PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Notes on vocalizations of Brazilian amphibians IV: advertisement calls of 20 Atlantic Forest frog species
items: Analysis of small RNA changes in different Brassica napus synthetic allopolyploids
items: EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model
items: Screening and identification of SipC-interacting proteins in Salmonella enteritidis using Gal4 yeast two-hybrid system in duck
items: Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals
items: Red-crowned crane (Grus japonensis) prefers postharvest reed beds during winter period in Yancheng National Nature Reserve
items: Niches and climate-change refugia in hundreds of species from one of the most arid places on Earth
items: Antimicrobial photodynamic therapy on Staphylococcus aureus and Escherichia coli using malachite green encapsulated mesoporous silica nanoparticles: an in vitro study
items: Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known
items: Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses

Notes on vocalizations of Brazilian amphibians IV: advertisement calls of 20 Atlantic Forest frog species
type: item
type: AcademicArticle
description: Bioacoustics is a powerful tool used for anuran species diagnoses, given that advertisement calls are signals related to specific recognition and mate attraction. Thus, call descriptions can support species taxonomy. In spite of that, call descriptions are lacking for many species, delaying advances in biodiversity research. Here, we describe the advertisement calls of 20 anuran species from the Brazilian Atlantic Forest. We accessed 50 digital recordings deposited in the Fonoteca Neotropical Jacques Vielliard. Acoustic analyses were carried out in the software Raven pro 1.5. We provide a general comparison of call structure among species inside taxonomic groups and genera. The vocalizations described here belong to poorly known species, which are representatives of six families: Brachycephalidae, Bufonidae, Ceratophryidae, Cycloramphidae, Hylidae, and Phyllomedusidae. Despite this, still there are 163 species of anurans from Atlantic Forest with calls not formally described. Our work represents an important step in providing data for a taxonomic perspective and improving the knowledge of the Atlantic Forest anuran diversity.
format: application/pdf
format: text/html
creator: Lucas Rodriguez Forti
creator: Célio Fernando Baptista Haddad
creator: Felipe Leite
creator: Leandro de Oliveira Drummond
creator: Clodoaldo de Assis
creator: Lucas Batista Crivellari
creator: Caio Marinho Mello
creator: Paulo Christiano Anchietta Garcia
creator: Camila Zornosa-Torres
creator: Luís Felipe Toledo
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.7612
publisher: PeerJ Inc.
rights: © 2019 Forti et al.
abstract: Bioacoustics is a powerful tool used for anuran species diagnoses, given that advertisement calls are signals related to specific recognition and mate attraction. Thus, call descriptions can support species taxonomy. In spite of that, call descriptions are lacking for many species, delaying advances in biodiversity research. Here, we describe the advertisement calls of 20 anuran species from the Brazilian Atlantic Forest. We accessed 50 digital recordings deposited in the Fonoteca Neotropical Jacques Vielliard. Acoustic analyses were carried out in the software Raven pro 1.5. We provide a general comparison of call structure among species inside taxonomic groups and genera. The vocalizations described here belong to poorly known species, which are representatives of six families: Brachycephalidae, Bufonidae, Ceratophryidae, Cycloramphidae, Hylidae, and Phyllomedusidae. Despite this, still there are 163 species of anurans from Atlantic Forest with calls not formally described. Our work represents an important step in providing data for a taxonomic perspective and improving the knowledge of the Atlantic Forest anuran diversity.
