PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: A stepping stone to compositionality in chimpanzee communication
items: Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)
items: Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035
items: Dietary fermented products using koji mold and sweet potato-shochu distillery by-product promotes hepatic and serum cholesterol levels and modulates gut microbiota in mice fed a high-cholesterol diet

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.

A stepping stone to compositionality in chimpanzee communication
type: item
type: AcademicArticle
description: Compositionality refers to a structural property of human language, according to which the meaning of a complex expression is a function of the meaning of its parts and the way they are combined. Compositionality is a defining characteristic of all human language, spoken and signed. Comparative research into the emergence of human language aims at identifying precursors to such key features of human language in the communication of other primates. While it is known that chimpanzees, our closest relatives, produce a variety of gestures, facial expressions and vocalizations in interactions with their group members, little is known about how these signals combine simultaneously. Therefore, the aim of the current study is to investigate whether there is evidence for compositional structures in the communication of chimpanzees. We investigated two semi-wild groups of chimpanzees, with focus on their manual gestures and their combinations with facial expressions across different social contexts. If there are compositional structures in chimpanzee communication, adding a facial expression to a gesture should convey a different message than the gesture alone, a difference that we expect to be measurable by the recipient’s response. Furthermore, we expect context-dependent usage of these combinations. Based on a form-based coding procedure of the collected video footage, we identified two frequently used manual gestures (stretched arm gesture and bent arm gesture) and two facial expression (bared teeth face and funneled lip face). We analyzed whether the recipients’ response varied depending on the signaler’s usage of a given gesture + face combination and the context in which these were used. Overall, our results suggest that, in positive contexts, such as play or grooming, specific combinations had an impact on the likelihood of the occurrence of particular responses. Specifically, adding a bared teeth face to a gesture either increased the likelihood of affiliative behavi…
format: application/pdf
format: text/html
creator: Linda S. Oña
creator: Wendy Sandler
creator: Katja Liebal
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
description: doi:10.7717/peerj.7623
publisher: PeerJ Inc.
rights: © 2019 Oña et al.
abstract: Compositionality refers to a structural property of human language, according to which the meaning of a complex expression is a function of the meaning of its parts and the way they are combined. Compositionality is a defining characteristic of all human language, spoken and signed. Comparative research into the emergence of human language aims at identifying precursors to such key features of human language in the communication of other primates. While it is known that chimpanzees, our closest relatives, produce a variety of gestures, facial expressions and vocalizations in interactions with their group members, little is known about how these signals combine simultaneously. Therefore, the aim of the current study is to investigate whether there is evidence for compositional structures in the communication of chimpanzees. We investigated two semi-wild groups of chimpanzees, with focus on their manual gestures and their combinations with facial expressions across different social contexts. If there are compositional structures in chimpanzee communication, adding a facial expression to a gesture should convey a different message than the gesture alone, a difference that we expect to be measurable by the recipient’s response. Furthermore, we expect context-dependent usage of these combinations. Based on a form-based coding procedure of the collected video footage, we identified two frequently used manual gestures (stretched arm gesture and bent arm gesture) and two facial expression (bared teeth face and funneled lip face). We analyzed whether the recipients’ response varied depending on the signaler’s usage of a given gesture + face combination and the context in which these were used. Overall, our results suggest that, in positive contexts, such as play or grooming, specific combinations had an impact on the likelihood of the occurrence of particular responses. Specifically, adding a bared teeth face to a gesture either increased the likelihood of affiliative behavi…
bibliographic citation: Oña et al. (2019) A stepping stone to compositionality in chimpanzee communication. PeerJ 7:e7623 https://doi.org/10.7717/peerj.7623
date submitted: 2019-06-12
date accepted: 2019-08-05
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oña
  given name: Linda S.
author list: Agent
  family name: Sandler
  given name: Wendy
author list: Agent
  family name: Liebal
  given name: Katja
doi: 10.7717/peerj.7623
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: © 2019 Oña et al.
attribution name: Oña et al.

Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)
type: item
type: AcademicArticle
description: Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237–323 amino acids, with a theoretical molecular weight (MW) of 24.31–31.80 kDa and an isoelectric point (pI) value of 4.73–10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.
format: application/pdf
format: text/html
creator: Weiguo Qian
creator: Xiaomin Yang
creator: Jiawen Li
creator: Rui Luo
creator: Xiufeng Yan
creator: Qiuying Pang
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7664
publisher: PeerJ Inc.
rights: © 2019 Qian et al.
abstract: Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237–323 amino acids, with a theoretical molecular weight (MW) of 24.31–31.80 kDa and an isoelectric point (pI) value of 4.73–10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.
bibliographic citation: Qian et al. (2019) Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum). PeerJ 7:e7664 https://doi.org/10.7717/peerj.7664
date submitted: 2019-03-02
date accepted: 2019-08-13
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qian
  given name: Weiguo
author list: Agent
  family name: Yang
  given name: Xiaomin
author list: Agent
  family name: Li
  given name: Jiawen
author list: Agent
  family name: Luo
  given name: Rui
author list: Agent
  family name: Yan
  given name: Xiufeng
author list: Agent
  family name: Pang
  given name: Qiuying
doi: 10.7717/peerj.7664
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: ©2019 Qian et al.
attribution name: Qian et al.

Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035
type: item
type: AcademicArticle
description: Acute farmland expansion and rapid urbanization in Central Asia have accelerated land use/land cover changes, which have substantial effects on ecosystem services. However, the spatiotemporal variations in ecosystem service values (ESVs) in Central Asia are not well understood. Here, based on land use products with 300-m resolution for the years 1995, 2005 and 2015 and transfer methodology, we predicted land use and land cover (LULC) for 2025 and 2035 using CA-Markov, assessed changes in ESVs in response to LULC dynamics, and explored the elasticity of the response of ESV to LULC changes. We found significant expansions of cropland (+22.10%) and urban areas (+322.40%) and shrinking of water bodies (−38.43%) and bare land (−9.42%) during 1995–2035. The combined value of ecosystem services of water bodies, cropland, and grassland accounted for over 90% of the total ESVs. Our study showed that cropland ecosystem services value increased by 93.45 billion US$ from 1995 to 2035, which was mainly caused by the expansion of cropland area. However, the area of water bodies decreased sharply during 1995–2035, causing a loss of 64.38 billion US$. Biodiversity, food production and water regulation were major ecosystem service functions, accounting for 80.52% of the total ESVs. Our results demonstrated that effective land-use policies should be made to control farmland expansion and protect water bodies, grassland and forestland for more sustainable ecosystem services.
format: application/pdf
format: text/html
creator: Jiangyue Li
creator: Hongxing Chen
creator: Chi Zhang
creator: Tao Pan
subject: Ecosystem Science
subject: Natural Resource Management
subject: Environmental Impacts
subject: Food, Water and Energy Nexus
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.7665
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Acute farmland expansion and rapid urbanization in Central Asia have accelerated land use/land cover changes, which have substantial effects on ecosystem services. However, the spatiotemporal variations in ecosystem service values (ESVs) in Central Asia are not well understood. Here, based on land use products with 300-m resolution for the years 1995, 2005 and 2015 and transfer methodology, we predicted land use and land cover (LULC) for 2025 and 2035 using CA-Markov, assessed changes in ESVs in response to LULC dynamics, and explored the elasticity of the response of ESV to LULC changes. We found significant expansions of cropland (+22.10%) and urban areas (+322.40%) and shrinking of water bodies (−38.43%) and bare land (−9.42%) during 1995–2035. The combined value of ecosystem services of water bodies, cropland, and grassland accounted for over 90% of the total ESVs. Our study showed that cropland ecosystem services value increased by 93.45 billion US$ from 1995 to 2035, which was mainly caused by the expansion of cropland area. However, the area of water bodies decreased sharply during 1995–2035, causing a loss of 64.38 billion US$. Biodiversity, food production and water regulation were major ecosystem service functions, accounting for 80.52% of the total ESVs. Our results demonstrated that effective land-use policies should be made to control farmland expansion and protect water bodies, grassland and forestland for more sustainable ecosystem services.
bibliographic citation: Li et al. (2019) Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035. PeerJ 7:e7665 https://doi.org/10.7717/peerj.7665
date submitted: 2019-04-10
date accepted: 2019-08-13
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiangyue
author list: Agent
  family name: Chen
  given name: Hongxing
author list: Agent
  family name: Zhang
  given name: Chi
author list: Agent
  family name: Pan
  given name: Tao
doi: 10.7717/peerj.7665
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: ©2019 Li et al.
attribution name: Li et al.

