaves, while other lipids only accumulated in local leaves or in systemic leaves. PA (16:0_18:2), PE (34:5) and PE (16:0_18:2) had higher levels in both local leaves inoculated with Psm ES4326 or Psm avrRpm1 and systemic leaves of the plants locally infected with Psm avrRpm1 or Psm ES4326. PC (32:5) had high levels in leaves inoculated with Psm ES4326. Other differentially regulated metabolites, including PA (18:2_18:2), PA (16:0_18:3), PA (18:3_18:2), PE (16:0_18:3), PE (16:1_16:1), PE (34:4) and TGs showed higher levels in systemic leaves of the plants locally infected with Psm avrRpm1 or Psm ES4326. These findings will help direct future studies on the molecular mechanisms of SAR.
bibliographic citation: Song et al. (2022) Lipids associated with plant-bacteria interaction identified using a metabolomics approach in an Arabidopsis thaliana model. PeerJ 10:e13293 https://doi.org/10.7717/peerj.13293
date submitted: 2021-08-23
date accepted: 2022-03-28
issued: 2022-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Jian-Bo
author list: Agent
  family name: Huang
  given name: Rui-Ke
author list: Agent
  family name: Guo
  given name: Miao-Jie
author list: Agent
  family name: Zhou
  given name: Qian
author list: Agent
  family name: Guo
  given name: Rui
author list: Agent
  family name: Zhang
  given name: Shu-Yuan
author list: Agent
  family name: Yao
  given name: Jing-Wen
author list: Agent
  family name: Bai
  given name: Ya-Ni
author list: Agent
  family name: Huang
  given name: Xuan
doi: 10.7717/peerj.13293
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: ©2022 Song et al.
attribution name: Song et al.

Winter diet of Burrowing Owls in the Llano La Soledad, Galeana, Nuevo León, México
type: item
type: AcademicArticle
description: The dietary niche breadth of the Burrowing Owl was determined (Athene cunicularia Molina, 1782) in Llano La Soledad, Galeana, Nuevo Leon in northern Mexico, by considering prey type, numerical percentage, weight, weight percentage, frequency of occurrence percentage, and IRI percentage. The study compared data from three winters (2002–2003, 2003–2004, 2004–2005) by analyzing 358 pellets, identifying 850 prey items. Invertebrates constituted 90% of prey items, which mostly included insects (85%); beetles were the most common insects found in pellets (70%). Vertebrates made up 84% of consumed weight, of which 83% were mammals. Most of the mammals were cricetid rodents (41%). Niche breadth based on the numerical and weight percentage confirmed the Burrowing Owl as a generalist species with mean values per year ranging between 0.65 and 0.82. Additionally, there was a strong association between the weight of rodent species in winter. This association was mainly driven by changes in composition and frequency of these prey species during the second winter, probably caused by high annual rainfall. The second season also showed a statistically significant narrower niche (Ro = 0.96) and the smallest overlap (0.45 vs. 0.76) among the three winters.
format: application/pdf
format: text/html
creator: Jose I. Gonzalez Rojas
creator: Miguel Angel Cruz Nieto
creator: Antonio Guzmán Velasco
creator: Irene Ruvalcaba-Ortega
creator: Alina Olalla-Kerstupp
creator: Gabriel Ruiz-Ayma
subject: Animal Behavior
subject: Ecology
subject: Ecosystem Science
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.13324
publisher: PeerJ Inc.
rights: © 2022 Gonzalez Rojas et al.
abstract: The dietary niche breadth of the Burrowing Owl was determined (Athene cunicularia Molina, 1782) in Llano La Soledad, Galeana, Nuevo Leon in northern Mexico, by considering prey type, numerical percentage, weight, weight percentage, frequency of occurrence percentage, and IRI percentage. The study compared data from three winters (2002–2003, 2003–2004, 2004–2005) by analyzing 358 pellets, identifying 850 prey items. Invertebrates constituted 90% of prey items, which mostly included insects (85%); beetles were the most common insects found in pellets (70%). Vertebrates made up 84% of consumed weight, of which 83% were mammals. Most of the mammals were cricetid rodents (41%). Niche breadth based on the numerical and weight percentage confirmed the Burrowing Owl as a generalist species with mean values per year ranging between 0.65 and 0.82. Additionally, there was a strong association between the weight of rodent species in winter. This association was mainly driven by changes in composition and frequency of these prey species during the second winter, probably caused by high annual rainfall. The second season also showed a statistically significant narrower niche (Ro = 0.96) and the smallest overlap (0.45 vs. 0.76) among the three winters.
