PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: An epidemiological investigation of porcine circovirus type 2 and porcine circovirus type 3 infections in Tianjin, North China
items: Contributions of burning incense on indoor air pollution levels and on the health status of patients with chronic obstructive pulmonary disease
items: Response of grassland productivity to climate change and anthropogenic activities in arid regions of Central Asia
items: Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi
items: Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan
items: Effects of cowpea mild mottle virus on soybean cultivars in Brazil
items: Double lives: transfer of fungal endophytes from leaves to woody substrates
items: Comparison of serum exosome isolation methods on co-precipitated free microRNAs
items: Investigating self-recognition in bonobos: mirror exposure reduces looking time to self but not unfamiliar conspecifics
items: Biomass, abundances, and abundance and geographical range size relationship of birds along a rainforest elevational gradient in Papua New Guinea

An epidemiological investigation of porcine circovirus type 2 and porcine circovirus type 3 infections in Tianjin, North China
type: item
type: AcademicArticle
description: Novel porcine circovirus type 3 (PCV3), first identified in the United States, has been detected in many other countries. Porcine circovirus is associated with postweaning multisystemic wasting syndrome, reproductive failure, congenital tremors, and other clinical symptoms. In this study, we established a double polymerase chain reaction assay for detecting both porcine circovirus type 2 (PCV2) and PCV3. This is the first study to detect and characterize the PCV3 genome in the Tianjin region of North China. We collected a total of 169 tissue samples from seven farms between 2016 and 2018. The PCV3-positive rate of all tissue samples was 37.3% (63/169) and the rate of PCV2 and PCV3 coinfection was 14.8% (25/169). PCV2 and PCV3 coinfections with more serious clinical symptoms were found in only three farms. We sequenced three PCV3 strains selected from tissue samples that were positively identified. The complete genome sequences of the three strains shared 97.6–99.4% nucleotide identities with the PCV3 strains in GenBank. Our results showed the extent of PCV3’s spread in Tianjin, and the need to further study PCV3’s pathobiology, epidemiology, isolation, and coinfection.
format: application/pdf
format: text/html
creator: Shuai-Yong Wang
creator: Ying-Feng Sun
creator: Qi Wang
creator: Ling-Xue Yu
creator: Shi-Qiang Zhu
creator: Xiao-Min Liu
creator: Yun Yao
creator: Juan Wang
creator: Tong-Ling Shan
creator: Hao Zheng
creator: Yan-Jun Zhou
creator: Wu Tong
creator: Ning Kong
creator: Guang-Zhi Tong
creator: Hai Yu
subject: Genomics
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.9735
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Novel porcine circovirus type 3 (PCV3), first identified in the United States, has been detected in many other countries. Porcine circovirus is associated with postweaning multisystemic wasting syndrome, reproductive failure, congenital tremors, and other clinical symptoms. In this study, we established a double polymerase chain reaction assay for detecting both porcine circovirus type 2 (PCV2) and PCV3. This is the first study to detect and characterize the PCV3 genome in the Tianjin region of North China. We collected a total of 169 tissue samples from seven farms between 2016 and 2018. The PCV3-positive rate of all tissue samples was 37.3% (63/169) and the rate of PCV2 and PCV3 coinfection was 14.8% (25/169). PCV2 and PCV3 coinfections with more serious clinical symptoms were found in only three farms. We sequenced three PCV3 strains selected from tissue samples that were positively identified. The complete genome sequences of the three strains shared 97.6–99.4% nucleotide identities with the PCV3 strains in GenBank. Our results showed the extent of PCV3’s spread in Tianjin, and the need to further study PCV3’s pathobiology, epidemiology, isolation, and coinfection.