Dietary fermented products using koji mold and sweet potato-shochu distillery by-product promotes hepatic and serum cholesterol levels and modulates gut microbiota in mice fed a high-cholesterol diet
type: item
type: AcademicArticle
description: It has been reported that fermented products (FPs) prepared from sweet potato-shochu distillery by-product suppressed weight gain and decreased serum cholesterol levels in mice under normal dietary conditions. Furthermore, from the information gained from the above data regarding health benefits of the FPs, the aim of this study was evaluating the effects of dietary FPs on lipid accumulation and gut microbiota in mice with or without cholesterol-load in the diet. C57BL/6N mice were fed normal (CO) diet, CO with 10% FPs (CO + FPs) diet, cholesterol loaded (HC) diet, or HC with 10% FPs (HC + FPs) diet for 8 weeks. The mice were then euthanized, and blood samples, tissue samples, and feces were collected. The adipose tissue weight and liver triglyceride levels in the HC + FPs diet groups were significantly reduced compared to that in the HC diet groups. However, FPs significantly increased the serum non-high-density lipoprotein cholesterol (HDL-C) levels, the ratio of non-HDL-C to HDL-C and hepatic total cholesterol levels in mice fed cholesterol-loaded diet compared with that of the HC diet group. Since dietary FPs significantly decreased the protein expression levels of cholesterol 7 alpha-hydroxylase 1 in the HC + FPs diet groups, the cholesterol accumulation in FPs group may be explained by insufficient catabolism from cholesterol to bile acid. In addition, the dietary FPs tended to increase Clostridium cluster IV and XIVa, which are butyrate-producing bacteria. Related to the result, n-butyrate was significantly increased in the CO + FPs and the HC + FPs diet groups compared to their respective control groups. These findings suggested that dietary FPs modulated the lipid pool and gut microbiota.
format: application/pdf
format: text/html
creator: Toshiki Kosakai
creator: Hirotaka Kato
creator: Cho Sho
creator: Kuniaki Kawano
creator: Ken-ichi Iwai
creator: Yoshikazu Takase
creator: Kenjiro Ogawa
creator: Kazuo Nishiyama
creator: Masao Yamasaki
subject: Food Science and Technology
subject: Microbiology
subject: Nutrition
description: doi:10.7717/peerj.7671
publisher: PeerJ Inc.
rights: © 2019 Kosakai et al.
abstract: It has been reported that fermented products (FPs) prepared from sweet potato-shochu distillery by-product suppressed weight gain and decreased serum cholesterol levels in mice under normal dietary conditions. Furthermore, from the information gained from the above data regarding health benefits of the FPs, the aim of this study was evaluating the effects of dietary FPs on lipid accumulation and gut microbiota in mice with or without cholesterol-load in the diet. C57BL/6N mice were fed normal (CO) diet, CO with 10% FPs (CO + FPs) diet, cholesterol loaded (HC) diet, or HC with 10% FPs (HC + FPs) diet for 8 weeks. The mice were then euthanized, and blood samples, tissue samples, and feces were collected. The adipose tissue weight and liver triglyceride levels in the HC + FPs diet groups were significantly reduced compared to that in the HC diet groups. However, FPs significantly increased the serum non-high-density lipoprotein cholesterol (HDL-C) levels, the ratio of non-HDL-C to HDL-C and hepatic total cholesterol levels in mice fed cholesterol-loaded diet compared with that of the HC diet group. Since dietary FPs significantly decreased the protein expression levels of cholesterol 7 alpha-hydroxylase 1 in the HC + FPs diet groups, the cholesterol accumulation in FPs group may be explained by insufficient catabolism from cholesterol to bile acid. In addition, the dietary FPs tended to increase Clostridium cluster IV and XIVa, which are butyrate-producing bacteria. Related to the result, n-butyrate was significantly increased in the CO + FPs and the HC + FPs diet groups compared to their respective control groups. These findings suggested that dietary FPs modulated the lipid pool and gut microbiota.
bibliographic citation: Kosakai et al. (2019) Dietary fermented products using koji mold and sweet potato-shochu distillery by-product promotes hepatic and serum cholesterol levels and modulates gut microbiota in mice fed a high-cholesterol diet. PeerJ 7:e7671 https://doi.org/10.7717/peerj.7671
date submitted: 2019-05-23
date accepted: 2019-08-13
issued: 2019-09-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kosakai
  given name: Toshiki
author list: Agent
  family name: Kato
  given name: Hirotaka
author list: Agent
  family name: Sho
  given name: Cho
author list: Agent
  family name: Kawano
  given name: Kuniaki
author list: Agent
  family name: Iwai
  given name: Ken-ichi
author list: Agent
  family name: Takase
  given name: Yoshikazu
author list: Agent
  family name: Ogawa
  given name: Kenjiro
author list: Agent
  family name: Nishiyama
  given name: Kazuo
author list: Agent
  family name: Yamasaki
  given name: Masao
doi: 10.7717/peerj.7671
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-12
copyright: © 2019 Kosakai et al.
attribution name: Kosakai et al.

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