PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Distribution, evolution and expression of GATA-TFs provide new insights into their functions in light response and fruiting body development of Tolypocladium guangdongense
items: Physiological, biochemical and genetic responses of Caucasian tea (Camellia sinensis (L.) Kuntze) genotypes under cold and frost stress
items: The effect of an image of watchful eyes on the evaluation of the appearance of food
items: Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve
items: A new genus Vittaliana belonging to the tribe Opsiini (Hemiptera: Cicadellidae) from India and its molecular phylogeny
items: Effects of supplementation levels of Allium fistulosum L. extract on in vitro ruminal fermentation characteristics and methane emission
items: The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific
items: The influence of bait on remote underwater video observations in shallow-water coastal environments associated with the North-Eastern Atlantic
items: High moon brightness and low ambient temperatures affect sloth predation by harpy eagles
items: Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution

Distribution, evolution and expression of GATA-TFs provide new insights into their functions in light response and fruiting body development of Tolypocladium guangdongense
type: item
type: AcademicArticle
description: Background Fungal GATA-type transcription factors (GATA-TFs) are a class of transcriptional regulators involved in various biological processes. However, their functions are rarely analyzed systematically, especially in edible or medicinal fungi, such as Tolypocladium guangdongense, which has various medicinal and food safety properties with a broad range of potential applications in healthcare products and the pharmaceutical industry. Methods GATA-TFs in T. guangdongense (TgGATAs) were identified using InterProScan. The type, distribution, and gene structure of TgGATAs were analyzed by genome-wide analyses. A phylogenetic tree was constructed to analyze their evolutionary relationships using the neighbor-joining (NJ) method. To explore the functions of GATA-TFs, conserved domains were analyzed using MEME, and cis-elements were predicted using the PlantCARE database. In addition, the expression patterns of TgGATAs under different light conditions and developmental stages were studied using qPCR. Results Seven TgGATAs were identified. They were randomly distributed on four chromosomes and contained one to four exons. Phylogenetic analysis indicated that GATA-TFs in each subgroup are highly conserved, especially for GATA1 to GATA5. Intron distribution analyses suggested that GATA1 and GATA3 possessed the most conserved gene structures. Light treatments induced the expression levels of TgGATA1 and TgGATA5-7, but the expression levels varied depending on the duration of illumination. The predicted protein structures indicate that TgGATA1 and TgGATA2 possess typical light-responsive domains and may function as photoreceptors to regulate downstream biological processes. TgGATA3 and TgGATA5 may be involved in nitrogen metabolism and siderophore biosynthesis, respectively. TgGATA6 and TgGATA7 possess unique Zn finger loop sequences, suggesting that they may have special functions. Furthermore, gene expression analysis indicated that TgGATA1 (WC1) was notably involved in myc…
format: application/pdf
format: text/html
creator: Chenghua Zhang
creator: Gangzheng Wang
creator: Wangqiu Deng
creator: Taihui Li
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.9784
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Fungal GATA-type transcription factors (GATA-TFs) are a class of transcriptional regulators involved in various biological processes. However, their functions are rarely analyzed systematically, especially in edible or medicinal fungi, such as Tolypocladium guangdongense, which has various medicinal and food safety properties with a broad range of potential applications in healthcare products and the pharmaceutical industry. Methods GATA-TFs in T. guangdongense (TgGATAs) were identified using InterProScan. The type, distribution, and gene structure of TgGATAs were analyzed by genome-wide analyses. A phylogenetic tree was constructed to analyze their evolutionary relationships using the neighbor-joining (NJ) method. To explore the functions of GATA-TFs, conserved domains were analyzed using MEME, and cis-elements were predicted using the PlantCARE database. In addition, the expression patterns of TgGATAs under different light conditions and developmental stages were studied using qPCR. Results Seven TgGATAs were identified. They were randomly distributed on four chromosomes and contained one to four exons. Phylogenetic analysis indicated that GATA-TFs in each subgroup are highly conserved, especially for GATA1 to GATA5. Intron distribution analyses suggested that GATA1 and GATA3 possessed the most conserved gene structures. Light treatments induced the expression levels of TgGATA1 and TgGATA5-7, but the expression levels varied depending on the duration of illumination. The predicted protein structures indicate that TgGATA1 and TgGATA2 possess typical light-responsive domains and may function as photoreceptors to regulate downstream biological processes. TgGATA3 and TgGATA5 may be involved in nitrogen metabolism and siderophore biosynthesis, respectively. TgGATA6 and TgGATA7 possess unique Zn finger loop sequences, suggesting that they may have special functions. Furthermore, gene expression analysis indicated that TgGATA1 (WC1) was notably involved in myc…