bibliographic citation: Wang et al. (2020) An epidemiological investigation of porcine circovirus type 2 and porcine circovirus type 3 infections in Tianjin, North China. PeerJ 8:e9735 https://doi.org/10.7717/peerj.9735
date submitted: 2019-12-09
date accepted: 2020-07-25
issued: 2020-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shuai-Yong
author list: Agent
  family name: Sun
  given name: Ying-Feng
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Yu
  given name: Ling-Xue
author list: Agent
  family name: Zhu
  given name: Shi-Qiang
author list: Agent
  family name: Liu
  given name: Xiao-Min
author list: Agent
  family name: Yao
  given name: Yun
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Shan
  given name: Tong-Ling
author list: Agent
  family name: Zheng
  given name: Hao
author list: Agent
  family name: Zhou
  given name: Yan-Jun
author list: Agent
  family name: Tong
  given name: Wu
author list: Agent
  family name: Kong
  given name: Ning
author list: Agent
  family name: Tong
  given name: Guang-Zhi
author list: Agent
  family name: Yu
  given name: Hai
doi: 10.7717/peerj.9735
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-31
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Contributions of burning incense on indoor air pollution levels and on the health status of patients with chronic obstructive pulmonary disease
type: item
type: AcademicArticle
description: Background Among Buddhist or Taoist Taiwanese residents, burning incense is a common source of indoor particulate matter (PM), including PM10 and PM2.5, and can adversely affect the health status of patients with chronic obstructive pulmonary diseases (COPD). However, few studies have focused on the effects of intermittent burning of incense on PM concentration levels and the health status of patients with COPD. This correlational cohort study aimed to investigate the association between burning incense exposure duration, indoor air pollution levels, and lung function in patients with COPD in Taiwan. Methods We assessed 18 outpatients at seven time points with moderate-to-severe COPD using the COPD Assessment Test (CAT), and lung function tests. PM level changes were assessed at seven intervals using generalized estimating equations. Results Participants were primarily male (84%), with a mean age of 72.1 (standard deviation (SD) ± 9.3) years, and with a mean COPD duration of 3.7 (SD ± 3.1) years. Both PM10 and PM2.5 levels were the same as the background levels 1 h after incense burning. Burning incense may not influence lung function or symptom severity in patients with COPD in a short-time period. Air quality returned to baseline levels 1 h after burning incense. Conclusion Patients with COPD should avoid staying in rooms where incense is burnt, for up to 1 h. The small sample size and short study period may have influenced our results. Future longitudinal studies with larger sample sizes and long-term follow-ups are recommended.
format: application/pdf
format: text/html
creator: Su-Er Guo
creator: Miao-Ching Chi
creator: Chieh-Mo Lin
creator: Tsung-Ming Yang
subject: Public Health
subject: Respiratory Medicine
subject: Environmental Impacts
description: doi:10.7717/peerj.9768
publisher: PeerJ Inc.
rights: © 2020 Guo et al.
abstract: Background Among Buddhist or Taoist Taiwanese residents, burning incense is a common source of indoor particulate matter (PM), including PM10 and PM2.5, and can adversely affect the health status of patients with chronic obstructive pulmonary diseases (COPD). However, few studies have focused on the effects of intermittent burning of incense on PM concentration levels and the health status of patients with COPD. This correlational cohort study aimed to investigate the association between burning incense exposure duration, indoor air pollution levels, and lung function in patients with COPD in Taiwan. Methods We assessed 18 outpatients at seven time points with moderate-to-severe COPD using the COPD Assessment Test (CAT), and lung function tests. PM level changes were assessed at seven intervals using generalized estimating equations. Results Participants were primarily male (84%), with a mean age of 72.1 (standard deviation (SD) ± 9.3) years, and with a mean COPD duration of 3.7 (SD ± 3.1) years. Both PM10 and PM2.5 levels were the same as the background levels 1 h after incense burning. Burning incense may not influence lung function or symptom severity in patients with COPD in a short-time period. Air quality returned to baseline levels 1 h after burning incense. Conclusion Patients with COPD should avoid staying in rooms where incense is burnt, for up to 1 h. The small sample size and short study period may have influenced our results. Future longitudinal studies with larger sample sizes and long-term follow-ups are recommended.
bibliographic citation: Guo et al. (2020) Contributions of burning incense on indoor air pollution levels and on the health status of patients with chronic obstructive pulmonary disease. PeerJ 8:e9768 https://doi.org/10.7717/peerj.9768
date submitted: 2020-04-07
date accepted: 2020-07-30
issued: 2020-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Guo
  given name: Su-Er
author list: Agent
  family name: Chi
  given name: Miao-Ching
author list: Agent
  family name: Lin
  given name: Chieh-Mo
author list: Agent
  family name: Yang
  given name: Tsung-Ming
doi: 10.7717/peerj.9768
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-31
copyright: ©2020 Guo et al.
attribution name: Guo et al.