bibliographic citation: Forti et al. (2019) Notes on vocalizations of Brazilian amphibians IV: advertisement calls of 20 Atlantic Forest frog species. PeerJ 7:e7612 https://doi.org/10.7717/peerj.7612
date submitted: 2019-05-03
date accepted: 2019-08-05
issued: 2019-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Forti
  given name: Lucas Rodriguez
author list: Agent
  family name: Haddad
  given name: Célio Fernando Baptista
author list: Agent
  family name: Leite
  given name: Felipe
author list: Agent
  family name: Drummond
  given name: Leandro de Oliveira
author list: Agent
  family name: de Assis
  given name: Clodoaldo
author list: Agent
  family name: Crivellari
  given name: Lucas Batista
author list: Agent
  family name: Mello
  given name: Caio Marinho
author list: Agent
  family name: Garcia
  given name: Paulo Christiano Anchietta
author list: Agent
  family name: Zornosa-Torres
  given name: Camila
author list: Agent
  family name: Toledo
  given name: Luís Felipe
doi: 10.7717/peerj.7612
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-13
copyright: © 2019 Forti et al.
attribution name: Forti et al.

Analysis of small RNA changes in different Brassica napus synthetic allopolyploids
type: item
type: AcademicArticle
description: Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.
format: application/pdf
format: text/html
creator: Yunxiao Wei
creator: Fei Li
creator: Shujiang Zhang
creator: Shifan Zhang
creator: Hui Zhang
creator: Rifei Sun
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.7621
publisher: PeerJ Inc.
rights: © 2019 Wei et al.
abstract: Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.
bibliographic citation: Wei et al. (2019) Analysis of small RNA changes in different Brassica napus synthetic allopolyploids. PeerJ 7:e7621 https://doi.org/10.7717/peerj.7621
date submitted: 2019-04-03
date accepted: 2019-08-05
issued: 2019-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Yunxiao
author list: Agent
  family name: Li
  given name: Fei
author list: Agent
  family name: Zhang
  given name: Shujiang
author list: Agent
  family name: Zhang
  given name: Shifan
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Sun
  given name: Rifei
doi: 10.7717/peerj.7621
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-13
copyright: ©2019 Wei et al.
attribution name: Wei et al.

EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model
type: item
type: AcademicArticle
description: Chromatin contacts between regulatory elements are of crucial importance for the interpretation of transcriptional regulation and the understanding of disease mechanisms. However, existing computational methods mainly focus on the prediction of interactions between enhancers and promoters, leaving enhancer-enhancer (E-E) interactions not well explored. In this work, we develop a novel deep learning approach, named Enhancer-enhancer contacts prediction (EnContact), to predict E-E contacts using genomic sequences as input. We statistically demonstrated the predicting ability of EnContact using training sets and testing sets derived from HiChIP data of seven cell lines. We also show that our model significantly outperforms other baseline methods. Besides, our model identifies finer-mapping E-E interactions from region-based chromatin contacts, where each region contains several enhancers. In addition, we identify a class of hub enhancers using the predicted E-E interactions and find that hub enhancers tend to be active across cell lines. We summarize that our EnContact model is capable of predicting E-E interactions using features automatically learned from genomic sequences.
format: application/pdf
format: text/html
creator: Mingxin Gan
creator: Wenran Li
creator: Rui Jiang
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.7657
publisher: PeerJ Inc.
rights: © 2019 Gan et al.
abstract: Chromatin contacts between regulatory elements are of crucial importance for the interpretation of transcriptional regulation and the understanding of disease mechanisms. However, existing computational methods mainly focus on the prediction of interactions between enhancers and promoters, leaving enhancer-enhancer (E-E) interactions not well explored. In this work, we develop a novel deep learning approach, named Enhancer-enhancer contacts prediction (EnContact), to predict E-E contacts using genomic sequences as input. We statistically demonstrated the predicting ability of EnContact using training sets and testing sets derived from HiChIP data of seven cell lines. We also show that our model significantly outperforms other baseline methods. Besides, our model identifies finer-mapping E-E interactions from region-based chromatin contacts, where each region contains several enhancers. In addition, we identify a class of hub enhancers using the predicted E-E interactions and find that hub enhancers tend to be active across cell lines. We summarize that our EnContact model is capable of predicting E-E interactions using features automatically learned from genomic sequences.
bibliographic citation: Gan et al. (2019) EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model. PeerJ 7:e7657 https://doi.org/10.7717/peerj.7657
date submitted: 2019-05-14
date accepted: 2019-08-10
issued: 2019-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Mingxin
author list: Agent
  family name: Li
  given name: Wenran
author list: Agent
  family name: Jiang
  given name: Rui
doi: 10.7717/peerj.7657
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-13
copyright: © 2019 Gan et al.
attribution name: Gan et al.