bibliographic citation: Gonzalez Rojas et al. (2022) Winter diet of Burrowing Owls in the Llano La Soledad, Galeana, Nuevo León, México. PeerJ 10:e13324 https://doi.org/10.7717/peerj.13324
date submitted: 2020-06-18
date accepted: 2022-04-01
issued: 2022-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzalez Rojas
  given name: Jose I.
author list: Agent
  family name: Cruz Nieto
  given name: Miguel Angel
author list: Agent
  family name: Guzmán Velasco
  given name: Antonio
author list: Agent
  family name: Ruvalcaba-Ortega
  given name: Irene
author list: Agent
  family name: Olalla-Kerstupp
  given name: Alina
author list: Agent
  family name: Ruiz-Ayma
  given name: Gabriel
doi: 10.7717/peerj.13324
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: © 2022 Gonzalez Rojas et al.
attribution name: Gonzalez Rojas et al.

Polyphenolic extract from Punica granatum peel causes cytoskeleton-related damage on Giardia lamblia trophozoites in vitro
type: item
type: AcademicArticle
description: Background Diarrheal diseases caused by protozoa have a great impact on human health around the world. Giardia lamblia is one of the most common flagellates in the intestinal tract. Factors such as adverse effects to first-line drugs or the appearance of drug-resistant strains, make it necessary to identify new treatment alternatives. Agroindustry waste, like pomegranate peel, are a source of phenolic compounds, which possess antiparasitic activities. In vivo studies demonstrated antigiardiasic potential by reducing cyst shedding and protecting intestinal cells; however, they did not identify the compounds or elucidate any mechanism of action in the parasite. The objective of this study is to identify potential molecular targets and to test the in vitro effects of polyphenols from Punica granatum on Giardia lamblia. Methods The in vitro antigiardial potential of polyphenolic extract from pomegranate peel (Punica granatum L.) obtained using microwave-ultrasound methodology was evaluated on Giardia lamblia trophozoites. Extract phytochemical identification was performed by HPLC/MS analysis. The effect of polyphenolic extract on growth and adhesion capacity was determined by parasite kinetics; morphological damage was evaluated by SEM, alteration on α-tubulin expression and distribution were analyzed by western blot and immunofluorescence, respectively. Results The pomegranate peel extract showed the presence of ellagitannins (punicalin and punicalagin, galloyl-dihexahydroxydiphenoyl-hexoside), flavones (luteolin), and ellagic acid, that caused an inhibitory effect on growth and adhesion capacity, particularly on cells treated with 200 µg/mL, where growth inhibition of 74.36%, trophozoite adherence inhibition of 46.8% and IC50 of 179 µg/mL at 48 h were demonstrated. The most important findings were that the extract alters α-tubulin expression and distribution in Giardia trophozoites in a concentration-independent manner. Also, an increase in α-tubulin expression at 200…
format: application/pdf
format: text/html
creator: Lissethe Palomo-Ligas
creator: Job Estrada-Camacho
creator: Mariana Garza-Ontiveros
creator: José Roberto Vargas-Villanueva
creator: Filiberto Gutiérrez-Gutiérrez
creator: Sendar Daniel Nery-Flores
creator: Jorge Arturo Cañas Montoya
creator: Juan Ascacio-Valdés
creator: Lizeth Guadalupe Campos-Muzquiz
creator: Raul Rodriguez-Herrera
subject: Cell Biology
subject: Microbiology
subject: Parasitology
subject: Pharmacology
description: doi:10.7717/peerj.13350
publisher: PeerJ Inc.
rights: © 2022 Palomo-Ligas et al.