Response of grassland productivity to climate change and anthropogenic activities in arid regions of Central Asia
type: item
type: AcademicArticle
description: Background Quantitative evaluations of the relative impacts of climate change and anthropogenic activity on grasslands are significant for understanding grassland degradation mechanisms and controlling degraded grasslands. However, our knowledge about the effects of anthropogenic activities and climate change on the grassland in a mountain basin system in arid regions of Central Asia is still subject to great uncertainties. Methods In this research, we have chosen the net primary productivity (NPP) as an index for revealing grassland dynamics processes. Moreover, the human appropriation of net primary production (NPPH), which was calculated as the potential NPP (NPPP) minus the actual NPP (NPPA), was applied to distinguish the relative influences of climate change and human activities on the grassland NPP variations in a mountain basin system of Central Asia from 2001–2015. Results The results indicated that the grassland NPPA showed an increasing trend (35.88%) that was smaller than the decreasing trend (64.12%). The respective contributions of human activity, climate change and the two together to the increase in the NPPA were 6.19%, 81.30% and 12.51%, respectively. Human activity was largely responsible for the decrease in the grassland NPPA, with the area experiencing human-induced decreases accounting for 98.21% of the total decreased area, which mainly occurred during spring/autumn pasture and winter pasture. Furthermore, the average grazing pressure index (GPI) values of summer pastures, spring/autumn pasture and winter pastures were 1.04, 3.03 and 1.83, respectively, from 2001–2015. In addition, negative correlations between the NPP and GPI occupied most of the research area (92.41%). Discussion Our results indicate that: (i) anthropogenic activities were the primary cause of the reduction in the grassland NPP, especially grazing activities. (ii) For areas where the grassland NPP has increased, precipitation was the dominant climatic factor over temperature …
format: application/pdf
format: text/html
creator: Xu Bi
creator: Bo Li
creator: Lixin Zhang
creator: Bo Nan
creator: Xinshi Zhang
creator: Zihan Yang
subject: Ecology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9797
publisher: PeerJ Inc.
rights: © 2020 Bi et al.
abstract: Background Quantitative evaluations of the relative impacts of climate change and anthropogenic activity on grasslands are significant for understanding grassland degradation mechanisms and controlling degraded grasslands. However, our knowledge about the effects of anthropogenic activities and climate change on the grassland in a mountain basin system in arid regions of Central Asia is still subject to great uncertainties. Methods In this research, we have chosen the net primary productivity (NPP) as an index for revealing grassland dynamics processes. Moreover, the human appropriation of net primary production (NPPH), which was calculated as the potential NPP (NPPP) minus the actual NPP (NPPA), was applied to distinguish the relative influences of climate change and human activities on the grassland NPP variations in a mountain basin system of Central Asia from 2001–2015. Results The results indicated that the grassland NPPA showed an increasing trend (35.88%) that was smaller than the decreasing trend (64.12%). The respective contributions of human activity, climate change and the two together to the increase in the NPPA were 6.19%, 81.30% and 12.51%, respectively. Human activity was largely responsible for the decrease in the grassland NPPA, with the area experiencing human-induced decreases accounting for 98.21% of the total decreased area, which mainly occurred during spring/autumn pasture and winter pasture. Furthermore, the average grazing pressure index (GPI) values of summer pastures, spring/autumn pasture and winter pastures were 1.04, 3.03 and 1.83, respectively, from 2001–2015. In addition, negative correlations between the NPP and GPI occupied most of the research area (92.41%). Discussion Our results indicate that: (i) anthropogenic activities were the primary cause of the reduction in the grassland NPP, especially grazing activities. (ii) For areas where the grassland NPP has increased, precipitation was the dominant climatic factor over temperature …
bibliographic citation: Bi et al. (2020) Response of grassland productivity to climate change and anthropogenic activities in arid regions of Central Asia. PeerJ 8:e9797 https://doi.org/10.7717/peerj.9797
date submitted: 2020-01-14
date accepted: 2020-08-01
issued: 2020-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bi
  given name: Xu
author list: Agent
  family name: Li
  given name: Bo
author list: Agent
  family name: Zhang
  given name: Lixin
author list: Agent
  family name: Nan
  given name: Bo
author list: Agent
  family name: Zhang
  given name: Xinshi
author list: Agent
  family name: Yang
  given name: Zihan
doi: 10.7717/peerj.9797
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-31
copyright: ©2020 Bi et al.
attribution name: Bi et al.

Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi
type: item
type: AcademicArticle
description: Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri, the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.
format: application/pdf
format: text/html
creator: Ken A. Sterling
creator: Melvin L. Warren, Jr.
