PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Resumption of donor-origin spermatogenesis in senescent goldfish Carassius auratus (Linnaeus, 1758) following spermatogonial cell therapy
items: The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research
items: Effects of Sr2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation
items: Steroid hormones and chondrichthyan reproduction: physiological functions, scientific research, and implications for conservation
items: The evolution of feeding within Euchelicerata: data from the fossil groups Eurypterida and Trigonotarbida illustrate possible evolutionary pathways
items: Vegetation influences soil properties along riparian zones of the Beijiang River in Southern China
items: Evaluation of salt tolerance in Eruca sativa accessions based on morpho-physiological traits
items: Prevalence of and risk factors associated with latent tuberculosis infection in a Latin American region
items: Perils and pitfalls of mixed-effects regression models in biology
items: Nectar robbing in the trainbearers (Lesbia, Trochilidae)

Resumption of donor-origin spermatogenesis in senescent goldfish Carassius auratus (Linnaeus, 1758) following spermatogonial cell therapy
type: item
type: AcademicArticle
description: Stem cell research has come into prominence because of its applications in assisted reproductive technology and the treatment of deadly diseases. In teleost fishes, spermatogonial stem cells have been effectively used to produce surrogate gametes and progeny through germ cell transplantation technique. The present study is the first report of an innovative application of stem cell therapy in fish species for revitalising the reproductive competence of senescent individuals. Senescent male goldfish, Carassius auratus, approximately 10 years of age were procured from a fish-breeding farm and were reared locally in the lab for an additional two years. The senescence of the individuals was then evaluated and confirmed using histological analysis, gonadal index assessment, and germ-cell specific vasa gene expression. Analyses revealed absence of spermatogonial cells and other germ cells in the testes of the senescent fish (n = 5). Spermatogonial cells from sexually immature C. auratus male donor were isolated using discontinuous percoll gradients, labelled with the fluorescent dye PKH-26, and transplanted into the gonads of senescent C. auratus males through urogenital papilla. Six months after the transplant, spermatozoa were collected through applying gentle manual pressure on the abdomen and were observed under a microscope. All C. auratus males with the transplant had produced spermatozoa from the transplanted cells. This was confirmed by the retention of PKH-26 in the spermatozoa and diagnostic SSR locus. Gravid C. auratus females were artificially inseminated with the spermatozoa of those senescent males and natural spawning was allowed. As a result viable progeny were produced. These observation suggests that the reproductive competence of senescent male fishes can be revitalised through spermatogonial stem cell therapy to produce functional gametes.
format: application/pdf
format: text/html
creator: Sullip K. Majhi
creator: Mog Chowdhury
creator: Santosh Kumar
creator: Rajeev K. Singh
creator: Vindhya Mohindra
creator: Kuldeep K. Lal
subject: Aquaculture, Fisheries and Fish Science
subject: Biotechnology
subject: Developmental Biology
description: doi:10.7717/peerj.9116
publisher: PeerJ Inc.
rights: © 2020 Majhi et al.
abstract: Stem cell research has come into prominence because of its applications in assisted reproductive technology and the treatment of deadly diseases. In teleost fishes, spermatogonial stem cells have been effectively used to produce surrogate gametes and progeny through germ cell transplantation technique. The present study is the first report of an innovative application of stem cell therapy in fish species for revitalising the reproductive competence of senescent individuals. Senescent male goldfish, Carassius auratus, approximately 10 years of age were procured from a fish-breeding farm and were reared locally in the lab for an additional two years. The senescence of the individuals was then evaluated and confirmed using histological analysis, gonadal index assessment, and germ-cell specific vasa gene expression. Analyses revealed absence of spermatogonial cells and other germ cells in the testes of the senescent fish (n = 5). Spermatogonial cells from sexually immature C. auratus male donor were isolated using discontinuous percoll gradients, labelled with the fluorescent dye PKH-26, and transplanted into the gonads of senescent C. auratus males through urogenital papilla. Six months after the transplant, spermatozoa were collected through applying gentle manual pressure on the abdomen and were observed under a microscope. All C. auratus males with the transplant had produced spermatozoa from the transplanted cells. This was confirmed by the retention of PKH-26 in the spermatozoa and diagnostic SSR locus. Gravid C. auratus females were artificially inseminated with the spermatozoa of those senescent males and natural spawning was allowed. As a result viable progeny were produced. These observation suggests that the reproductive competence of senescent male fishes can be revitalised through spermatogonial stem cell therapy to produce functional gametes.