bibliographic citation: Zhang et al. (2020) Distribution, evolution and expression of GATA-TFs provide new insights into their functions in light response and fruiting body development of Tolypocladium guangdongense. PeerJ 8:e9784 https://doi.org/10.7717/peerj.9784
date submitted: 2020-02-27
date accepted: 2020-07-30
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Chenghua
author list: Agent
  family name: Wang
  given name: Gangzheng
author list: Agent
  family name: Deng
  given name: Wangqiu
author list: Agent
  family name: Li
  given name: Taihui
doi: 10.7717/peerj.9784
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Physiological, biochemical and genetic responses of Caucasian tea (Camellia sinensis (L.) Kuntze) genotypes under cold and frost stress
type: item
type: AcademicArticle
description: Background Cold and frost are two serious factors limiting the yield of many crops worldwide, including the tea plant (Camellia sinensis (L.) Kuntze). The acclimatization of tea plant from tropical to temperate climate regions resulted in unique germplasm in the North–Western Caucasus with extremely frost-tolerant genotypes. Methods The aim of the current research was to evaluate the physiological, biochemical and genetic responses of tolerant and sensitive tea cultivars exposed to cold (0 to +2 °C for 7 days) and frost (−6 to −8 °C for 5 days). Relative water content, cell membranes integrity, pH of the cell sap, water soluble protein, cations, sugars, amino acids were measured under cold and frost. Comparative expression of the following genes ICE1, CBF1, WRKY2, DHN1, DHN2, DHN3, NAC17, NAC26, NAC30, SnRK1.1, SnRK1.2, SnRK1.3, bHLH7, bHLH43, P5CS, LOX1, LOX6, LOX7 were analyzed. Results We found elevated protein (by 3–4 times) and cations (potassium, calcium and magnesium) contents in the leaves of both cultivars under cold and frost treatments. Meanwhile, Leu, Met, Val, Thr, Ser were increased under cold and frost, however tolerant cv. Gruzinskii7 showed earlier accumulation of these amino acids. Out of 18 studied genes, 11 were expressed at greater level in the frost- tolerant cultivar comparing with frost-sensitive one: ICE1, CBF1, WRKY2, DHN2, NAC17, NAC26, SnRK1.1, SnRK1.3, bHLH43, P5CS and LOX6. Positive correlations between certain amino acids namely, Met, Thr, Leu and Ser and studied genes were found. Taken together, the revealed cold responses in Caucasian tea cultivars help better understanding of tea tolerance to low temperature stress and role of revealed metabolites need to be further evaluated in different tea genotypes.
format: application/pdf
format: text/html
creator: Lidiia S. Samarina
creator: Lyudmila S. Malyukova
creator: Alexander M. Efremov
creator: Taisiya A. Simonyan
creator: Alexandra O. Matskiv
creator: Natalia G. Koninskaya
creator: Ruslan S. Rakhmangulov
creator: Maya V. Gvasaliya
creator: Valentina I. Malyarovskaya
creator: Alexey V. Ryndin
creator: Yuriy L. Orlov
creator: Wei Tong
creator: Magda-Viola Hanke
subject: Agricultural Science
subject: Food Science and Technology
subject: Genetics
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9787
publisher: PeerJ Inc.
rights: © 2020 Samarina et al.
abstract: Background Cold and frost are two serious factors limiting the yield of many crops worldwide, including the tea plant (Camellia sinensis (L.) Kuntze). The acclimatization of tea plant from tropical to temperate climate regions resulted in unique germplasm in the North–Western Caucasus with extremely frost-tolerant genotypes. Methods The aim of the current research was to evaluate the physiological, biochemical and genetic responses of tolerant and sensitive tea cultivars exposed to cold (0 to +2 °C for 7 days) and frost (−6 to −8 °C for 5 days). Relative water content, cell membranes integrity, pH of the cell sap, water soluble protein, cations, sugars, amino acids were measured under cold and frost. Comparative expression of the following genes ICE1, CBF1, WRKY2, DHN1, DHN2, DHN3, NAC17, NAC26, NAC30, SnRK1.1, SnRK1.2, SnRK1.3, bHLH7, bHLH43, P5CS, LOX1, LOX6, LOX7 were analyzed. Results We found elevated protein (by 3–4 times) and cations (potassium, calcium and magnesium) contents in the leaves of both cultivars under cold and frost treatments. Meanwhile, Leu, Met, Val, Thr, Ser were increased under cold and frost, however tolerant cv. Gruzinskii7 showed earlier accumulation of these amino acids. Out of 18 studied genes, 11 were expressed at greater level in the frost- tolerant cultivar comparing with frost-sensitive one: ICE1, CBF1, WRKY2, DHN2, NAC17, NAC26, SnRK1.1, SnRK1.3, bHLH43, P5CS and LOX6. Positive correlations between certain amino acids namely, Met, Thr, Leu and Ser and studied genes were found. Taken together, the revealed cold responses in Caucasian tea cultivars help better understanding of tea tolerance to low temperature stress and role of revealed metabolites need to be further evaluated in different tea genotypes.