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.9807
publisher: PeerJ Inc.
rights: © 2020 Sterling and Warren, Jr
abstract: Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri, the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.
bibliographic citation: Sterling et al. (2020) Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi. PeerJ 8:e9807 https://doi.org/10.7717/peerj.9807
date submitted: 2020-05-01
date accepted: 2020-08-03
issued: 2020-08-31
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Sterling
  given name: Ken A.
author list: Agent
  family name: Warren, Jr.
  given name: Melvin L.
doi: 10.7717/peerj.9807
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-31
copyright: ©2020 Sterling and Warren, Jr
attribution name: Sterling and Warren, Jr

Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan
type: item
type: AcademicArticle
description: Common or bread wheat (Triticum aestivum L.) is the most important cereal crop in the world, including Kazakhstan, where it is a major agricultural commodity. Fungal pathogens producing leaf, stem, and yellow (stripe) rusts of wheat may cause yield losses of up to 50–60%. One of the most effective methods for preventing these losses is to develop resistant cultivars with high yield potential. This goal can be achieved using complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. In this study, a panel consisting of 215 common wheat cultivars and breeding lines from Kazakhstan, Russia, Europe, USA, Canada, Mexico, and Australia, with a wide range of resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR) diseases, was analyzed under field conditions in Southern Kazakhstan. The collection was genotyped using the 20K Illumina iSelect DNA array, where 11,510 informative single-nucleotide polymorphism markers were selected for further genome-wide association study (GWAS). Evaluation of the phenotypic diversity over 2 years showed a mostly mixed reaction to LR, mixed reaction/moderate susceptibility to SR, and moderate resistance to YR among wheat accessions from Kazakhstan. GWAS revealed 45 marker–trait associations (MTAs), including 23 for LR, 14 for SR, and eight for YR resistances. Three MTAs for LR resistance and one for SR resistance appeared to be novel. The MTAs identified in this work can be used for marker-assisted selection of common wheat in Kazakhstan in breeding new cultivars resistant to LR, SR, and YR diseases. These findings can be helpful for pyramiding genes with favorable alleles in promising cultivars and lines.
format: application/pdf
format: text/html
creator: Yuliya Genievskaya
creator: Yerlan Turuspekov
creator: Aralbek Rsaliyev
creator: Saule Abugalieva
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9820
publisher: PeerJ Inc.
rights: © 2020
abstract: Common or bread wheat (Triticum aestivum L.) is the most important cereal crop in the world, including Kazakhstan, where it is a major agricultural commodity. Fungal pathogens producing leaf, stem, and yellow (stripe) rusts of wheat may cause yield losses of up to 50–60%. One of the most effective methods for preventing these losses is to develop resistant cultivars with high yield potential. This goal can be achieved using complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. In this study, a panel consisting of 215 common wheat cultivars and breeding lines from Kazakhstan, Russia, Europe, USA, Canada, Mexico, and Australia, with a wide range of resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR) diseases, was analyzed under field conditions in Southern Kazakhstan. The collection was genotyped using the 20K Illumina iSelect DNA array, where 11,510 informative single-nucleotide polymorphism markers were selected for further genome-wide association study (GWAS). Evaluation of the phenotypic diversity over 2 years showed a mostly mixed reaction to LR, mixed reaction/moderate susceptibility to SR, and moderate resistance to YR among wheat accessions from Kazakhstan. GWAS revealed 45 marker–trait associations (MTAs), including 23 for LR, 14 for SR, and eight for YR resistances. Three MTAs for LR resistance and one for SR resistance appeared to be novel. The MTAs identified in this work can be used for marker-assisted selection of common wheat in Kazakhstan in breeding new cultivars resistant to LR, SR, and YR diseases. These findings can be helpful for pyramiding genes with favorable alleles in promising cultivars and lines.
bibliographic citation: Genievskaya et al. (2020) Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan. PeerJ 8:e9820 https://doi.org/10.7717/peerj.9820
date submitted: 2020-04-24
date accepted: 2020-08-05
issued: 2020-08-31
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Genievskaya
  given name: Yuliya
author list: Agent
  family name: Turuspekov
  given name: Yerlan
author list: Agent
  family name: Rsaliyev
  given name: Aralbek
author list: Agent
  family name: Abugalieva
  given name: Saule
doi: 10.7717/peerj.9820
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-31

Effects of cowpea mild mottle virus on soybean cultivars in Brazil
type: item
type: AcademicArticle
description: Soybean stem necrosis is caused by cowpea mild mottle virus (CPMMV), transmitted by the whitefly Bemisia tabaci. CPMMV has already been recorded in all major soybean-producing areas of Brazil. The impacts caused by CPMMV to the current Brazilian soybean production are unknown, thus the main objective of this study was to evaluate the effects of CPMMV infection on the main important soybean cultivars grown in the Southern and Midwestern regions of Brazil. Although asymptomatic in some of the tested cultivars, CPMMV infection significantly reduced the plant height, the number of pods per plant and the 1,000-grain weight. In addition, estimated yield losses ranged from 174 to 638 kg ha−1, depending on the cultivar. Evidence of seed transmission of CPMMV was observed in the BMX POTÊNCIA RR cultivar. These results suggest that CPMMV could have an important role in the reduction of soybean productivity in Brazil, but symptomless infections might be hiding the actual impact of this pathogen in commercial fields and infected seeds could be the primary inoculum source of the virus in the field.