bibliographic citation: Majhi et al. (2020) Resumption of donor-origin spermatogenesis in senescent goldfish Carassius auratus (Linnaeus, 1758) following spermatogonial cell therapy. PeerJ 8:e9116 https://doi.org/10.7717/peerj.9116
date submitted: 2019-11-11
date accepted: 2020-04-12
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Majhi
  given name: Sullip K.
author list: Agent
  family name: Chowdhury
  given name: Mog
author list: Agent
  family name: Kumar
  given name: Santosh
author list: Agent
  family name: Singh
  given name: Rajeev K.
author list: Agent
  family name: Mohindra
  given name: Vindhya
author list: Agent
  family name: Lal
  given name: Kuldeep K.
doi: 10.7717/peerj.9116
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: ©2020 Majhi et al.
attribution name: Majhi et al.

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research
type: item
type: AcademicArticle
description: Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.
format: application/pdf
format: text/html
creator: Benjamin Bolduc
creator: Suzanne B. Hodgkins
creator: Ruth K. Varner
creator: Patrick M. Crill
creator: Carmody K. McCalley
creator: Jeffrey P. Chanton
creator: Gene W. Tyson
creator: William J. Riley
creator: Michael Palace
creator: Melissa B. Duhaime
creator: Moira A. Hough
creator: Scott R. Saleska
creator: Matthew B. Sullivan
creator: Virginia I. Rich
subject: Bioinformatics
subject: Ecosystem Science
subject: Data Science
description: doi:10.7717/peerj.9467
publisher: PeerJ Inc.
rights: © 2020 Bolduc et al.
abstract: Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.
bibliographic citation: Bolduc et al. (2020) The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ 8:e9467 https://doi.org/10.7717/peerj.9467
date submitted: 2019-12-03
date accepted: 2020-06-11
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bolduc
  given name: Benjamin
author list: Agent
  family name: Hodgkins
  given name: Suzanne B.
author list: Agent
  family name: Varner
  given name: Ruth K.
author list: Agent
  family name: Crill
  given name: Patrick M.
author list: Agent
  family name: McCalley
  given name: Carmody K.
author list: Agent
  family name: Chanton
  given name: Jeffrey P.
author list: Agent
  family name: Tyson
  given name: Gene W.
author list: Agent
  family name: Riley
  given name: William J.
author list: Agent
  family name: Palace
  given name: Michael
author list: Agent
  family name: Duhaime
  given name: Melissa B.
author list: Agent
  family name: Hough
  given name: Moira A.
author list: Agent
  family name: Saleska
  given name: Scott R.
author list: Agent
  family name: Sullivan
  given name: Matthew B.
author list: Agent
  family name: Rich
  given name: Virginia I.
doi: 10.7717/peerj.9467
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: © 2020 Bolduc et al.
attribution name: Bolduc et al.