Screening and identification of SipC-interacting proteins in Salmonella enteritidis using Gal4 yeast two-hybrid system in duck
type: item
type: AcademicArticle
description: The zoonotic pathogen Salmonella not only reduces the production performance in ducks, but also poses a serious threat to human health through eggs and pollutes water bodies through feces. SipC, an effector protein of type III secretion systems (T3SS) in Salmonella, mediates translocation of effectors into the eukaryotic host. However, the precise role of SipC effectors remains unknown in ducks. In this study, the SipC from duck granulosa cells (dGCs) was selected as bait, and the SipC-interacting proteins in Salmonella enteritidis (SE) were screened using Gal4 yeast two-hybrid system in duck. Twelve SipC-interacting proteins were identified. Among those, the p53-effector related to PMP-22 (PERP) and TGF-β activated kinase 1-binding protein 2 (TAB2) were selected to further confirm the function by GST pull-down in vitro. Over-expression of PERP resulted in not only increasing SE adhesion and invasion but also triggering the production of IL-1β and IFN-α in SE infected dGCs, while knock-down PERP showed the opposite tendency (P < 0.01). In addition, TAB2 significantly induced the production of IL-6, IL-1β, IFN-α, and INF-γ in SE infected dGCs (P < 0.05), but did not cause obvious changes in SE adhesion and invasion. When the sipC in SE was deleted, the activities of duck PERP and TAB2 were abolished because they could not bind to SipC. Taken together, although the protein of PERP and TAB2 can interact with SipC, their mechanisms were different in duck challenged by SE. Therefore, PERP was involved in SE invasion and inflammatory response of dGC ovaries, and TAB2 only contributed to dGCs inflammatory response, which provided critical insights about the mechanism in host- bacterium protein interactions during Salmonella invasion in duck.
format: application/pdf
format: text/html
creator: Yu Zhang
creator: Tiantian Gu
creator: Yang Chen
creator: Guoqiang Zhu
creator: Wanwipa Vongsangnak
creator: Qi Xu
creator: Guohong Chen
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.7663
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: The zoonotic pathogen Salmonella not only reduces the production performance in ducks, but also poses a serious threat to human health through eggs and pollutes water bodies through feces. SipC, an effector protein of type III secretion systems (T3SS) in Salmonella, mediates translocation of effectors into the eukaryotic host. However, the precise role of SipC effectors remains unknown in ducks. In this study, the SipC from duck granulosa cells (dGCs) was selected as bait, and the SipC-interacting proteins in Salmonella enteritidis (SE) were screened using Gal4 yeast two-hybrid system in duck. Twelve SipC-interacting proteins were identified. Among those, the p53-effector related to PMP-22 (PERP) and TGF-β activated kinase 1-binding protein 2 (TAB2) were selected to further confirm the function by GST pull-down in vitro. Over-expression of PERP resulted in not only increasing SE adhesion and invasion but also triggering the production of IL-1β and IFN-α in SE infected dGCs, while knock-down PERP showed the opposite tendency (P < 0.01). In addition, TAB2 significantly induced the production of IL-6, IL-1β, IFN-α, and INF-γ in SE infected dGCs (P < 0.05), but did not cause obvious changes in SE adhesion and invasion. When the sipC in SE was deleted, the activities of duck PERP and TAB2 were abolished because they could not bind to SipC. Taken together, although the protein of PERP and TAB2 can interact with SipC, their mechanisms were different in duck challenged by SE. Therefore, PERP was involved in SE invasion and inflammatory response of dGC ovaries, and TAB2 only contributed to dGCs inflammatory response, which provided critical insights about the mechanism in host- bacterium protein interactions during Salmonella invasion in duck.