format: application/pdf
format: text/html
creator: Felipe Barreto da Silva
creator: Cristiane Muller
creator: Vinicius Henrique Bello
creator: Luís Fernando Maranho Watanabe
creator: Bruno Rossitto De Marchi
creator: Lucas Machado Fusco
creator: Marcos Roberto Ribeiro-Junior
creator: Guilherme Barbosa Minozzi
creator: Lucia Madalena Vivan
creator: Marco Antonio Tamai
creator: Juliano Ricardo Farias
creator: Angélica Maria Nogueira
creator: Maria Márcia Pereira Sartori
creator: Renate Krause-Sakate
subject: Agricultural Science
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.9828
publisher: PeerJ Inc.
rights: © 2020 Barreto da Silva et al.
abstract: Soybean stem necrosis is caused by cowpea mild mottle virus (CPMMV), transmitted by the whitefly Bemisia tabaci. CPMMV has already been recorded in all major soybean-producing areas of Brazil. The impacts caused by CPMMV to the current Brazilian soybean production are unknown, thus the main objective of this study was to evaluate the effects of CPMMV infection on the main important soybean cultivars grown in the Southern and Midwestern regions of Brazil. Although asymptomatic in some of the tested cultivars, CPMMV infection significantly reduced the plant height, the number of pods per plant and the 1,000-grain weight. In addition, estimated yield losses ranged from 174 to 638 kg ha−1, depending on the cultivar. Evidence of seed transmission of CPMMV was observed in the BMX POTÊNCIA RR cultivar. These results suggest that CPMMV could have an important role in the reduction of soybean productivity in Brazil, but symptomless infections might be hiding the actual impact of this pathogen in commercial fields and infected seeds could be the primary inoculum source of the virus in the field.
bibliographic citation: Barreto da Silva et al. (2020) Effects of cowpea mild mottle virus on soybean cultivars in Brazil. PeerJ 8:e9828 https://doi.org/10.7717/peerj.9828
date submitted: 2020-04-06
date accepted: 2020-08-05
issued: 2020-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barreto da Silva
  given name: Felipe
author list: Agent
  family name: Muller
  given name: Cristiane
author list: Agent
  family name: Bello
  given name: Vinicius Henrique
author list: Agent
  family name: Watanabe
  given name: Luís Fernando Maranho
author list: Agent
  family name: Rossitto De Marchi
  given name: Bruno
author list: Agent
  family name: Fusco
  given name: Lucas Machado
author list: Agent
  family name: Ribeiro-Junior
  given name: Marcos Roberto
author list: Agent
  family name: Minozzi
  given name: Guilherme Barbosa
author list: Agent
  family name: Vivan
  given name: Lucia Madalena
author list: Agent
  family name: Tamai
  given name: Marco Antonio
author list: Agent
  family name: Farias
  given name: Juliano Ricardo
author list: Agent
  family name: Nogueira
  given name: Angélica Maria
author list: Agent
  family name: Sartori
  given name: Maria Márcia Pereira
author list: Agent
  family name: Krause-Sakate
  given name: Renate
doi: 10.7717/peerj.9828
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-31
copyright: © 2020 Barreto da Silva et al.
attribution name: Barreto da Silva et al.

Double lives: transfer of fungal endophytes from leaves to woody substrates
type: item
type: AcademicArticle
description: Fungal endophytes are a ubiquitous feature of plants, yet for many fungi the benefits of endophytism are still unknown. The Foraging Ascomycete (FA) hypothesis proposes that saprotrophic fungi can utilize leaves both as dispersal vehicles and as resource havens during times of scarcity. The presence of saprotrophs in leaf endophyte communities has been previously observed but their ability to transfer to non-foliar saprobic substrates has not been well investigated. To assess this ability, we conducted a culture study by placing surface-sterilized leaves from a single tropical angiosperm tree (Nectandra lineatifolia) directly onto sterile wood fragments and incubating them for 6 weeks. Fungi from the wood were subsequently isolated in culture and identified to the genus level by ITS sequences or morphology. Four-hundred and seventy-seven fungal isolates comprising 24 taxa were cultured from the wood. Of these, 70.8% of taxa (82.3% of isolates) belong to saprotrophic genera according to the FUNGuild database. Furthermore, 27% of OTUs (6% of isolates) were basidiomycetes, an unusually high proportion compared to typical endophyte communities. Xylaria flabelliformis, although absent in our original isolations, formed anamorphic fruiting structures on the woody substrates. We introduce the term viaphyte (literally, “by way of plant”) to refer to fungi that undergo an interim stage as leaf endophytes and, after leaf senescence, colonize other woody substrates via hyphal growth. Our results support the FA hypothesis and suggest that viaphytism may play a significant role in fungal dispersal.