bibliographic citation: Samarina et al. (2020) Physiological, biochemical and genetic responses of Caucasian tea (Camellia sinensis (L.) Kuntze) genotypes under cold and frost stress. PeerJ 8:e9787 https://doi.org/10.7717/peerj.9787
date submitted: 2020-05-04
date accepted: 2020-07-31
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Samarina
  given name: Lidiia S.
author list: Agent
  family name: Malyukova
  given name: Lyudmila S.
author list: Agent
  family name: Efremov
  given name: Alexander M.
author list: Agent
  family name: Simonyan
  given name: Taisiya A.
author list: Agent
  family name: Matskiv
  given name: Alexandra O.
author list: Agent
  family name: Koninskaya
  given name: Natalia G.
author list: Agent
  family name: Rakhmangulov
  given name: Ruslan S.
author list: Agent
  family name: Gvasaliya
  given name: Maya V.
author list: Agent
  family name: Malyarovskaya
  given name: Valentina I.
author list: Agent
  family name: Ryndin
  given name: Alexey V.
author list: Agent
  family name: Orlov
  given name: Yuriy L.
author list: Agent
  family name: Tong
  given name: Wei
author list: Agent
  family name: Hanke
  given name: Magda-Viola
doi: 10.7717/peerj.9787
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: ©2020 Samarina et al.
attribution name: Samarina et al.

The effect of an image of watchful eyes on the evaluation of the appearance of food
type: item
type: AcademicArticle
description: It is known that an eye-like image promotes generosity. It is also known that the evaluation of the visual deliciousness of food is improved in the presence of an emotionally positive stimulus. The purpose of the present study was to examine whether the presence of open eyes (OPEN) causes generous behavior altering the evaluation of the visual deliciousness of food, and how the images of open and closed eyes (CLOSED) affect human emotions. Seventeen women participated in the present study. A picture of food was presented on a computer screen, and the participants predicted and evaluated its visual deliciousness. An image of OPEN or that of CLOSED was presented simultaneously with a picture of food. There was a significant difference between the OPEN and CLOSED conditions, as demonstrated by the scores on a nine-point Likert scale for visual deliciousness; the ratings in the OPEN condition were significantly higher than those in the CLOSED condition (p = 0.004). There was no significant difference in the image of watchful eyes for the perceived relaxation state; the ratings in the OPEN condition were not significantly higher than those in the CLOSED condition (p = 0.716). The results of the present study revealed that the evaluation of the visual deliciousness of food based on its appearance was likely due to the presence of an image of open watchful eyes, increasing the perceived visual deliciousness of the food without any changes in the participants’ emotions.
format: application/pdf
format: text/html
creator: Kenichi Shibuya
creator: Mana Miyamoto
creator: Risa Santa
creator: Chihiro Homma
creator: Sumire Hosono
creator: Naoto Sato
subject: Anthropology
subject: Food Science and Technology
subject: Nutrition
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9804
publisher: PeerJ Inc.
rights: © 2020 Shibuya et al.
abstract: It is known that an eye-like image promotes generosity. It is also known that the evaluation of the visual deliciousness of food is improved in the presence of an emotionally positive stimulus. The purpose of the present study was to examine whether the presence of open eyes (OPEN) causes generous behavior altering the evaluation of the visual deliciousness of food, and how the images of open and closed eyes (CLOSED) affect human emotions. Seventeen women participated in the present study. A picture of food was presented on a computer screen, and the participants predicted and evaluated its visual deliciousness. An image of OPEN or that of CLOSED was presented simultaneously with a picture of food. There was a significant difference between the OPEN and CLOSED conditions, as demonstrated by the scores on a nine-point Likert scale for visual deliciousness; the ratings in the OPEN condition were significantly higher than those in the CLOSED condition (p = 0.004). There was no significant difference in the image of watchful eyes for the perceived relaxation state; the ratings in the OPEN condition were not significantly higher than those in the CLOSED condition (p = 0.716). The results of the present study revealed that the evaluation of the visual deliciousness of food based on its appearance was likely due to the presence of an image of open watchful eyes, increasing the perceived visual deliciousness of the food without any changes in the participants’ emotions.
bibliographic citation: Shibuya et al. (2020) The effect of an image of watchful eyes on the evaluation of the appearance of food. PeerJ 8:e9804 https://doi.org/10.7717/peerj.9804
date submitted: 2020-06-17
date accepted: 2020-08-03
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shibuya
  given name: Kenichi
author list: Agent
  family name: Miyamoto
  given name: Mana
author list: Agent
  family name: Santa
  given name: Risa
author list: Agent
  family name: Homma
  given name: Chihiro
author list: Agent
  family name: Hosono
  given name: Sumire
author list: Agent
  family name: Sato
  given name: Naoto
doi: 10.7717/peerj.9804
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: © 2020 Shibuya et al.
attribution name: Shibuya et al.

Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve
type: item
type: AcademicArticle
description: Background During fertility treatment, diminished ovarian reserve (DOR) is a challenge that can seriously affect a patient’s reproductive potential. However, the pathogenesis of DOR is still unclear and its treatment options are limited. This study aimed to explore DOR’s molecular mechanisms. Methods We used R software to analyze the mRNA microarray dataset E-MTAB-391 downloaded from ArrayExpress, screen for differentially expressed genes (DEGs), and perform functional enrichment analyses. We also constructed the protein-protein interaction (PPI) and miRNA-mRNA networks. Ovarian granulosa cells (GCs) from women with DOR and the control group were collected to perform untargeted metabolomics analyses. Additionally, small molecule drugs were identified using the Connectivity Map database. Results We ultimately identified 138 DEGs. Our gene ontology (GO) analysis indicated that DEGs were mainly enriched in cytokine and steroid biosynthetic processes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the DEGs were mainly enriched in the AGE (advanced glycation end-product)-RAGE (receptor for AGE) signaling pathway in diabetic complications and steroid biosynthesis. In the PPI network, we determined that JUN, EGR1, HMGCR, ATF3, and SQLE were hub genes that may be involved in steroid biosynthesis and inflammation. miRNAs also played a role in DOR development by regulating target genes. We validated the differences in steroid metabolism across GCs using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We selected 31 small molecules with potentially positive or negative influences on DOR development. Conclusion We found that steroidogenesis and inflammation played critical roles in DOR development, and our results provide promising insights for predicting and treating DOR.
format: application/pdf
format: text/html
creator: Ruifen He
creator: Zhongying Zhao
creator: Yongxiu Yang
creator: Xiaolei Liang
subject: Bioinformatics
subject: Women’s Health
description: doi:10.7717/peerj.9812
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Background During fertility treatment, diminished ovarian reserve (DOR) is a challenge that can seriously affect a patient’s reproductive potential. However, the pathogenesis of DOR is still unclear and its treatment options are limited. This study aimed to explore DOR’s molecular mechanisms. Methods We used R software to analyze the mRNA microarray dataset E-MTAB-391 downloaded from ArrayExpress, screen for differentially expressed genes (DEGs), and perform functional enrichment analyses. We also constructed the protein-protein interaction (PPI) and miRNA-mRNA networks. Ovarian granulosa cells (GCs) from women with DOR and the control group were collected to perform untargeted metabolomics analyses. Additionally, small molecule drugs were identified using the Connectivity Map database. Results We ultimately identified 138 DEGs. Our gene ontology (GO) analysis indicated that DEGs were mainly enriched in cytokine and steroid biosynthetic processes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the DEGs were mainly enriched in the AGE (advanced glycation end-product)-RAGE (receptor for AGE) signaling pathway in diabetic complications and steroid biosynthesis. In the PPI network, we determined that JUN, EGR1, HMGCR, ATF3, and SQLE were hub genes that may be involved in steroid biosynthesis and inflammation. miRNAs also played a role in DOR development by regulating target genes. We validated the differences in steroid metabolism across GCs using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We selected 31 small molecules with potentially positive or negative influences on DOR development. Conclusion We found that steroidogenesis and inflammation played critical roles in DOR development, and our results provide promising insights for predicting and treating DOR.
bibliographic citation: He et al. (2020) Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve. PeerJ 8:e9812 https://doi.org/10.7717/peerj.9812
date submitted: 2020-03-06
date accepted: 2020-08-04
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Ruifen
author list: Agent
  family name: Zhao
  given name: Zhongying
author list: Agent
  family name: Yang
  given name: Yongxiu
author list: Agent
  family name: Liang
  given name: Xiaolei
doi: 10.7717/peerj.9812
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: ©2020 He et al.
attribution name: He et al.

A new genus Vittaliana belonging to the tribe Opsiini (Hemiptera: Cicadellidae) from India and its molecular phylogeny
type: item
type: AcademicArticle
description: The new leafhopper genus Vittalianareticulata gen. nov., sp. nov., is described from India, and placed in the tribe Opsiini based on ocelli close to eyes, without carina on anterior margin of the face and bifurcate aedeagus with two gonopores. Phylogenetic analysis with maximum likelihood (ML) using IQtree v1.4.1 of combined data (Histone H3 and 28S rDNA) reveals that the new genus Vittaliana belongs to a clade consisting of Opsius versicolor (Distant, 1908), Opsiini gen. sp., Libengaia sp., Hishimonus phycitis (Distant, 1908) and Yinfomibus menglaensis Du, Liang & Dai (2019) with good branch support, and that the tribe Opsiini is paraphyletic. This resolves the placement of a new genus in the tribe Opsiini under Deltocephalinae.
format: application/pdf
format: text/html
creator: Sunil
creator: Naresh M. Meshram
creator: Tahseen Raza Hashmi
creator: Pathour R. Shashank
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.9515
publisher: PeerJ Inc.
rights: © 2020 Sunil et al.