bibliographic citation: Zhang et al. (2019) Screening and identification of SipC-interacting proteins in Salmonella enteritidis using Gal4 yeast two-hybrid system in duck. PeerJ 7:e7663 https://doi.org/10.7717/peerj.7663
date submitted: 2019-03-19
date accepted: 2019-08-12
issued: 2019-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Gu
  given name: Tiantian
author list: Agent
  family name: Chen
  given name: Yang
author list: Agent
  family name: Zhu
  given name: Guoqiang
author list: Agent
  family name: Vongsangnak
  given name: Wanwipa
author list: Agent
  family name: Xu
  given name: Qi
author list: Agent
  family name: Chen
  given name: Guohong
doi: 10.7717/peerj.7663
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-13
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals
type: item
type: AcademicArticle
description: Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.
format: application/pdf
format: text/html
creator: Sébastien Leveque
creator: Lutfi Afiq-Rosli
creator: Yin Cheong Aden Ip
creator: Sudhanshi S. Jain
creator: Danwei Huang
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.7669
publisher: PeerJ Inc.
rights: © 2019 Leveque et al.
abstract: Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.
bibliographic citation: Leveque et al. (2019) Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals. PeerJ 7:e7669 https://doi.org/10.7717/peerj.7669
date submitted: 2019-04-16
date accepted: 2019-08-13
issued: 2019-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leveque
  given name: Sébastien
author list: Agent
  family name: Afiq-Rosli
  given name: Lutfi
author list: Agent
  family name: Ip
  given name: Yin Cheong Aden
author list: Agent
  family name: Jain
  given name: Sudhanshi S.
author list: Agent
  family name: Huang
  given name: Danwei
doi: 10.7717/peerj.7669
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-13
copyright: ©2019 Leveque et al.
attribution name: Leveque et al.

Red-crowned crane (Grus japonensis) prefers postharvest reed beds during winter period in Yancheng National Nature Reserve
type: item
type: AcademicArticle
description: Reed beds represent an important habitat for the survival of birds by providing favorable foraging and reproduction conditions. Reed management, as a traditional agricultural activity, primarily includes water level control and vegetation removal by cutting. Red-crowned crane (Grus japonensis) is one of the most endangered cranes, and their population continues to decline due to habitat loss caused by artificial activities. A lack of research relating to how reed management affects crane habitat distribution patterns throughout the wintering period hinders our ability to offer conservation recommendations. In the present study, we explored the effect of reed management on the habitat distribution patterns and analyzed the food resources of red-crowned crane in the Yancheng National Nature Reserve (YNNR). According to the reed management activities in December, we divided the wintering period into two phases: the preharvest period and the postharvest period. Throughout the wintering period, the number of cranes recorded in the common seepweed (Suaeda glauca) tidal flats remained stable, but cranes were rarely recorded in the smooth cordgrass (Spartina alterniflora) tidal flats and aquaculture fish ponds. The number of cranes, however, showed a noticeable fluctuation in the reed beds during the two periods. Before the reed harvest, only a small proportion of cranes were recorded in the reed beds (relative abundance = 2.9%). However, more cranes (relative abundance = 61.0%) were recorded after the reed harvest. Water was introduced from adjacent rivers and fish ponds to submerge the cut reed beds. Changes in potential animal food resources (items and biomass) might be one of the vital reasons for the preference of cranes to the postharvest reed beds. Our results suggest that traditional reed management in the YNNR could benefit this flagship crane species that winters in the wetland system. However, as reed harvest has been forbidden in the core zone for conservation p…
format: application/pdf
format: text/html
creator: Peng Xu
creator: Yalan Zhang
creator: Xiaoran Zhang
creator: Hao Chen
creator: Changhu Lu
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Science Policy
subject: Natural Resource Management
description: doi:10.7717/peerj.7682