format: application/pdf
format: text/html
creator: Aaron Nelson
creator: Roo Vandegrift
creator: George C. Carroll
creator: Bitty A. Roy
subject: Biodiversity
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.9341
publisher: PeerJ Inc.
rights: © 2020 Nelson et al.
abstract: Fungal endophytes are a ubiquitous feature of plants, yet for many fungi the benefits of endophytism are still unknown. The Foraging Ascomycete (FA) hypothesis proposes that saprotrophic fungi can utilize leaves both as dispersal vehicles and as resource havens during times of scarcity. The presence of saprotrophs in leaf endophyte communities has been previously observed but their ability to transfer to non-foliar saprobic substrates has not been well investigated. To assess this ability, we conducted a culture study by placing surface-sterilized leaves from a single tropical angiosperm tree (Nectandra lineatifolia) directly onto sterile wood fragments and incubating them for 6 weeks. Fungi from the wood were subsequently isolated in culture and identified to the genus level by ITS sequences or morphology. Four-hundred and seventy-seven fungal isolates comprising 24 taxa were cultured from the wood. Of these, 70.8% of taxa (82.3% of isolates) belong to saprotrophic genera according to the FUNGuild database. Furthermore, 27% of OTUs (6% of isolates) were basidiomycetes, an unusually high proportion compared to typical endophyte communities. Xylaria flabelliformis, although absent in our original isolations, formed anamorphic fruiting structures on the woody substrates. We introduce the term viaphyte (literally, “by way of plant”) to refer to fungi that undergo an interim stage as leaf endophytes and, after leaf senescence, colonize other woody substrates via hyphal growth. Our results support the FA hypothesis and suggest that viaphytism may play a significant role in fungal dispersal.
bibliographic citation: Nelson et al. (2020) Double lives: transfer of fungal endophytes from leaves to woody substrates. PeerJ 8:e9341 https://doi.org/10.7717/peerj.9341
date submitted: 2019-09-12
date accepted: 2020-05-20
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nelson
  given name: Aaron
author list: Agent
  family name: Vandegrift
  given name: Roo
author list: Agent
  family name: Carroll
  given name: George C.
author list: Agent
  family name: Roy
  given name: Bitty A.
doi: 10.7717/peerj.9341
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: © 2020 Nelson et al.
attribution name: Nelson et al.

Comparison of serum exosome isolation methods on co-precipitated free microRNAs
type: item
type: AcademicArticle
description: Background Exosomes are nano-sized extracellular vesicles containing different biomolecules such as proteins and microRNAs (miRNAs) that mediate intercellular communication. Recently, numerous studies have reported the important functions of exosomal miRNAs in disease development and the potential clinical application as diagnostic biomarkers. Up to now, the most commonly used methods to extract exosomes are ultracentrifugation (UC) and precipitation-based commercial kit (e.g., ExoQuick). Generally, both UC and ExoQuick method could co-isolate contaminating proteins along with exosomes, with the UC method yielding even purer exosomes than ExoQuick. However, the comparison of these two methods on co-precipitated free miRNAs is still unknown. Methods In this study, we isolated exosomes from the human serum with exogenously added cel-miR-39 by UC and ExoQuick and compared the proportion of cel-miR-39 co-precipitated with exosomes extracted by these two methods. Results Using exogenous cel-miR-39 as free miRNAs in serum, we concluded that ExoQuick co-isolates a small proportion of free miRNAs while UC hardly precipitates any free miRNAs. We also found that incubation at 37 °C for 1 h could decrease the proportion of free miRNAs, and exosomal miRNAs like miR-126 and miR-152 also decreased when RNase A was used. In conclusion, our findings provide essential information about the details of serum exosome isolation methods for further research on exosomal miRNAs.