abstract: The new leafhopper genus Vittalianareticulata gen. nov., sp. nov., is described from India, and placed in the tribe Opsiini based on ocelli close to eyes, without carina on anterior margin of the face and bifurcate aedeagus with two gonopores. Phylogenetic analysis with maximum likelihood (ML) using IQtree v1.4.1 of combined data (Histone H3 and 28S rDNA) reveals that the new genus Vittaliana belongs to a clade consisting of Opsius versicolor (Distant, 1908), Opsiini gen. sp., Libengaia sp., Hishimonus phycitis (Distant, 1908) and Yinfomibus menglaensis Du, Liang & Dai (2019) with good branch support, and that the tribe Opsiini is paraphyletic. This resolves the placement of a new genus in the tribe Opsiini under Deltocephalinae.
bibliographic citation: Sunil et al. (2020) A new genus Vittaliana belonging to the tribe Opsiini (Hemiptera: Cicadellidae) from India and its molecular phylogeny. PeerJ 8:e9515 https://doi.org/10.7717/peerj.9515
date submitted: 2019-12-30
date accepted: 2020-06-19
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sunil
author list: Agent
  family name: Meshram
  given name: Naresh M.
author list: Agent
  family name: Hashmi
  given name: Tahseen Raza
author list: Agent
  family name: Shashank
  given name: Pathour R.
doi: 10.7717/peerj.9515
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: ©2020 Sunil et al.
attribution name: Sunil et al.

Effects of supplementation levels of Allium fistulosum L. extract on in vitro ruminal fermentation characteristics and methane emission
type: item
type: AcademicArticle
description: Background Ruminants release the majority of agricultural methane, an important greenhouse gas. Different feeds and additives are used to reduce emissions, but each has its drawbacks. This experiment was conducted to determine the effects of Allium fistulosum L. (A. fistulosum) extract on in vitro ruminal fermentation characteristics, and on methane emission. Methods Rumen fluid was taken from two cannulated rumen Hanwoo cow (with mean initial body weight 450 ± 30 kg, standard deviation = 30). Rumen fluid and McDougall’s buffer (1:2; 15 mL) were dispensed anaerobically into 50 mL serum bottles containing 300 mg (DM basis) of timothy substrate and A. fistulosum extracts (based on timothy substrate; 0%, 1%, 3%, 5%, 7%, or 9%). This experiment followed a completely randomized design performed in triplicate, using 126 individual serum bottles (six treatments × seven incubation times × three replicates). Results Dry matter degradability was not significantly affected (p-value > 0.05) by any A. fistulosum treatment other than 1% extract at 24 h incubation. Methane emission linearly decreased A. fistulosum extract concentration increased at 12 and 24 h incubation (p-value < 0.0001; p-value = 0.0003, respectively). Acetate concentration linearly decreased (p-value = 0.003) as A. fistulosum extract concentration increased at 12 h incubation. Methanogenic archaea abundance tendency decreased (p-value = 0.055) in the 1%, 7%, and 9% A. fistulosum extract groups compared to that in the 0% group, and quadratically decreased (p-value < 0.0001) as A. fistulosum extract concentration increased at 24 h incubation. Conclusion A. fistulosum extract had no apparent effect on ruminal fermentation characteristics or dry matter degradability. However, it reduced methane emission and methanogenic archaea abundance.
format: application/pdf
format: text/html
creator: Jun Sik Eom
creator: Shin Ja Lee
creator: Yejun Lee
creator: Hyun Sang Kim
creator: You Young Choi
creator: Hyeong Suk Kim
creator: Do Hyung Kim
creator: Sung Sill Lee
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.9651
publisher: PeerJ Inc.
rights: © 2020 Eom et al.
abstract: Background Ruminants release the majority of agricultural methane, an important greenhouse gas. Different feeds and additives are used to reduce emissions, but each has its drawbacks. This experiment was conducted to determine the effects of Allium fistulosum L. (A. fistulosum) extract on in vitro ruminal fermentation characteristics, and on methane emission. Methods Rumen fluid was taken from two cannulated rumen Hanwoo cow (with mean initial body weight 450 ± 30 kg, standard deviation = 30). Rumen fluid and McDougall’s buffer (1:2; 15 mL) were dispensed anaerobically into 50 mL serum bottles containing 300 mg (DM basis) of timothy substrate and A. fistulosum extracts (based on timothy substrate; 0%, 1%, 3%, 5%, 7%, or 9%). This experiment followed a completely randomized design performed in triplicate, using 126 individual serum bottles (six treatments × seven incubation times × three replicates). Results Dry matter degradability was not significantly affected (p-value > 0.05) by any A. fistulosum treatment other than 1% extract at 24 h incubation. Methane emission linearly decreased A. fistulosum extract concentration increased at 12 and 24 h incubation (p-value < 0.0001; p-value = 0.0003, respectively). Acetate concentration linearly decreased (p-value = 0.003) as A. fistulosum extract concentration increased at 12 h incubation. Methanogenic archaea abundance tendency decreased (p-value = 0.055) in the 1%, 7%, and 9% A. fistulosum extract groups compared to that in the 0% group, and quadratically decreased (p-value < 0.0001) as A. fistulosum extract concentration increased at 24 h incubation. Conclusion A. fistulosum extract had no apparent effect on ruminal fermentation characteristics or dry matter degradability. However, it reduced methane emission and methanogenic archaea abundance.
