PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea
items: Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
items: No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators
items: A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods
items: A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides
items: Nest-site selection and breeding success of passerines in the world’s southernmost forests
items: Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)
items: Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam
items: Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
items: Confidence intervals for the common coefficient of variation of rainfall in Thailand

Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea
type: item
type: AcademicArticle
description: We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormis sp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcata Lang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.
format: application/pdf
format: text/html
creator: Jaehyun Kim
creator: Eunjung Nam
creator: Wonchoel Lee
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10007
publisher: PeerJ Inc.
rights: © 2020 Kim et al.
abstract: We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormis sp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcata Lang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.
bibliographic citation: Kim et al. (2020) Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea. PeerJ 8:e10007 https://doi.org/10.7717/peerj.10007
date submitted: 2020-06-17
date accepted: 2020-08-31
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Jaehyun
author list: Agent
  family name: Nam
  given name: Eunjung
author list: Agent
  family name: Lee
  given name: Wonchoel
doi: 10.7717/peerj.10007
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Kim et al.
attribution name: Kim et al.

Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
type: item
type: AcademicArticle
description: Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.
format: application/pdf
format: text/html
creator: Youmei Huang
creator: Yanhui Liu
creator: Man Zhang
creator: Mengnan Chai
creator: Qing He
creator: Bello Hassan Jakada
creator: Fangqian Chen
creator: Huihuang Chen
creator: Xingyue Jin
creator: Hanyang Cai
creator: Yuan Qin
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10014
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.
bibliographic citation: Huang et al. (2020) Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.). PeerJ 8:e10014 https://doi.org/10.7717/peerj.10014
date submitted: 2020-04-21
date accepted: 2020-09-01
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Youmei
author list: Agent
  family name: Liu
  given name: Yanhui
author list: Agent
  family name: Zhang
  given name: Man
author list: Agent
  family name: Chai
  given name: Mengnan
author list: Agent
  family name: He
  given name: Qing
author list: Agent
  family name: Jakada
  given name: Bello Hassan
author list: Agent
  family name: Chen
  given name: Fangqian
author list: Agent
  family name: Chen
  given name: Huihuang
author list: Agent
  family name: Jin
  given name: Xingyue
author list: Agent
  family name: Cai
  given name: Hanyang
author list: Agent
  family name: Qin
  given name: Yuan
doi: 10.7717/peerj.10014
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Huang et al.
attribution name: Huang et al.

No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators
type: item
type: AcademicArticle
description: No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in the yards of a subset of homes (N = 20) located near regularly mowed urban parks (N = 15) at the end of the month. We found that homes that participated in No Mow May had more diverse and abundant flora than regularly mowed green spaces throughout the city. No Mow May homes had three times higher bee richness and five times higher bee abundances than frequently mowed greenspaces. Using generalized linear models, we found that the best predictor of bee richness was the size of the designated unmowed area, and the best predictors of bee abundances were the size of the unmowed area as well as floral richness. While our findings cannot conclusively attribute increases in bee abundances and richness to the No Mow May efforts, our data does show that bee pollinators make use of no mow spaces as key floral resources during early spring in the upper midwestern United States. A post-No Mow May survey revealed that the participants were keen to increase native floral resources in their yards, increase native bee nesting habitat, reduce mowing intensities, and limit herbicide, pesticide, and fertilizer applications to their lawns. The No Mow May initiative educated an engaged community on best practices to improve the conservation of urban pollinators in future years.
format: application/pdf
format: text/html
creator: Israel Del Toro
creator: Relena R. Ribbons
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.10021
publisher: PeerJ Inc.
rights: © 2020 Del Toro et al.