format: application/pdf
format: text/html
creator: Yirui Cheng
creator: Xiangyun Qu
creator: Zhaonan Dong
creator: Qingyu Zeng
creator: Xueqing Ma
creator: Yunli Jia
creator: Ruochen Li
creator: Xiaoxu Jiang
creator: Cecilia Williams
creator: Tao Wang
creator: Weiliang Xia
subject: Bioengineering
subject: Biotechnology
subject: Cell Biology
description: doi:10.7717/peerj.9434
publisher: PeerJ Inc.
rights: © 2020 Cheng et al.
abstract: Background Exosomes are nano-sized extracellular vesicles containing different biomolecules such as proteins and microRNAs (miRNAs) that mediate intercellular communication. Recently, numerous studies have reported the important functions of exosomal miRNAs in disease development and the potential clinical application as diagnostic biomarkers. Up to now, the most commonly used methods to extract exosomes are ultracentrifugation (UC) and precipitation-based commercial kit (e.g., ExoQuick). Generally, both UC and ExoQuick method could co-isolate contaminating proteins along with exosomes, with the UC method yielding even purer exosomes than ExoQuick. However, the comparison of these two methods on co-precipitated free miRNAs is still unknown. Methods In this study, we isolated exosomes from the human serum with exogenously added cel-miR-39 by UC and ExoQuick and compared the proportion of cel-miR-39 co-precipitated with exosomes extracted by these two methods. Results Using exogenous cel-miR-39 as free miRNAs in serum, we concluded that ExoQuick co-isolates a small proportion of free miRNAs while UC hardly precipitates any free miRNAs. We also found that incubation at 37 °C for 1 h could decrease the proportion of free miRNAs, and exosomal miRNAs like miR-126 and miR-152 also decreased when RNase A was used. In conclusion, our findings provide essential information about the details of serum exosome isolation methods for further research on exosomal miRNAs.
bibliographic citation: Cheng et al. (2020) Comparison of serum exosome isolation methods on co-precipitated free microRNAs. PeerJ 8:e9434 https://doi.org/10.7717/peerj.9434
date submitted: 2020-03-05
date accepted: 2020-06-06
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Yirui
author list: Agent
  family name: Qu
  given name: Xiangyun
author list: Agent
  family name: Dong
  given name: Zhaonan
author list: Agent
  family name: Zeng
  given name: Qingyu
author list: Agent
  family name: Ma
  given name: Xueqing
author list: Agent
  family name: Jia
  given name: Yunli
author list: Agent
  family name: Li
  given name: Ruochen
author list: Agent
  family name: Jiang
  given name: Xiaoxu
author list: Agent
  family name: Williams
  given name: Cecilia
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Xia
  given name: Weiliang
doi: 10.7717/peerj.9434
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: ©2020 Cheng et al.
attribution name: Cheng et al.

Investigating self-recognition in bonobos: mirror exposure reduces looking time to self but not unfamiliar conspecifics
type: item
type: AcademicArticle
description: The question of whether animals have some sort of self-awareness is a topic of continued debate. A necessary precondition for self-awareness is the ability to visually discriminate the self from others, which has traditionally been investigated through mirror self-recognition experiments. Although great apes generally pass such experiments, interpretations of results have remained controversial. The aim of this study was to investigate how bonobos (Pan paniscus) respond to different types of images of themselves and others, both before and after prolonged mirror exposure. We first presented presumably mirror-naive subjects with representations of themselves in three different ways (mirror image, contingent and non-contingent video footage) as well as representations of others (video footage of known and unknown conspecifics). We found that subjects paid significantly less attention to contingent images of themselves (mirror image, video footage) than to non-contingent images of themselves and unfamiliar individuals, suggesting they perceived the non-contingent self-images as novel. We then provided subjects with three months of access to a large mirror centrally positioned in the enclosure. Following this manipulation, subjects showed significantly reduced interest in the non-contingent self-images, while interest in unknown individuals remained unchanged, suggesting that the mirror experience has led to a fuller understanding of their own self. We discuss implications of this preliminary investigation for the on-going debate on self-awareness in animals.
format: application/pdf
format: text/html
creator: Gladez Shorland
creator: Emilie Genty
creator: Jean-Pascal Guéry
creator: Klaus Zuberbühler
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.9685
publisher: PeerJ Inc.
rights: © 2020 Shorland et al.