Effects of Sr2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation
type: item
type: AcademicArticle
description: Bacterial gene transformation used with Escherichia coli as a desired microorganism is one of the important techniques in genetic engineering. In this study, the preparation of E. coli DH5α competent cells treated with SrCl2 and transformation by heat-shock with pUC19 plasmid was optimized by Response Surface Methodology (RSM). Other five E. coli strains including BL21 (DE3), HB-101, JM109, TOP10 and TG1, three different sizes plasmids (pUC19, pET32a, pPIC9k) were used to verify the protocol, respectively. The transformation mechanism was explored by scanning electron microscope combined with energy dispersive spectrometer (SEM-EDS), atomic absorption spectroscopy (AAS) and Fourier-transform infrared spectroscopy (FT-IR). An equation of regression model was obtained, and the ideal parameters were Sr2 + ions of 90 mM, heat-shock time of 90 s and 9 ng of plasmid. Under this conditions, the transformation efficiency could almost reach to 106 CFU/µg DNA. A small change of the cell surface structure has been observed between E. coli DH5α strain and competent cells by abovementioned spectrum technologies, which implied that a strict regulation mechanism involved in the formation of competent cells and transformation of plasmids. An equation of regression model for the competent cells preparation and plasmid transformation could be applied in gene cloning technology
format: application/pdf
format: text/html
creator: Yonggang Wang
creator: Xinjian Wang
creator: Linmiao Yu
creator: Yuan Tian
creator: Shaowei Li
creator: Feifan Leng
creator: Jianzhong Ma
creator: Jixiang Chen
subject: Biochemistry
subject: Bioengineering
subject: Microbiology
description: doi:10.7717/peerj.9480
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Bacterial gene transformation used with Escherichia coli as a desired microorganism is one of the important techniques in genetic engineering. In this study, the preparation of E. coli DH5α competent cells treated with SrCl2 and transformation by heat-shock with pUC19 plasmid was optimized by Response Surface Methodology (RSM). Other five E. coli strains including BL21 (DE3), HB-101, JM109, TOP10 and TG1, three different sizes plasmids (pUC19, pET32a, pPIC9k) were used to verify the protocol, respectively. The transformation mechanism was explored by scanning electron microscope combined with energy dispersive spectrometer (SEM-EDS), atomic absorption spectroscopy (AAS) and Fourier-transform infrared spectroscopy (FT-IR). An equation of regression model was obtained, and the ideal parameters were Sr2 + ions of 90 mM, heat-shock time of 90 s and 9 ng of plasmid. Under this conditions, the transformation efficiency could almost reach to 106 CFU/µg DNA. A small change of the cell surface structure has been observed between E. coli DH5α strain and competent cells by abovementioned spectrum technologies, which implied that a strict regulation mechanism involved in the formation of competent cells and transformation of plasmids. An equation of regression model for the competent cells preparation and plasmid transformation could be applied in gene cloning technology
bibliographic citation: Wang et al. (2020) Effects of Sr2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation. PeerJ 8:e9480 https://doi.org/10.7717/peerj.9480
date submitted: 2019-10-29
date accepted: 2020-06-14
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yonggang
author list: Agent
  family name: Wang
  given name: Xinjian
author list: Agent
  family name: Yu
  given name: Linmiao
author list: Agent
  family name: Tian
  given name: Yuan
author list: Agent
  family name: Li
  given name: Shaowei
author list: Agent
  family name: Leng
  given name: Feifan
author list: Agent
  family name: Ma
  given name: Jianzhong
author list: Agent
  family name: Chen
  given name: Jixiang
doi: 10.7717/peerj.9480
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Steroid hormones and chondrichthyan reproduction: physiological functions, scientific research, and implications for conservation
type: item
type: AcademicArticle
description: The study of the reproductive aspects of chondrichthyans through the analysis of steroid hormones has been carried out for more than five decades in several species around the world. This scientific knowledge constitutes the basis of the reproductive endocrinology of chondrichthyans, which has provided information regarding their sexual maturation, gametogenesis, mating seasons, gestation periods, and parturition. The present review summarises the existing literature on steroid hormones in chondrichthyan reproduction and identifies future research directions addressing critical knowledge gaps in the reproductive physiology of this taxon. A total of 59 peer reviewed scientific papers from 1963 to 2020 were reviewed and the following parameters analysed: species, steroid hormones, biological matrix, field sampling (year, location), and methodology (assays, sample size, precision, and recoveries). We provided a summary of the methods, biological matrices, and the functions of up to 19 hormones on the biology of 34 species of chondrichthyans that have been analysed to date. The majority of the studies used radioimmunoassay as the main methodology (76.3%; n = 45/49); while the most frequent biological matrix used was plasma (69.5%; n = 41/49). A Kernel’s heat map was generated to present the scientific effort according to geographic location and evidenced a lack of research in high biodiversity areas for chondrichthyans worldwide. The implications of the study of steroid hormones for the conservation of chondrichthyans are discussed, as only 2.9% of the species of this group have been analysed and most of the scientific effort (93.2%; n = 55/59 papers) has focused on the analysis of less than six hormones.