bibliographic citation: Eom et al. (2020) Effects of supplementation levels of Allium fistulosum L. extract on in vitro ruminal fermentation characteristics and methane emission. PeerJ 8:e9651 https://doi.org/10.7717/peerj.9651
date submitted: 2019-10-04
date accepted: 2020-07-13
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eom
  given name: Jun Sik
author list: Agent
  family name: Lee
  given name: Shin Ja
author list: Agent
  family name: Lee
  given name: Yejun
author list: Agent
  family name: Kim
  given name: Hyun Sang
author list: Agent
  family name: Choi
  given name: You Young
author list: Agent
  family name: Kim
  given name: Hyeong Suk
author list: Agent
  family name: Kim
  given name: Do Hyung
author list: Agent
  family name: Lee
  given name: Sung Sill
doi: 10.7717/peerj.9651
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: ©2020 Eom et al.
attribution name: Eom et al.

The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific
type: item
type: AcademicArticle
description: The extant genera of fur seals and sea lions of the family Otariidae (Carnivora: Pinnipedia) are thought to have emerged in the Pliocene or the early Pleistocene in the North Pacific. Among them, the Steller sea lion (Eumetopias jubatus) is the largest and distributed both in the western and eastern North Pacific. In contrast to the limited distribution of the current population around the Japanese Islands that is now only along the coast of Hokkaido, their fossil records have been known from the middle and late Pleistocene of Honshu Island. One such important fossil specimen has been recorded from the upper lower Pleistocene Omma Formation (ca. 1.36–0.83 Ma) in Kanazawa, Ishikawa Prefecture, Japan, which now bears the institutional number GKZ-N 00001. Because GKZ-N 00001 is the earliest fossil having been identified as a species of the sea lion genus Eumetopias, it is of importance to elucidate the evolutionary history of that genus. The morphometric comparisons were made among 51 mandibles of fur seals and sea lions with GKZ-N 00001. As results of bivariate analyses and PCA based on 39 measurements for external morphologies with internal structures by CT scan data, there is almost no difference between GKZ-N 00001 and extant male individuals of E. jubatus. In this regard, GKZ-N 00001 is identified specifically as the Steller sea lion E. jubatus. Consequently, it is recognized as the oldest Steller sea lion in the North Pacific. About 0.8 Ma, the distribution of the Steller sea lion had been already established at least in the Japan Sea side of the western North Pacific.
format: application/pdf
format: text/html
creator: Nahoko Tsuzuku
creator: Naoki Kohno
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9709
publisher: PeerJ Inc.
rights: © 2020 Tsuzuku and Kohno
abstract: The extant genera of fur seals and sea lions of the family Otariidae (Carnivora: Pinnipedia) are thought to have emerged in the Pliocene or the early Pleistocene in the North Pacific. Among them, the Steller sea lion (Eumetopias jubatus) is the largest and distributed both in the western and eastern North Pacific. In contrast to the limited distribution of the current population around the Japanese Islands that is now only along the coast of Hokkaido, their fossil records have been known from the middle and late Pleistocene of Honshu Island. One such important fossil specimen has been recorded from the upper lower Pleistocene Omma Formation (ca. 1.36–0.83 Ma) in Kanazawa, Ishikawa Prefecture, Japan, which now bears the institutional number GKZ-N 00001. Because GKZ-N 00001 is the earliest fossil having been identified as a species of the sea lion genus Eumetopias, it is of importance to elucidate the evolutionary history of that genus. The morphometric comparisons were made among 51 mandibles of fur seals and sea lions with GKZ-N 00001. As results of bivariate analyses and PCA based on 39 measurements for external morphologies with internal structures by CT scan data, there is almost no difference between GKZ-N 00001 and extant male individuals of E. jubatus. In this regard, GKZ-N 00001 is identified specifically as the Steller sea lion E. jubatus. Consequently, it is recognized as the oldest Steller sea lion in the North Pacific. About 0.8 Ma, the distribution of the Steller sea lion had been already established at least in the Japan Sea side of the western North Pacific.