abstract: Background Diarrheal diseases caused by protozoa have a great impact on human health around the world. Giardia lamblia is one of the most common flagellates in the intestinal tract. Factors such as adverse effects to first-line drugs or the appearance of drug-resistant strains, make it necessary to identify new treatment alternatives. Agroindustry waste, like pomegranate peel, are a source of phenolic compounds, which possess antiparasitic activities. In vivo studies demonstrated antigiardiasic potential by reducing cyst shedding and protecting intestinal cells; however, they did not identify the compounds or elucidate any mechanism of action in the parasite. The objective of this study is to identify potential molecular targets and to test the in vitro effects of polyphenols from Punica granatum on Giardia lamblia. Methods The in vitro antigiardial potential of polyphenolic extract from pomegranate peel (Punica granatum L.) obtained using microwave-ultrasound methodology was evaluated on Giardia lamblia trophozoites. Extract phytochemical identification was performed by HPLC/MS analysis. The effect of polyphenolic extract on growth and adhesion capacity was determined by parasite kinetics; morphological damage was evaluated by SEM, alteration on α-tubulin expression and distribution were analyzed by western blot and immunofluorescence, respectively. Results The pomegranate peel extract showed the presence of ellagitannins (punicalin and punicalagin, galloyl-dihexahydroxydiphenoyl-hexoside), flavones (luteolin), and ellagic acid, that caused an inhibitory effect on growth and adhesion capacity, particularly on cells treated with 200 µg/mL, where growth inhibition of 74.36%, trophozoite adherence inhibition of 46.8% and IC50 of 179 µg/mL at 48 h were demonstrated. The most important findings were that the extract alters α-tubulin expression and distribution in Giardia trophozoites in a concentration-independent manner. Also, an increase in α-tubulin expression at 200…
bibliographic citation: Palomo-Ligas et al. (2022) Polyphenolic extract from Punica granatum peel causes cytoskeleton-related damage on Giardia lamblia trophozoites in vitro. PeerJ 10:e13350 https://doi.org/10.7717/peerj.13350
date submitted: 2022-01-21
date accepted: 2022-04-07
issued: 2022-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palomo-Ligas
  given name: Lissethe
author list: Agent
  family name: Estrada-Camacho
  given name: Job
author list: Agent
  family name: Garza-Ontiveros
  given name: Mariana
author list: Agent
  family name: Vargas-Villanueva
  given name: José Roberto
author list: Agent
  family name: Gutiérrez-Gutiérrez
  given name: Filiberto
author list: Agent
  family name: Nery-Flores
  given name: Sendar Daniel
author list: Agent
  family name: Cañas Montoya
  given name: Jorge Arturo
author list: Agent
  family name: Ascacio-Valdés
  given name: Juan
author list: Agent
  family name: Campos-Muzquiz
  given name: Lizeth Guadalupe
author list: Agent
  family name: Rodriguez-Herrera
  given name: Raul
doi: 10.7717/peerj.13350
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: © 2022 Palomo-Ligas et al.
attribution name: Palomo-Ligas et al.

Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
type: item
type: AcademicArticle
description: The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
format: application/pdf
format: text/html
creator: Stepan Nersisyan
creator: Anton Zhiyanov
creator: Maria Zakharova
creator: Irina Ishina
creator: Inna Kurbatskaia
creator: Azad Mamedov
creator: Alexei Galatenko
creator: Maxim Shkurnikov
creator: Alexander Gabibov
creator: Alexander Tonevitsky
subject: Bioinformatics
subject: Cell Biology
subject: Virology
description: doi:10.7717/peerj.13354
publisher: PeerJ Inc.
rights: © 2022 Nersisyan et al.
abstract: The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
bibliographic citation: Nersisyan et al. (2022) Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. PeerJ 10:e13354 https://doi.org/10.7717/peerj.13354
date submitted: 2022-03-01
date accepted: 2022-04-08
issued: 2022-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nersisyan
  given name: Stepan
author list: Agent
  family name: Zhiyanov
  given name: Anton
author list: Agent
  family name: Zakharova
  given name: Maria
author list: Agent
  family name: Ishina
  given name: Irina
author list: Agent
  family name: Kurbatskaia
  given name: Inna
author list: Agent
  family name: Mamedov
  given name: Azad
author list: Agent
  family name: Galatenko
  given name: Alexei
author list: Agent
  family name: Shkurnikov
  given name: Maxim
author list: Agent
  family name: Gabibov
  given name: Alexander
author list: Agent
  family name: Tonevitsky
  given name: Alexander
doi: 10.7717/peerj.13354
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: © 2022 Nersisyan et al.
attribution name: Nersisyan et al.

Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica
type: item
type: AcademicArticle
description: Many conservation projects relocate sea turtle eggs to hatcheries to protect the sea turtle nests from the anthropogenic and natural threats they face in the early stages of development. The Rescue Center for Endangered Marine Species (CREMA) manages four sea turtle conservation projects on the nesting beaches of the Southern Nicoya Peninsula in Costa Rica, where the predominant nesting activity is from olive ridley turtles (Lepidochelys olivacea). Two of these nesting projects are based in Costa de Oro and San Miguel, which are adjacent beaches divided by an estuary. In this study, we compared the dynamics and rates of human and animal predation of nests prior to being relocated to the hatchery on both nesting beaches from 2012 to 2018. We hypothesized that human take and animal predation were compensatory threats, meaning that lower human take may result in higher animal predation, and vice versa, resulting in a similar number of nests lost to predation overall. We discuss the community-based conservation programs on both beaches, one of which has been monitored since 1998 (San Miguel) and the other of which has been monitored since 2012 (Costa de Oro). We found that Costa de Oro exhibited high rates of human take with up to 51% of nests being extracted per season, which has decreased since the conservation project was established. Human take was significantly higher than animal predation on both beaches and human take was significantly higher in Costa de Oro. While San Miguel exhibited higher animal predation, the difference was not statistically significant. Higher depredation by animals corresponded to higher overall nest abundance on both beaches. We were unable to find evidence that human take or animal predation increased in the absence of the other threat, suggesting a lack of compensatory effects of predation. Our findings support further analysis of animal predation and a continuation of patrol-based conservation efforts as well as community outreach to a…
format: application/pdf
format: text/html
creator: Janie L. Reavis
creator: Daniela Rojas-Cañizales
creator: Carmen Mejías-Balsalobre
creator: Isabel Naranjo
creator: Randall Arauz
creator: Jesse F. Senko
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.12925
publisher: PeerJ Inc.
rights: © 2022 Reavis et al.
abstract: Many conservation projects relocate sea turtle eggs to hatcheries to protect the sea turtle nests from the anthropogenic and natural threats they face in the early stages of development. The Rescue Center for Endangered Marine Species (CREMA) manages four sea turtle conservation projects on the nesting beaches of the Southern Nicoya Peninsula in Costa Rica, where the predominant nesting activity is from olive ridley turtles (Lepidochelys olivacea). Two of these nesting projects are based in Costa de Oro and San Miguel, which are adjacent beaches divided by an estuary. In this study, we compared the dynamics and rates of human and animal predation of nests prior to being relocated to the hatchery on both nesting beaches from 2012 to 2018. We hypothesized that human take and animal predation were compensatory threats, meaning that lower human take may result in higher animal predation, and vice versa, resulting in a similar number of nests lost to predation overall. We discuss the community-based conservation programs on both beaches, one of which has been monitored since 1998 (San Miguel) and the other of which has been monitored since 2012 (Costa de Oro). We found that Costa de Oro exhibited high rates of human take with up to 51% of nests being extracted per season, which has decreased since the conservation project was established. Human take was significantly higher than animal predation on both beaches and human take was significantly higher in Costa de Oro. While San Miguel exhibited higher animal predation, the difference was not statistically significant. Higher depredation by animals corresponded to higher overall nest abundance on both beaches. We were unable to find evidence that human take or animal predation increased in the absence of the other threat, suggesting a lack of compensatory effects of predation. Our findings support further analysis of animal predation and a continuation of patrol-based conservation efforts as well as community outreach to a…
bibliographic citation: Reavis et al. (2022) Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica. PeerJ 10:e12925 https://doi.org/10.7717/peerj.12925
date submitted: 2021-08-12
date accepted: 2022-01-20
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reavis
  given name: Janie L.
author list: Agent
  family name: Rojas-Cañizales
  given name: Daniela
author list: Agent
  family name: Mejías-Balsalobre
  given name: Carmen
author list: Agent
  family name: Naranjo
  given name: Isabel
author list: Agent
  family name: Arauz
  given name: Randall
author list: Agent
  family name: Senko
  given name: Jesse F.
doi: 10.7717/peerj.12925
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Reavis et al.
attribution name: Reavis et al.

Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies
type: item
type: AcademicArticle
description: Research on the biological role of exosomes is rapidly developing, and recent evidence suggests that exosomal effects involve ferroptosis. Exosomes derived from different tissues inhibit ferroptosis, which increases tumour cell chemoresistance. Therefore, exosome-mediated regulation of ferroptosis may be leveraged to design anticancer drugs. This review discusses three pathways of exosome-mediated inhibition of ferroptosis: (1) the Fenton reaction; (2) the ferroptosis defence system, including the Xc-GSH-GPX4 axis and the FSP1/CoQ10/NAD(P)H axis; and (3) lipid peroxidation. We also summarize three recent approaches for combining exosomes and ferroptosis in oncology therapy: (1) promoting exosome-inhibited ferroptosis to enhance chemotherapy; (2) encapsulating exosomes with ferroptosis inducers to inhibit cancers; and (3) developing therapies that combine exosomal inhibitors and ferroptosis inducers. This review will contribute toward establishing effective cancer therapies.
format: application/pdf
format: text/html
creator: Yixin Shi
creator: Bingrun Qiu
creator: Linyang Huang
creator: Jie Lin
creator: Yiling Li
creator: Yiting Ze
creator: Chenglong Huang
creator: Yang Yao
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.13238
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: Research on the biological role of exosomes is rapidly developing, and recent evidence suggests that exosomal effects involve ferroptosis. Exosomes derived from different tissues inhibit ferroptosis, which increases tumour cell chemoresistance. Therefore, exosome-mediated regulation of ferroptosis may be leveraged to design anticancer drugs. This review discusses three pathways of exosome-mediated inhibition of ferroptosis: (1) the Fenton reaction; (2) the ferroptosis defence system, including the Xc-GSH-GPX4 axis and the FSP1/CoQ10/NAD(P)H axis; and (3) lipid peroxidation. We also summarize three recent approaches for combining exosomes and ferroptosis in oncology therapy: (1) promoting exosome-inhibited ferroptosis to enhance chemotherapy; (2) encapsulating exosomes with ferroptosis inducers to inhibit cancers; and (3) developing therapies that combine exosomal inhibitors and ferroptosis inducers. This review will contribute toward establishing effective cancer therapies.
bibliographic citation: Shi et al. (2022) Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies. PeerJ 10:e13238 https://doi.org/10.7717/peerj.13238
date submitted: 2021-12-15
date accepted: 2022-03-18
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yixin
author list: Agent
  family name: Qiu
  given name: Bingrun
author list: Agent
  family name: Huang
  given name: Linyang
author list: Agent
  family name: Lin
  given name: Jie
author list: Agent
  family name: Li
  given name: Yiling
author list: Agent
  family name: Ze
  given name: Yiting
author list: Agent
  family name: Huang
  given name: Chenglong
author list: Agent
  family name: Yao
  given name: Yang
doi: 10.7717/peerj.13238
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Shi et al.
attribution name: Shi et al.

Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)
type: item
type: AcademicArticle
description: We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the d…
format: application/pdf
format: text/html
creator: Vladimir E. Fedosov
creator: Anna V. Shkurko
creator: Alina V. Fedorova
creator: Elena A. Ignatova
creator: Evgeniya N. Solovyeva
creator: John C. Brinda
creator: Michael S. Ignatov
creator: Jan Kučera
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.13260
publisher: PeerJ Inc.
rights: © 2022 Fedosov et al.
abstract: We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the d…
bibliographic citation: Fedosov et al. (2022) Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta). PeerJ 10:e13260 https://doi.org/10.7717/peerj.13260
date submitted: 2021-11-10
date accepted: 2022-03-22
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fedosov
  given name: Vladimir E.
author list: Agent
  family name: Shkurko
  given name: Anna V.
author list: Agent
  family name: Fedorova
  given name: Alina V.
author list: Agent
  family name: Ignatova
  given name: Elena A.
author list: Agent
  family name: Solovyeva
  given name: Evgeniya N.
author list: Agent
  family name: Brinda
  given name: John C.
author list: Agent
  family name: Ignatov
  given name: Michael S.
author list: Agent
  family name: Kučera
  given name: Jan
doi: 10.7717/peerj.13260
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Fedosov et al.
attribution name: Fedosov et al.

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