format: application/pdf
format: text/html
creator: Edgar Eduardo Becerril-García
creator: Marcial Arellano-Martínez
creator: Daniela Bernot-Simon
creator: Edgar Mauricio Hoyos-Padilla
creator: Felipe Galván-Magaña
creator: Céline Godard-Codding
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.9686
publisher: PeerJ Inc.
rights: © 2020 Becerril-García et al.
abstract: The study of the reproductive aspects of chondrichthyans through the analysis of steroid hormones has been carried out for more than five decades in several species around the world. This scientific knowledge constitutes the basis of the reproductive endocrinology of chondrichthyans, which has provided information regarding their sexual maturation, gametogenesis, mating seasons, gestation periods, and parturition. The present review summarises the existing literature on steroid hormones in chondrichthyan reproduction and identifies future research directions addressing critical knowledge gaps in the reproductive physiology of this taxon. A total of 59 peer reviewed scientific papers from 1963 to 2020 were reviewed and the following parameters analysed: species, steroid hormones, biological matrix, field sampling (year, location), and methodology (assays, sample size, precision, and recoveries). We provided a summary of the methods, biological matrices, and the functions of up to 19 hormones on the biology of 34 species of chondrichthyans that have been analysed to date. The majority of the studies used radioimmunoassay as the main methodology (76.3%; n = 45/49); while the most frequent biological matrix used was plasma (69.5%; n = 41/49). A Kernel’s heat map was generated to present the scientific effort according to geographic location and evidenced a lack of research in high biodiversity areas for chondrichthyans worldwide. The implications of the study of steroid hormones for the conservation of chondrichthyans are discussed, as only 2.9% of the species of this group have been analysed and most of the scientific effort (93.2%; n = 55/59 papers) has focused on the analysis of less than six hormones.
bibliographic citation: Becerril-García et al. (2020) Steroid hormones and chondrichthyan reproduction: physiological functions, scientific research, and implications for conservation. PeerJ 8:e9686 https://doi.org/10.7717/peerj.9686
date submitted: 2020-04-21
date accepted: 2020-07-18
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Becerril-García
  given name: Edgar Eduardo
author list: Agent
  family name: Arellano-Martínez
  given name: Marcial
author list: Agent
  family name: Bernot-Simon
  given name: Daniela
author list: Agent
  family name: Hoyos-Padilla
  given name: Edgar Mauricio
author list: Agent
  family name: Galván-Magaña
  given name: Felipe
author list: Agent
  family name: Godard-Codding
  given name: Céline
doi: 10.7717/peerj.9686
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: © 2020 Becerril-García et al.
attribution name: Becerril-García et al.

The evolution of feeding within Euchelicerata: data from the fossil groups Eurypterida and Trigonotarbida illustrate possible evolutionary pathways
type: item
type: AcademicArticle
description: When the evolution of Euarthropoda is discussed, often the lineage of Chelicerata s. str. is assumed to be the more ‘primitive’ or ‘basal’ part of the tree, especially when compared to the other major lineage, Mandibulata. This claimed primitiveness is (at least partly) based on the assumption that different morphological structures are still in an ancestral state and did not evolve any further. One of these sets of structures is the feeding apparatus, which has been stated to be highly advanced in Mandibulata, but not ‘properly’ developed, or at least not to such a high degree, within Chelicerata s. str. In this study, I reinvestigate the feeding apparatus of different ingroups of Euchelicerata, with a focus on assumed ‘primitive’ groups such as Eurypterida and Trigonotarbida. The basis of this study is a large amount of material from different museum collections, with fossils with the entire feeding apparatuses being exceptionally well preserved. Based on high-resolution micro-photography and three-dimensional imaging, it is possible to resolve fine details of the feeding apparatuses. The results make clear that the feeding apparatuses of different ingroups of Euchelicerata are highly specialised and often possess morphological structures comparable to those of the feeding apparatuses of representatives of Mandibulata, apparently convergently evolved. Though the reconstruction of the evolution of the feeding apparatus within Euchelicerata is to a certain degree hampered by unclear phylogenetic relationships, there was clearly a shortening of the feeding apparatus from posterior (i.e. only the anterior appendages being involved in the feeding apparatus), probably linked to the colonisation of land in Arachnida.
format: application/pdf
format: text/html
creator: Carolin Haug
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.9696
publisher: PeerJ Inc.