bibliographic citation: Tsuzuku et al. (2020) The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific. PeerJ 8:e9709 https://doi.org/10.7717/peerj.9709
date submitted: 2020-02-19
date accepted: 2020-07-22
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsuzuku
  given name: Nahoko
author list: Agent
  family name: Kohno
  given name: Naoki
doi: 10.7717/peerj.9709
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: © 2020 Tsuzuku and Kohno
attribution name: Tsuzuku and Kohno

The influence of bait on remote underwater video observations in shallow-water coastal environments associated with the North-Eastern Atlantic
type: item
type: AcademicArticle
description: The use of baited remote underwater video (BRUV) for examining and monitoring marine biodiversity in temperate marine environments is rapidly growing, however many aspects of their effectiveness relies on assumptions based on studies from the Southern Hemisphere. The addition of bait to underwater camera systems acts as a stimulus for attracting individuals towards the camera field of view, however knowledge of the effectiveness of different bait types in northern temperate climbs is limited, particularly in dynamic coastal environments. Studies in the Southern Hemisphere indicate that oily baits are most effective whilst bait volume and weight do not impact BRUV effectiveness to any great degree. The present study assesses the influence of four bait types (mackerel, squid, crab and no bait (control)) on the relative abundance, taxonomic diversity and faunal assemblage composition at two independent locations within the North-Eastern Atlantic region; Swansea Bay, UK and Ria Formosa Lagoon, Portugal. Two different bait quantities (50 g and 350 g) were further trialled in Swansea Bay. Overall, patterns showed that baited deployments recorded statistically higher values of relative abundance and taxonomic diversity when compared to un-baited deployments in Swansea Bay but not in Ria Formosa Lagoon. No statistical evidence singled out one bait type as best performing for attracting higher abundances and taxonomic diversity in both locations. Faunal assemblage composition was however found to differ with bait type in Swansea Bay, with mackerel and squid attracting higher abundances of scavenging species compared to the crab and control treatments. With the exception of squid, bait quantity had minimal influence on bait attractiveness. It is recommended for consistency that a minimum of 50 g of cheap, oily fish such as mackerel is used as bait for BRUV deployments in shallow dynamic coastal environments in the North-Eastern Atlantic Region.
format: application/pdf
format: text/html
creator: Robyn E. Jones
creator: Ross A. Griffin
creator: Stephanie R. Januchowski-Hartley
creator: Richard K.F. Unsworth
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
description: doi:10.7717/peerj.9744
publisher: PeerJ Inc.
rights: © 2020 Jones et al.
abstract: The use of baited remote underwater video (BRUV) for examining and monitoring marine biodiversity in temperate marine environments is rapidly growing, however many aspects of their effectiveness relies on assumptions based on studies from the Southern Hemisphere. The addition of bait to underwater camera systems acts as a stimulus for attracting individuals towards the camera field of view, however knowledge of the effectiveness of different bait types in northern temperate climbs is limited, particularly in dynamic coastal environments. Studies in the Southern Hemisphere indicate that oily baits are most effective whilst bait volume and weight do not impact BRUV effectiveness to any great degree. The present study assesses the influence of four bait types (mackerel, squid, crab and no bait (control)) on the relative abundance, taxonomic diversity and faunal assemblage composition at two independent locations within the North-Eastern Atlantic region; Swansea Bay, UK and Ria Formosa Lagoon, Portugal. Two different bait quantities (50 g and 350 g) were further trialled in Swansea Bay. Overall, patterns showed that baited deployments recorded statistically higher values of relative abundance and taxonomic diversity when compared to un-baited deployments in Swansea Bay but not in Ria Formosa Lagoon. No statistical evidence singled out one bait type as best performing for attracting higher abundances and taxonomic diversity in both locations. Faunal assemblage composition was however found to differ with bait type in Swansea Bay, with mackerel and squid attracting higher abundances of scavenging species compared to the crab and control treatments. With the exception of squid, bait quantity had minimal influence on bait attractiveness. It is recommended for consistency that a minimum of 50 g of cheap, oily fish such as mackerel is used as bait for BRUV deployments in shallow dynamic coastal environments in the North-Eastern Atlantic Region.
bibliographic citation: Jones et al. (2020) The influence of bait on remote underwater video observations in shallow-water coastal environments associated with the North-Eastern Atlantic. PeerJ 8:e9744 https://doi.org/10.7717/peerj.9744
date submitted: 2020-04-06
date accepted: 2020-07-27
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jones
  given name: Robyn E.
author list: Agent
  family name: Griffin
  given name: Ross A.
author list: Agent
  family name: Januchowski-Hartley
  given name: Stephanie R.
author list: Agent
  family name: Unsworth
  given name: Richard K.F.
doi: 10.7717/peerj.9744
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: © 2020 Jones et al.
attribution name: Jones et al.