abstract: No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in the yards of a subset of homes (N = 20) located near regularly mowed urban parks (N = 15) at the end of the month. We found that homes that participated in No Mow May had more diverse and abundant flora than regularly mowed green spaces throughout the city. No Mow May homes had three times higher bee richness and five times higher bee abundances than frequently mowed greenspaces. Using generalized linear models, we found that the best predictor of bee richness was the size of the designated unmowed area, and the best predictors of bee abundances were the size of the unmowed area as well as floral richness. While our findings cannot conclusively attribute increases in bee abundances and richness to the No Mow May efforts, our data does show that bee pollinators make use of no mow spaces as key floral resources during early spring in the upper midwestern United States. A post-No Mow May survey revealed that the participants were keen to increase native floral resources in their yards, increase native bee nesting habitat, reduce mowing intensities, and limit herbicide, pesticide, and fertilizer applications to their lawns. The No Mow May initiative educated an engaged community on best practices to improve the conservation of urban pollinators in future years.
bibliographic citation: Del Toro et al. (2020) No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators. PeerJ 8:e10021 https://doi.org/10.7717/peerj.10021
date submitted: 2020-06-26
date accepted: 2020-09-02
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Del Toro
  given name: Israel
author list: Agent
  family name: Ribbons
  given name: Relena R.
doi: 10.7717/peerj.10021
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Del Toro and Ribbons
attribution name: Del Toro et al.

A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods
type: item
type: AcademicArticle
description: Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the populatio…
format: application/pdf
format: text/html
creator: Sara M. Burns
creator: Frances Bonier
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.10037
publisher: PeerJ Inc.
rights: © 2020 Burns and Bonier
abstract: Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the populatio…
bibliographic citation: Burns et al. (2020) A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods. PeerJ 8:e10037 https://doi.org/10.7717/peerj.10037
date submitted: 2020-03-04
date accepted: 2020-09-03
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burns
  given name: Sara M.
author list: Agent
  family name: Bonier
  given name: Frances
doi: 10.7717/peerj.10037
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: © 2020 Burns and Bonier
attribution name: Burns and Bonier

A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides
type: item
type: AcademicArticle
description: Background In semi-arid regions, the use of plastic mulch and pesticides in conventional agriculture is nearly ubiquitous. Although the sorption of pesticides on Low Density Polyethylene (LDPE) has been previously studied, no data are available for other plastics such as Pro-oxidant Additive Containing (PAC) plastics or “biodegradable” (Bio) plastics. The aim of this research was to measure the sorption pattern of active substances from pesticides on LDPE, PAC and Bio plastic mulches and to compare the decay of the active substances in the presence and absence of plastic debris. Methods For this purpose, 38 active substances from 17 insecticides, 15 fungicides and six herbicides commonly applied with plastic mulching in South-east Spain were incubated with a 3 × 3 cm2 piece of plastic mulch (LDPE, PAC and Bio). The incubation was done in a solution of 10% acetonitrile and 90% distilled water at 35 °C for 15 days in the dark. The Quick Easy Cheap Effective Rugged Safe approach was adapted to extract the pesticides. Results The sorption behavior depended on both the pesticide and the plastic mulch type. On average, the sorption percentage was ~23% on LDPE and PAC and ~50% on Bio. The decay of active substances in the presence of plastic was ~30% lesser than the decay of active substances in solution alone. This study is the first attempt at assessing the behavior of a diversity of plastic mulches and pesticides to further define research needs.
format: application/pdf
format: text/html
creator: Nicolas Beriot
creator: Paul Zomer
creator: Raul Zornoza
creator: Violette Geissen
subject: Agricultural Science
subject: Soil Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Green Chemistry
description: doi:10.7717/peerj.9876
publisher: PeerJ Inc.
rights: © 2020 Beriot et al.