rights: © 2020 Haug
abstract: When the evolution of Euarthropoda is discussed, often the lineage of Chelicerata s. str. is assumed to be the more ‘primitive’ or ‘basal’ part of the tree, especially when compared to the other major lineage, Mandibulata. This claimed primitiveness is (at least partly) based on the assumption that different morphological structures are still in an ancestral state and did not evolve any further. One of these sets of structures is the feeding apparatus, which has been stated to be highly advanced in Mandibulata, but not ‘properly’ developed, or at least not to such a high degree, within Chelicerata s. str. In this study, I reinvestigate the feeding apparatus of different ingroups of Euchelicerata, with a focus on assumed ‘primitive’ groups such as Eurypterida and Trigonotarbida. The basis of this study is a large amount of material from different museum collections, with fossils with the entire feeding apparatuses being exceptionally well preserved. Based on high-resolution micro-photography and three-dimensional imaging, it is possible to resolve fine details of the feeding apparatuses. The results make clear that the feeding apparatuses of different ingroups of Euchelicerata are highly specialised and often possess morphological structures comparable to those of the feeding apparatuses of representatives of Mandibulata, apparently convergently evolved. Though the reconstruction of the evolution of the feeding apparatus within Euchelicerata is to a certain degree hampered by unclear phylogenetic relationships, there was clearly a shortening of the feeding apparatus from posterior (i.e. only the anterior appendages being involved in the feeding apparatus), probably linked to the colonisation of land in Arachnida.
bibliographic citation: Haug (2020) The evolution of feeding within Euchelicerata: data from the fossil groups Eurypterida and Trigonotarbida illustrate possible evolutionary pathways. PeerJ 8:e9696 https://doi.org/10.7717/peerj.9696
date submitted: 2019-10-02
date accepted: 2020-07-20
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haug
  given name: Carolin
doi: 10.7717/peerj.9696
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: © 2020 Haug
attribution name: Haug

Vegetation influences soil properties along riparian zones of the Beijiang River in Southern China
type: item
type: AcademicArticle
description: Riparian soils and vegetation are important factors influencing the biodiversity and biogeochemical processes of river ecosystems. Riparian soils and vegetation form the foundation for multiple ecosystem services provided by river ecosystems. However, it remains poorly understood how riparian soils and vegetation interact with one another to maintain these services. In this study, we sampled four common types of riparian vegetation associated with the Beijiang River in South China. These included forestland, bamboo forest, mixed forest, and grassland ecosystems. Specifically, we analyzed the spatial distribution of riparian soils and their response to environmental factors (i.e., coverage and height of trees, shrubs and grass, distance to river, and altitude). Our results indicate that soil properties in riparian zones were affected significantly by vegetation type. In particular, clay content, soil organic carbon, and nitrate nitrogen content were significantly correlated with vegetation type. In contrast, changes in soil total nitrogen, total phosphorus, and available phosphorus content were not associated with vegetation type. Moreover, soil physical and chemical properties interacted with one an other, as well as with vegetation characteristics. This was indicated by the significant correlation observed between soil organic carbon, total nitrogen, total phosphorus, and soil texture, with structural characteristics of the four vegetation types. We also found that height and cover of trees and shrubs were significantly correlated with soil chemical properties. However, the effects of topographic variables such as altitude and distance to river were not significant. Results from this study can thus provide a basis for the ecological restoration and land management of degraded iparian zones.