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Reed beds represent an important habitat for the survival of birds by providing favorable foraging and reproduction conditions. Reed management, as a traditional agricultural activity, primarily includes water level control and vegetation removal by cutting. Red-crowned crane (Grus japonensis) is one of the most endangered cranes, and their population continues to decline due to habitat loss caused by artificial activities. A lack of research relating to how reed management affects crane habitat distribution patterns throughout the wintering period hinders our ability to offer conservation recommendations. In the present study, we explored the effect of reed management on the habitat distribution patterns and analyzed the food resources of red-crowned crane in the Yancheng National Nature Reserve (YNNR). According to the reed management activities in December, we divided the wintering period into two phases: the preharvest period and the postharvest period. Throughout the wintering period, the number of cranes recorded in the common seepweed (Suaeda glauca) tidal flats remained stable, but cranes were rarely recorded in the smooth cordgrass (Spartina alterniflora) tidal flats and aquaculture fish ponds. The number of cranes, however, showed a noticeable fluctuation in the reed beds during the two periods. Before the reed harvest, only a small proportion of cranes were recorded in the reed beds (relative abundance = 2.9%). However, more cranes (relative abundance = 61.0%) were recorded after the reed harvest. Water was introduced from adjacent rivers and fish ponds to submerge the cut reed beds. Changes in potential animal food resources (items and biomass) might be one of the vital reasons for the preference of cranes to the postharvest reed beds. Our results suggest that traditional reed management in the YNNR could benefit this flagship crane species that winters in the wetland system. However, as reed harvest has been forbidden in the core zone for conservation p…
bibliographic citation: Xu et al. (2019) Red-crowned crane (Grus japonensis) prefers postharvest reed beds during winter period in Yancheng National Nature Reserve. PeerJ 7:e7682 https://doi.org/10.7717/peerj.7682
date submitted: 2019-05-22
date accepted: 2019-08-16
issued: 2019-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Peng
author list: Agent
  family name: Zhang
  given name: Yalan
author list: Agent
  family name: Zhang
  given name: Xiaoran
author list: Agent
  family name: Chen
  given name: Hao
author list: Agent
  family name: Lu
  given name: Changhu
doi: 10.7717/peerj.7682
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-13
copyright: ©2019 Xu et al.
attribution name: Xu et al.

Niches and climate-change refugia in hundreds of species from one of the most arid places on Earth
type: item
type: AcademicArticle
description: Background and Aims Global climate change is a major threat to biodiversity worldwide. Several arid areas might expand in the future, but it is not clear if this change would be positive or negative for arid-adapted lineages. Here, we explore whether climatic niche properties are involved in the configuration of climate refugia and thus in future species trends. Methods To estimate putative climate refugia and potential expansion areas, we used maximum entropy models and four climate-change models to generate current and future potential distributions of 142 plant species endemic to the Atacama and mediterranean Chilean ecosystems. We assessed the relationship between the similarity and breadth of thermal and precipitation niches with the size of climate refugia and areas of potential expansions. Key Results We found a positive relationship between breadth and similarity for thermal niche with the size of climate refugia, but only niche similarity of the thermal niche was positively related with the size of expansion areas. Although all lineages would reduce their distributions in the future, few species are predicted to be at risk of extinction in their current distribution, and all of them presented potential expansion areas. Conclusion Species with a broad niche and niche dissimilarity will have larger refugia, and species with niche dissimilarity will have larger expansion areas. In addition, our prediction for arid lineages shows that these species will be moderately affected by climate change.
format: application/pdf
format: text/html
creator: Milen Duarte
creator: Pablo C. Guerrero
creator: Mary T.K. Arroyo
creator: Ramiro O. Bustamante
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.7409
publisher: PeerJ Inc.
rights: © 2019 Duarte et al.