abstract: Background In semi-arid regions, the use of plastic mulch and pesticides in conventional agriculture is nearly ubiquitous. Although the sorption of pesticides on Low Density Polyethylene (LDPE) has been previously studied, no data are available for other plastics such as Pro-oxidant Additive Containing (PAC) plastics or “biodegradable” (Bio) plastics. The aim of this research was to measure the sorption pattern of active substances from pesticides on LDPE, PAC and Bio plastic mulches and to compare the decay of the active substances in the presence and absence of plastic debris. Methods For this purpose, 38 active substances from 17 insecticides, 15 fungicides and six herbicides commonly applied with plastic mulching in South-east Spain were incubated with a 3 × 3 cm2 piece of plastic mulch (LDPE, PAC and Bio). The incubation was done in a solution of 10% acetonitrile and 90% distilled water at 35 °C for 15 days in the dark. The Quick Easy Cheap Effective Rugged Safe approach was adapted to extract the pesticides. Results The sorption behavior depended on both the pesticide and the plastic mulch type. On average, the sorption percentage was ~23% on LDPE and PAC and ~50% on Bio. The decay of active substances in the presence of plastic was ~30% lesser than the decay of active substances in solution alone. This study is the first attempt at assessing the behavior of a diversity of plastic mulches and pesticides to further define research needs.
bibliographic citation: Beriot et al. (2020) A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides. PeerJ 8:e9876 https://doi.org/10.7717/peerj.9876
date submitted: 2020-02-26
date accepted: 2020-08-14
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beriot
  given name: Nicolas
author list: Agent
  family name: Zomer
  given name: Paul
author list: Agent
  family name: Zornoza
  given name: Raul
author list: Agent
  family name: Geissen
  given name: Violette
doi: 10.7717/peerj.9876
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: © 2020 Beriot et al.
attribution name: Beriot et al.

Nest-site selection and breeding success of passerines in the world’s southernmost forests
type: item
type: AcademicArticle
description: Background Birds can maximize their reproductive success through careful selection of nest-sites. The ‘total-foliage’ hypothesis predicts that nests concealed in vegetation should have higher survival. We propose an additional hypothesis, the ‘predator proximity’ hypothesis, which states that nests placed farther from predators would have higher survival. We examined these hypotheses in the world’s southernmost forests of Navarino Island, in the Cape Horn Biosphere reserve, Chile (55°S). This island has been free of mammalian ground predators until recently, and forest passerines have been subject to depredation only by diurnal and nocturnal raptors. Methods During three breeding seasons (2014–2017), we monitored 104 nests for the five most abundant open-cup forest-dwelling passerines (Elaenia albiceps, Zonotrichia capensis, Phrygilus patagonicus, Turdus falcklandii, and Anairetes parulus). We identified nest predators using camera traps and assessed whether habitat characteristics affected nest-site selection and survival. Results Nest predation was the main cause of nest failure (71% of failed nests). Milvago chimango was the most common predator, depredating 13 (87%) of the 15 nests where we could identify a predator. By contrast, the recently introduced mammal Neovison vison, the only ground predator, depredated one nest (7%). Species selected nest-sites with more understory cover and taller understory, which according to the total-foliage hypothesis would provide more concealment against both avian and mammal predators. However, these variables negatively influenced nest survival. The apparent disconnect between selecting nest-sites to avoid predation and the actual risk of predation could be due to recent changes in the predator assemblage driven by an increased abundance of native M. chimango associated with urban development, and/or the introduction of exotic mammalian ground predators to this island. These predator assemblage changes could have resulted in …
format: application/pdf
format: text/html
creator: Rocío Fernanda Jara
creator: Ramiro Daniel Crego
creator: Michael David Samuel
creator: Ricardo Rozzi
creator: Jaime Enrique Jiménez
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.9892
publisher: PeerJ Inc.
rights: © 2020 Jara et al.