abstract: The question of whether animals have some sort of self-awareness is a topic of continued debate. A necessary precondition for self-awareness is the ability to visually discriminate the self from others, which has traditionally been investigated through mirror self-recognition experiments. Although great apes generally pass such experiments, interpretations of results have remained controversial. The aim of this study was to investigate how bonobos (Pan paniscus) respond to different types of images of themselves and others, both before and after prolonged mirror exposure. We first presented presumably mirror-naive subjects with representations of themselves in three different ways (mirror image, contingent and non-contingent video footage) as well as representations of others (video footage of known and unknown conspecifics). We found that subjects paid significantly less attention to contingent images of themselves (mirror image, video footage) than to non-contingent images of themselves and unfamiliar individuals, suggesting they perceived the non-contingent self-images as novel. We then provided subjects with three months of access to a large mirror centrally positioned in the enclosure. Following this manipulation, subjects showed significantly reduced interest in the non-contingent self-images, while interest in unknown individuals remained unchanged, suggesting that the mirror experience has led to a fuller understanding of their own self. We discuss implications of this preliminary investigation for the on-going debate on self-awareness in animals.
bibliographic citation: Shorland et al. (2020) Investigating self-recognition in bonobos: mirror exposure reduces looking time to self but not unfamiliar conspecifics. PeerJ 8:e9685 https://doi.org/10.7717/peerj.9685
date submitted: 2018-05-01
date accepted: 2020-07-18
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shorland
  given name: Gladez
author list: Agent
  family name: Genty
  given name: Emilie
author list: Agent
  family name: Guéry
  given name: Jean-Pascal
author list: Agent
  family name: Zuberbühler
  given name: Klaus
doi: 10.7717/peerj.9685
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: ©2020 Shorland et al.
attribution name: Shorland et al.

Biomass, abundances, and abundance and geographical range size relationship of birds along a rainforest elevational gradient in Papua New Guinea
type: item
type: AcademicArticle
description: The usually positive inter-specific relationship between geographical range size and the abundance of local bird populations comes with exceptions. On continents, the majority of these exceptions have been described from tropical montane areas in Africa, where geographically-restricted bird species are unusually abundant. We asked how the local abundances of passerine and non-passerine bird species along an elevational gradient on Mt. Wilhelm, Papua New Guinea relate to their geographical range size. We collected data on bird assemblages at eight elevations (200–3,700 m, at 500 m elevational increments). We used a standardized point-counts at 16 points at each elevational study site. We partitioned the birds into feeding guilds, and we obtained data on geographical range sizes from the Bird-Life International data zone. We observed a positive relationship between abundance and geographical range size in the lowlands. This trend changed to a negative one towards higher elevations. The total abundances of the assemblage showed a hump-shaped pattern along the elevational gradient, with passerine birds, namely passerine insectivores, driving the observed pattern. In contrast to abundances, the mean biomass of the bird assemblages decreased with increasing elevation. Our results show that montane bird species maintain dense populations which compensate for the decreased available area near the top of the mountain.
format: application/pdf
format: text/html
creator: Katerina Sam
creator: Bonny Koane
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9727
publisher: PeerJ Inc.
rights: © 2020 Sam and Koane
abstract: The usually positive inter-specific relationship between geographical range size and the abundance of local bird populations comes with exceptions. On continents, the majority of these exceptions have been described from tropical montane areas in Africa, where geographically-restricted bird species are unusually abundant. We asked how the local abundances of passerine and non-passerine bird species along an elevational gradient on Mt. Wilhelm, Papua New Guinea relate to their geographical range size. We collected data on bird assemblages at eight elevations (200–3,700 m, at 500 m elevational increments). We used a standardized point-counts at 16 points at each elevational study site. We partitioned the birds into feeding guilds, and we obtained data on geographical range sizes from the Bird-Life International data zone. We observed a positive relationship between abundance and geographical range size in the lowlands. This trend changed to a negative one towards higher elevations. The total abundances of the assemblage showed a hump-shaped pattern along the elevational gradient, with passerine birds, namely passerine insectivores, driving the observed pattern. In contrast to abundances, the mean biomass of the bird assemblages decreased with increasing elevation. Our results show that montane bird species maintain dense populations which compensate for the decreased available area near the top of the mountain.
bibliographic citation: Sam et al. (2020) Biomass, abundances, and abundance and geographical range size relationship of birds along a rainforest elevational gradient in Papua New Guinea. PeerJ 8:e9727 https://doi.org/10.7717/peerj.9727
date submitted: 2019-07-24
date accepted: 2020-07-24
issued: 2020-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sam
  given name: Katerina
author list: Agent
  family name: Koane
  given name: Bonny
doi: 10.7717/peerj.9727
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-28
copyright: ©2020 Sam and Koane
attribution name: Sam and Koane

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