abstract: Background and Aims Global climate change is a major threat to biodiversity worldwide. Several arid areas might expand in the future, but it is not clear if this change would be positive or negative for arid-adapted lineages. Here, we explore whether climatic niche properties are involved in the configuration of climate refugia and thus in future species trends. Methods To estimate putative climate refugia and potential expansion areas, we used maximum entropy models and four climate-change models to generate current and future potential distributions of 142 plant species endemic to the Atacama and mediterranean Chilean ecosystems. We assessed the relationship between the similarity and breadth of thermal and precipitation niches with the size of climate refugia and areas of potential expansions. Key Results We found a positive relationship between breadth and similarity for thermal niche with the size of climate refugia, but only niche similarity of the thermal niche was positively related with the size of expansion areas. Although all lineages would reduce their distributions in the future, few species are predicted to be at risk of extinction in their current distribution, and all of them presented potential expansion areas. Conclusion Species with a broad niche and niche dissimilarity will have larger refugia, and species with niche dissimilarity will have larger expansion areas. In addition, our prediction for arid lineages shows that these species will be moderately affected by climate change.
bibliographic citation: Duarte et al. (2019) Niches and climate-change refugia in hundreds of species from one of the most arid places on Earth. PeerJ 7:e7409 https://doi.org/10.7717/peerj.7409
date submitted: 2018-10-18
date accepted: 2019-07-04
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duarte
  given name: Milen
author list: Agent
  family name: Guerrero
  given name: Pablo C.
author list: Agent
  family name: Arroyo
  given name: Mary T.K.
author list: Agent
  family name: Bustamante
  given name: Ramiro O.
doi: 10.7717/peerj.7409
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: © 2019 Duarte et al.
attribution name: Duarte et al.

Antimicrobial photodynamic therapy on Staphylococcus aureus and Escherichia coli using malachite green encapsulated mesoporous silica nanoparticles: an in vitro study
type: item
type: AcademicArticle
description: Background Rise in the number of healthcare associated or hospital acquired infections is a major problem affecting the global healthcare sector. We evaluated superior antibacterial and antibiofilm photodynamic therapy (aPDT) using malachite green encapsulated mesoporous silica nanoparticles (MG-MSN) against Staphylococcus aureus and Escherichia coli, which are known to be major causative agents of nosocomial infections. Methods Malachite green (MG) was encapsulated on mesoporous silica nanoparticles (MSN). Fourier-transform infrared spectroscopy, Transmission electron microscopy, and spectroscopic analysis were performed to characterize the MG-MSN. The antimicrobial efficacies of MSN, MG, and MG-MSN were investigated and the results were recorded. Results MG-MSN was effective against both the tested bacteria. S. aureus was more phototoxic to MG-MSN compared to E. coli. The antibiofilm efficacy of MG-MSN on E. coli and S. aureus was also studied. Biofilm inhibition was 65.68 ± 2.62% in E. coli and 79.66 ± 3.82% in S. aureus. Cell viability assay, exopolysaccharides quantification, and confocal laser scanning microscopy studies also revealed the enhanced antibiofilm activity of MG-MSN when used as a potential photosensitizer for aPDT. This study can be extended to eradicate these strains from localized superficial infections and medical appliances, preventing nosocomial infections.
format: application/pdf
format: text/html
creator: Parasuraman Paramanantham
creator: Busi Siddhardha
creator: Sruthil Lal SB
creator: Alok Sharan
creator: Abdullah A. Alyousef
creator: Mohammed Saeed Al Dosary
creator: Mohammed Arshad
creator: Asad Syed
subject: Biochemistry
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.7454
publisher: PeerJ Inc.
rights: © 2019 Paramanantham et al.