abstract: Background Birds can maximize their reproductive success through careful selection of nest-sites. The ‘total-foliage’ hypothesis predicts that nests concealed in vegetation should have higher survival. We propose an additional hypothesis, the ‘predator proximity’ hypothesis, which states that nests placed farther from predators would have higher survival. We examined these hypotheses in the world’s southernmost forests of Navarino Island, in the Cape Horn Biosphere reserve, Chile (55°S). This island has been free of mammalian ground predators until recently, and forest passerines have been subject to depredation only by diurnal and nocturnal raptors. Methods During three breeding seasons (2014–2017), we monitored 104 nests for the five most abundant open-cup forest-dwelling passerines (Elaenia albiceps, Zonotrichia capensis, Phrygilus patagonicus, Turdus falcklandii, and Anairetes parulus). We identified nest predators using camera traps and assessed whether habitat characteristics affected nest-site selection and survival. Results Nest predation was the main cause of nest failure (71% of failed nests). Milvago chimango was the most common predator, depredating 13 (87%) of the 15 nests where we could identify a predator. By contrast, the recently introduced mammal Neovison vison, the only ground predator, depredated one nest (7%). Species selected nest-sites with more understory cover and taller understory, which according to the total-foliage hypothesis would provide more concealment against both avian and mammal predators. However, these variables negatively influenced nest survival. The apparent disconnect between selecting nest-sites to avoid predation and the actual risk of predation could be due to recent changes in the predator assemblage driven by an increased abundance of native M. chimango associated with urban development, and/or the introduction of exotic mammalian ground predators to this island. These predator assemblage changes could have resulted in …
bibliographic citation: Jara et al. (2020) Nest-site selection and breeding success of passerines in the world’s southernmost forests. PeerJ 8:e9892 https://doi.org/10.7717/peerj.9892
date submitted: 2020-02-05
date accepted: 2020-08-17
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jara
  given name: Rocío Fernanda
author list: Agent
  family name: Crego
  given name: Ramiro Daniel
author list: Agent
  family name: Samuel
  given name: Michael David
author list: Agent
  family name: Rozzi
  given name: Ricardo
author list: Agent
  family name: Jiménez
  given name: Jaime Enrique
doi: 10.7717/peerj.9892
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Jara et al.
attribution name: Jara et al.

Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)
type: item
type: AcademicArticle
description: Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.
format: application/pdf
format: text/html
creator: Leta Dickinson
creator: Hilary Noble
creator: Elliot Gardner
creator: Aida Shafreena Ahmad Puad
creator: Wan Nuur Fatiha Wan Zakaria
creator: Nyree J.C. Zerega
subject: Biodiversity
subject: Genetics
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.9897
publisher: PeerJ Inc.
rights: © 2020 Dickinson et al.
abstract: Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.
bibliographic citation: Dickinson et al. (2020) Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus). PeerJ 8:e9897 https://doi.org/10.7717/peerj.9897
date submitted: 2020-02-24
date accepted: 2020-08-17
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dickinson
  given name: Leta
author list: Agent
  family name: Noble
  given name: Hilary
author list: Agent
  family name: Gardner
  given name: Elliot
author list: Agent
  family name: Puad
  given name: Aida Shafreena Ahmad
author list: Agent
  family name: Zakaria
  given name: Wan Nuur Fatiha Wan
author list: Agent
  family name: Zerega
  given name: Nyree J.C.
doi: 10.7717/peerj.9897
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Dickinson et al.
attribution name: Dickinson et al.

Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam
type: item
type: AcademicArticle
description: Background Deformed wing virus (DWV) is a virulent virus that causes honeybee disease. DWV can exist as a latent infection in honeybees, outbreak into epidemics, and cause serious damage to beekeeping cross the world, including Vietnam. Methods The two DWV strains circulating in Vietnamese honeybee, Apis cerana, were first isolated from adult honeybees in North Vietnam (DWV-NVN) and South Vietnam (DWV-SVN). Their complete nucleotide sequences were determined, aligned, and compared with other DWV strains. Results The two Vietnamese DWV strains comprised 10,113 bp and contained a large single open reading frame (ORF) of 2,893 amino acids, initiating at nucleotide 1,130 and terminating at nucleotide 9,812. Multiple nucleotide sequence alignment between these two DWV-VN strains and DWV strains in A. mellifera was performed. The DWV-VN strains showed a low genetic identity (from 91.4% to 92.0%) with almost of these strains, but lower identities (89.2% and 89.4%) with UK2 and (89.6%) with the China2 strain. Low identities (91.7% and 91.9%) were also observed between the China3 strain (in A. cerana) and the DWV-VN strains, respectively. The deduced amino acid sequence alignment showed high genetic similarities (97.0%–97.9%) when the USA1, Chile, Italy1, France, UK1, UK2, Japan, Korea2, China1, China2 and China3 strains were compared to the DWV-VN strains. This ratio was 96.7% and 96.8% when the Korea1 strain was compared to the DWV-SVN and DWV-NVN strains, respectively. Numerous amino acid substitutions were identified in the L, VP3, and RdRp sequences. Notably, we observed six substitutions positioned at amino acids 27 (E > I), 98 (S > T), 120 (A > V), 153 (M > T), 170 (D > F), and 174 (Y > F) in the L protein, two amino acid changes at positions 980 (S > A) and 1032 (E > T) in VP3, and one amino acid change at position 2627 (R > C) unique to the DWV-VN strains. Phylogenetic analysis based on complete genome sequences, RdRp sequences and Simplot analysis indicated that th…
format: application/pdf
format: text/html
creator: Ha T. Thu
creator: Nguyen T.K. Lien
creator: Pham T. Lanh
creator: Bui T.T. Duong
creator: Nguyen T. Hoa
creator: Man H. Phuoc
creator: Pham H. Thai
creator: Dong Van Quyen
subject: Biodiversity
subject: Genomics
subject: Microbiology
subject: Taxonomy
subject: Virology
description: doi:10.7717/peerj.9911
publisher: PeerJ Inc.
rights: © 2020 Thu et al.
abstract: Background Deformed wing virus (DWV) is a virulent virus that causes honeybee disease. DWV can exist as a latent infection in honeybees, outbreak into epidemics, and cause serious damage to beekeeping cross the world, including Vietnam. Methods The two DWV strains circulating in Vietnamese honeybee, Apis cerana, were first isolated from adult honeybees in North Vietnam (DWV-NVN) and South Vietnam (DWV-SVN). Their complete nucleotide sequences were determined, aligned, and compared with other DWV strains. Results The two Vietnamese DWV strains comprised 10,113 bp and contained a large single open reading frame (ORF) of 2,893 amino acids, initiating at nucleotide 1,130 and terminating at nucleotide 9,812. Multiple nucleotide sequence alignment between these two DWV-VN strains and DWV strains in A. mellifera was performed. The DWV-VN strains showed a low genetic identity (from 91.4% to 92.0%) with almost of these strains, but lower identities (89.2% and 89.4%) with UK2 and (89.6%) with the China2 strain. Low identities (91.7% and 91.9%) were also observed between the China3 strain (in A. cerana) and the DWV-VN strains, respectively. The deduced amino acid sequence alignment showed high genetic similarities (97.0%–97.9%) when the USA1, Chile, Italy1, France, UK1, UK2, Japan, Korea2, China1, China2 and China3 strains were compared to the DWV-VN strains. This ratio was 96.7% and 96.8% when the Korea1 strain was compared to the DWV-SVN and DWV-NVN strains, respectively. Numerous amino acid substitutions were identified in the L, VP3, and RdRp sequences. Notably, we observed six substitutions positioned at amino acids 27 (E > I), 98 (S > T), 120 (A > V), 153 (M > T), 170 (D > F), and 174 (Y > F) in the L protein, two amino acid changes at positions 980 (S > A) and 1032 (E > T) in VP3, and one amino acid change at position 2627 (R > C) unique to the DWV-VN strains. Phylogenetic analysis based on complete genome sequences, RdRp sequences and Simplot analysis indicated that th…
bibliographic citation: Thu et al. (2020) Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam. PeerJ 8:e9911 https://doi.org/10.7717/peerj.9911
date submitted: 2020-04-13
date accepted: 2020-08-18
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thu
  given name: Ha T.
author list: Agent
  family name: Lien
  given name: Nguyen T.K.
author list: Agent
  family name: Lanh
  given name: Pham T.
author list: Agent
  family name: Duong
  given name: Bui T.T.
author list: Agent
  family name: Hoa
  given name: Nguyen T.
author list: Agent
  family name: Phuoc
  given name: Man H.
author list: Agent
  family name: Thai
  given name: Pham H.
author list: Agent
  family name: Quyen
  given name: Dong Van
doi: 10.7717/peerj.9911
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Thu et al.
attribution name: Thu et al.

Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
type: item
type: AcademicArticle
description: Background Breast cancer is a heterogeneous disease. Compared with other subtypes of breast cancer, triple-negative breast cancer (TNBC) is easy to metastasize and has a short survival time, less choice of treatment options. Here, we aimed to identify the potential biomarkers to TNBC diagnosis and prognosis. Material/Methods Three independent data sets (GSE45827, GSE38959, GSE65194) were downloaded from the Gene Expression Omnibus (GEO). The R software packages were used to integrate the gene profiles and identify differentially expressed genes (DEGs). A variety of bioinformatics tools were used to explore the hub genes, including the DAVID database, STRING database and Cytoscape software. Reverse transcription quantitative PCR (RT-qPCR) was used to verify the hub genes in 14 pairs of TNBC paired tissues. Results In this study, we screened out 161 DEGs between 222 non-TNBC and 126 TNBC samples, of which 105 genes were up-regulated and 56 were down-regulated. These DEGs were enriched for 27 GO terms and two pathways. GO analysis enriched mainly in “cell division”, “chromosome, centromeric region” and “microtubule motor activity”. KEGG pathway analysis enriched mostly in “Cell cycle” and “Oocyte meiosis”. PPI network was constructed and then 10 top hub genes were screened. According to the analysis results of the Kaplan-Meier survival curve, the expression levels of only NUF2, FAM83D and CENPH were associated with the recurrence-free survival in TNBC samples (P < 0.05). RT-qPCR confirmed that the expression levels of NUF2 and FAM83D in TNBC tissues were indeed up-regulated significantly. Conclusions The comprehensive analysis showed that NUF2 and FAM83D could be used as potential biomarkers for diagnosis and prognosis of TNBC.
format: application/pdf
format: text/html
creator: Xiuming Zhai
creator: Zhaowei Yang
creator: Xiji Liu
creator: Zihe Dong
creator: Dandan Zhou
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.9975
publisher: PeerJ Inc.
rights: © 2020 Zhai et al.
abstract: Background Breast cancer is a heterogeneous disease. Compared with other subtypes of breast cancer, triple-negative breast cancer (TNBC) is easy to metastasize and has a short survival time, less choice of treatment options. Here, we aimed to identify the potential biomarkers to TNBC diagnosis and prognosis. Material/Methods Three independent data sets (GSE45827, GSE38959, GSE65194) were downloaded from the Gene Expression Omnibus (GEO). The R software packages were used to integrate the gene profiles and identify differentially expressed genes (DEGs). A variety of bioinformatics tools were used to explore the hub genes, including the DAVID database, STRING database and Cytoscape software. Reverse transcription quantitative PCR (RT-qPCR) was used to verify the hub genes in 14 pairs of TNBC paired tissues. Results In this study, we screened out 161 DEGs between 222 non-TNBC and 126 TNBC samples, of which 105 genes were up-regulated and 56 were down-regulated. These DEGs were enriched for 27 GO terms and two pathways. GO analysis enriched mainly in “cell division”, “chromosome, centromeric region” and “microtubule motor activity”. KEGG pathway analysis enriched mostly in “Cell cycle” and “Oocyte meiosis”. PPI network was constructed and then 10 top hub genes were screened. According to the analysis results of the Kaplan-Meier survival curve, the expression levels of only NUF2, FAM83D and CENPH were associated with the recurrence-free survival in TNBC samples (P < 0.05). RT-qPCR confirmed that the expression levels of NUF2 and FAM83D in TNBC tissues were indeed up-regulated significantly. Conclusions The comprehensive analysis showed that NUF2 and FAM83D could be used as potential biomarkers for diagnosis and prognosis of TNBC.
bibliographic citation: Zhai et al. (2020) Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer. PeerJ 8:e9975 https://doi.org/10.7717/peerj.9975
date submitted: 2020-06-12
date accepted: 2020-08-26
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhai
  given name: Xiuming
author list: Agent
  family name: Yang
  given name: Zhaowei
author list: Agent
  family name: Liu
  given name: Xiji
author list: Agent
  family name: Dong
  given name: Zihe
author list: Agent
  family name: Zhou
  given name: Dandan
doi: 10.7717/peerj.9975
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Zhai et al.
attribution name: Zhai et al.