High moon brightness and low ambient temperatures affect sloth predation by harpy eagles
type: item
type: AcademicArticle
description: Background Climate plays a key role in the life histories of tropical vertebrates. However, tropical forests are only weakly seasonal compared with temperate and boreal regions. For species with limited ability to control core body temperature, even mild climatic variation can determine major behavioural outcomes, such as foraging and predator avoidance. In tropical forests, sloths are the arboreal vertebrate attaining the greatest biomass density, but their capacity to regulate body temperature is limited, relying on behavioural adaptations to thermoregulate. Sloths are largely or strictly nocturnal, and depend on crypsis to avoid predation. The harpy eagle (Harpia harpyja) is a sloth-specialist and exerts strong top-down control over its prey species. Yet the role of environmental variables on the regulation of predator–prey interactions between sloths and harpy eagles are unknown. The harpy eagle is considered Near Threatened. This motivated a comprehensive eﬀort to reintroduce this species into parts of Mesoamerica. This eﬀort incidentally enabled us to understand the prey profile of harpy eagles over multiple seasons. Methods Our study was conducted between 2003 and 2009 at Soberanía National Park, Panamá. Telemetered harpy eagles were seen hunting and feeding on individual prey species. For each predation event, field assistants systematically recorded the species killed. We analysed the effects of climatic conditions and vegetation phenology on the prey species profile of harpy eagles using generalised linear mixed models. Results Here we show that sloth predation by harpy eagles was negatively aﬀected by nocturnal ambient light (i.e. bright moonshine) and positively aﬀected by seasonally cool temperatures. We suggest that the first ensured low detectability conditions for sloths foraging at night and the second posed a thermally unsuitable climate that forced sloths to forage under riskier daylight. We showed that even moderate seasonal variation in temperat…
format: application/pdf
format: text/html
creator: Everton B.P. de Miranda
creator: Caio F. Kenup
creator: Edwin Campbell-Thompson
creator: Felix H. Vargas
creator: Angel Muela
creator: Richard Watson
creator: Carlos A. Peres
creator: Colleen T. Downs
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9756
publisher: PeerJ Inc.
rights: © 2020 Miranda et al.
abstract: Background Climate plays a key role in the life histories of tropical vertebrates. However, tropical forests are only weakly seasonal compared with temperate and boreal regions. For species with limited ability to control core body temperature, even mild climatic variation can determine major behavioural outcomes, such as foraging and predator avoidance. In tropical forests, sloths are the arboreal vertebrate attaining the greatest biomass density, but their capacity to regulate body temperature is limited, relying on behavioural adaptations to thermoregulate. Sloths are largely or strictly nocturnal, and depend on crypsis to avoid predation. The harpy eagle (Harpia harpyja) is a sloth-specialist and exerts strong top-down control over its prey species. Yet the role of environmental variables on the regulation of predator–prey interactions between sloths and harpy eagles are unknown. The harpy eagle is considered Near Threatened. This motivated a comprehensive eﬀort to reintroduce this species into parts of Mesoamerica. This eﬀort incidentally enabled us to understand the prey profile of harpy eagles over multiple seasons. Methods Our study was conducted between 2003 and 2009 at Soberanía National Park, Panamá. Telemetered harpy eagles were seen hunting and feeding on individual prey species. For each predation event, field assistants systematically recorded the species killed. We analysed the effects of climatic conditions and vegetation phenology on the prey species profile of harpy eagles using generalised linear mixed models. Results Here we show that sloth predation by harpy eagles was negatively aﬀected by nocturnal ambient light (i.e. bright moonshine) and positively aﬀected by seasonally cool temperatures. We suggest that the first ensured low detectability conditions for sloths foraging at night and the second posed a thermally unsuitable climate that forced sloths to forage under riskier daylight. We showed that even moderate seasonal variation in temperat…
bibliographic citation: Miranda et al. (2020) High moon brightness and low ambient temperatures affect sloth predation by harpy eagles. PeerJ 8:e9756 https://doi.org/10.7717/peerj.9756
date submitted: 2020-03-25
date accepted: 2020-07-28
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miranda
  given name: Everton B.P. de
author list: Agent
  family name: Kenup
  given name: Caio F.
author list: Agent
  family name: Campbell-Thompson
  given name: Edwin
author list: Agent
  family name: Vargas
  given name: Felix H.
author list: Agent
  family name: Muela
  given name: Angel
author list: Agent
  family name: Watson
  given name: Richard
author list: Agent
  family name: Peres
  given name: Carlos A.
author list: Agent
  family name: Downs
  given name: Colleen T.
doi: 10.7717/peerj.9756
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: © 2020 Miranda et al.
attribution name: Miranda et al.

Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution
type: item
type: AcademicArticle
description: Subcellular relocalization of proteins determines an organism’s metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
format: application/pdf
format: text/html
creator: Ryan W. Christian
creator: Seanna L. Hewitt
creator: Grant Nelson
creator: Eric H. Roalson
creator: Amit Dhingra
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9772
publisher: PeerJ Inc.
rights: © 2020 Christian et al.
abstract: Subcellular relocalization of proteins determines an organism’s metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
bibliographic citation: Christian et al. (2020) Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ 8:e9772 https://doi.org/10.7717/peerj.9772
date submitted: 2019-12-09
date accepted: 2020-07-30
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Christian
  given name: Ryan W.
author list: Agent
  family name: Hewitt
  given name: Seanna L.
author list: Agent
  family name: Nelson
  given name: Grant
author list: Agent
  family name: Roalson
  given name: Eric H.
author list: Agent
  family name: Dhingra
  given name: Amit
doi: 10.7717/peerj.9772
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: © 2020 Christian et al.
attribution name: Christian et al.

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