abstract: Background Rise in the number of healthcare associated or hospital acquired infections is a major problem affecting the global healthcare sector. We evaluated superior antibacterial and antibiofilm photodynamic therapy (aPDT) using malachite green encapsulated mesoporous silica nanoparticles (MG-MSN) against Staphylococcus aureus and Escherichia coli, which are known to be major causative agents of nosocomial infections. Methods Malachite green (MG) was encapsulated on mesoporous silica nanoparticles (MSN). Fourier-transform infrared spectroscopy, Transmission electron microscopy, and spectroscopic analysis were performed to characterize the MG-MSN. The antimicrobial efficacies of MSN, MG, and MG-MSN were investigated and the results were recorded. Results MG-MSN was effective against both the tested bacteria. S. aureus was more phototoxic to MG-MSN compared to E. coli. The antibiofilm efficacy of MG-MSN on E. coli and S. aureus was also studied. Biofilm inhibition was 65.68 ± 2.62% in E. coli and 79.66 ± 3.82% in S. aureus. Cell viability assay, exopolysaccharides quantification, and confocal laser scanning microscopy studies also revealed the enhanced antibiofilm activity of MG-MSN when used as a potential photosensitizer for aPDT. This study can be extended to eradicate these strains from localized superficial infections and medical appliances, preventing nosocomial infections.
bibliographic citation: Paramanantham et al. (2019) Antimicrobial photodynamic therapy on Staphylococcus aureus and Escherichia coli using malachite green encapsulated mesoporous silica nanoparticles: an in vitro study. PeerJ 7:e7454 https://doi.org/10.7717/peerj.7454
date submitted: 2019-03-04
date accepted: 2019-07-10
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paramanantham
  given name: Parasuraman
author list: Agent
  family name: Siddhardha
  given name: Busi
author list: Agent
  family name: Lal SB
  given name: Sruthil
author list: Agent
  family name: Sharan
  given name: Alok
author list: Agent
  family name: Alyousef
  given name: Abdullah A.
author list: Agent
  family name: Al Dosary
  given name: Mohammed Saeed
author list: Agent
  family name: Arshad
  given name: Mohammed
author list: Agent
  family name: Syed
  given name: Asad
doi: 10.7717/peerj.7454
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: ©2019 Paramanantham et al.
attribution name: Paramanantham et al.

Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known
type: item
type: AcademicArticle
description: Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.
format: application/pdf
format: text/html
creator: Mikhail I. Schelkunov
creator: Maxim S. Nuraliev
creator: Maria D. Logacheva
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7500
publisher: PeerJ Inc.
rights: © 2019 Schelkunov et al.
abstract: Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.
bibliographic citation: Schelkunov et al. (2019) Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known. PeerJ 7:e7500 https://doi.org/10.7717/peerj.7500
date submitted: 2018-12-20
date accepted: 2019-07-16
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schelkunov
  given name: Mikhail I.
author list: Agent
  family name: Nuraliev
  given name: Maxim S.
author list: Agent
  family name: Logacheva
  given name: Maria D.
doi: 10.7717/peerj.7500
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: © 2019 Schelkunov et al.
attribution name: Schelkunov et al.

Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses
type: item
type: AcademicArticle
description: Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.
format: application/pdf
format: text/html
creator: Yanan Shi
creator: Huanlong Liu
creator: Yameng Gao
creator: Yujiao Wang
creator: Min Wu
creator: Yan Xiang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7510
publisher: PeerJ Inc.
rights: © 2019 Shi et al.
abstract: Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.
bibliographic citation: Shi et al. (2019) Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses. PeerJ 7:e7510 https://doi.org/10.7717/peerj.7510
date submitted: 2019-03-26
date accepted: 2019-07-17
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yanan
author list: Agent
  family name: Liu
  given name: Huanlong
author list: Agent
  family name: Gao
  given name: Yameng
author list: Agent
  family name: Wang
  given name: Yujiao
author list: Agent
  family name: Wu
  given name: Min
author list: Agent
  family name: Xiang
  given name: Yan
doi: 10.7717/peerj.7510
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: © 2019 Shi et al.
attribution name: Shi et al.

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