Confidence intervals for the common coefficient of variation of rainfall in Thailand
type: item
type: AcademicArticle
description: The log-normal distribution is often used to analyze environmental data like daily rainfall amounts. The rainfall is of interest in Thailand because high variable climates can lead to periodic water stress and scarcity. The mean, standard deviation or coefficient of variation of the rainfall in the area is usually estimated. The climate moisture index is the ratio of plant water demand to precipitation. The climate moisture index should use the coefficient of variation instead of the standard deviation for comparison between areas with widely different means. The larger coefficient of variation indicates greater dispersion, whereas the lower coefficient of variation indicates the lower risk. The common coefficient of variation, is the weighted coefficients of variation based on k areas, presents the average daily rainfall. Therefore, the common coefficient of variation is used to describe overall water problems of k areas. In this paper, we propose four novel approaches for the confidence interval estimation of the common coefficient of variation of log-normal distributions based on the fiducial generalized confidence interval (FGCI), method of variance estimates recovery (MOVER), computational, and Bayesian approaches. A Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths of the confidence intervals. In terms of coverage probability, the results show that the FGCI approach provided the best confidence interval estimates for most cases except for when the sample case was equal to six populations (k = 6) and the sample sizes were small (nI < 50), for which the MOVER confidence interval estimates were the best. The efficacies of the proposed approaches are illustrated with example using real-life daily rainfall datasets from regions of Thailand.
format: application/pdf
format: text/html
creator: Warisa Thangjai
creator: Sa-Aat Niwitpong
creator: Suparat Niwitpong
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.10004
publisher: PeerJ Inc.
rights: © 2020 Thangjai et al.
abstract: The log-normal distribution is often used to analyze environmental data like daily rainfall amounts. The rainfall is of interest in Thailand because high variable climates can lead to periodic water stress and scarcity. The mean, standard deviation or coefficient of variation of the rainfall in the area is usually estimated. The climate moisture index is the ratio of plant water demand to precipitation. The climate moisture index should use the coefficient of variation instead of the standard deviation for comparison between areas with widely different means. The larger coefficient of variation indicates greater dispersion, whereas the lower coefficient of variation indicates the lower risk. The common coefficient of variation, is the weighted coefficients of variation based on k areas, presents the average daily rainfall. Therefore, the common coefficient of variation is used to describe overall water problems of k areas. In this paper, we propose four novel approaches for the confidence interval estimation of the common coefficient of variation of log-normal distributions based on the fiducial generalized confidence interval (FGCI), method of variance estimates recovery (MOVER), computational, and Bayesian approaches. A Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths of the confidence intervals. In terms of coverage probability, the results show that the FGCI approach provided the best confidence interval estimates for most cases except for when the sample case was equal to six populations (k = 6) and the sample sizes were small (nI < 50), for which the MOVER confidence interval estimates were the best. The efficacies of the proposed approaches are illustrated with example using real-life daily rainfall datasets from regions of Thailand.
bibliographic citation: Thangjai et al. (2020) Confidence intervals for the common coefficient of variation of rainfall in Thailand. PeerJ 8:e10004 https://doi.org/10.7717/peerj.10004
date submitted: 2020-02-17
date accepted: 2020-08-30
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thangjai
  given name: Warisa
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
author list: Agent
  family name: Niwitpong
  given name: Suparat
doi: 10.7717/peerj.10004
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Thangjai et al.
attribution name: Thangjai et al.

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