format: application/pdf
format: text/html
creator: Qinghe Zhao
creator: Shengyan Ding
creator: Qian Liu
creator: Shuoqian Wang
creator: Yaru Jing
creator: Mengwen Lu
subject: Conservation Biology
subject: Ecology
subject: Soil Science
description: doi:10.7717/peerj.9699
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: Riparian soils and vegetation are important factors influencing the biodiversity and biogeochemical processes of river ecosystems. Riparian soils and vegetation form the foundation for multiple ecosystem services provided by river ecosystems. However, it remains poorly understood how riparian soils and vegetation interact with one another to maintain these services. In this study, we sampled four common types of riparian vegetation associated with the Beijiang River in South China. These included forestland, bamboo forest, mixed forest, and grassland ecosystems. Specifically, we analyzed the spatial distribution of riparian soils and their response to environmental factors (i.e., coverage and height of trees, shrubs and grass, distance to river, and altitude). Our results indicate that soil properties in riparian zones were affected significantly by vegetation type. In particular, clay content, soil organic carbon, and nitrate nitrogen content were significantly correlated with vegetation type. In contrast, changes in soil total nitrogen, total phosphorus, and available phosphorus content were not associated with vegetation type. Moreover, soil physical and chemical properties interacted with one an other, as well as with vegetation characteristics. This was indicated by the significant correlation observed between soil organic carbon, total nitrogen, total phosphorus, and soil texture, with structural characteristics of the four vegetation types. We also found that height and cover of trees and shrubs were significantly correlated with soil chemical properties. However, the effects of topographic variables such as altitude and distance to river were not significant. Results from this study can thus provide a basis for the ecological restoration and land management of degraded iparian zones.
bibliographic citation: Zhao et al. (2020) Vegetation influences soil properties along riparian zones of the Beijiang River in Southern China. PeerJ 8:e9699 https://doi.org/10.7717/peerj.9699
date submitted: 2019-12-16
date accepted: 2020-07-20
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Qinghe
author list: Agent
  family name: Ding
  given name: Shengyan
author list: Agent
  family name: Liu
  given name: Qian
author list: Agent
  family name: Wang
  given name: Shuoqian
author list: Agent
  family name: Jing
  given name: Yaru
author list: Agent
  family name: Lu
  given name: Mengwen
doi: 10.7717/peerj.9699
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Evaluation of salt tolerance in Eruca sativa accessions based on morpho-physiological traits
type: item
type: AcademicArticle
description: Background Salinity is one of the most lethal abiotic stresses which affect multiple aspects of plant physiology. Natural variations in plant germplasm are a great resource that could be exploited for improvement in salt tolerance. Eruca sativa (E. sativa) exhibits tolerance to abiotic stresses. However, thorough evaluation of its salt stress tolerance and screening for traits that could be reliably applied for salt tolerance needs to be studied. The current study was designed to characterize 25 E. sativa accessions, originating from diverse geographical regions of Pakistan, for the salt stress tolerance. Methods Salt stress (150 mM NaCl) was applied for 2 weeks to the plants at four leaf stage in hydroponics. Data of the following morpho-physiological traits were collected from control and treated plants of all the accessions: root length (RL), shoot length (SL), plant height (PH), leaf number (LN), leaf area (LA), fresh weight (FW), dry weight (DW), chlorophyl content (SPAD), electrolyte leakage (EL), relative water content (RWC), gas exchange parameters and mineral ion content. Salt tolerance was determined based on membership function value (MFV) of the tested traits. Results Compared with control, the salt-stressed group had significantly reduced mean SL, RL, PH, LN, LA, FW, DW and SPAD. NaCl treatment triggered a slight increase in EL in few accessions. Mean RWC of control and treated groups were not significantly different although few accessions exhibited variation in this trait. Salt stress caused a significant reduction in photosynthesis rate (PR), transpiration rate (TR) and stomatal conductance (SC) but intercellular CO2 (Ci) was not significantly different between control and treated groups. Compared with control, the salt-stressed plants accumulated significantly higher Na+, K+ and Ca2+ while significantly lower Mg2+. K+/Na+ ratio was significantly decreased in salt-stressed plants compared with control. Importantly, significant inter-accession variati…
format: application/pdf
format: text/html
creator: Sadia Afsar
creator: Gulnaz Bibi
creator: Raza Ahmad
creator: Muhammad Bilal
creator: Tatheer Alam Naqvi
creator: Ayesha Baig
creator: Mohammad Maroof Shah
creator: Bangquan Huang
creator: Jamshaid Hussain
subject: Agricultural Science
subject: Biodiversity
subject: Plant Science
subject: Biosphere Interactions
subject: Ecotoxicology
description: doi:10.7717/peerj.9749
publisher: PeerJ Inc.
rights: © 2020 Afsar et al.
abstract: Background Salinity is one of the most lethal abiotic stresses which affect multiple aspects of plant physiology. Natural variations in plant germplasm are a great resource that could be exploited for improvement in salt tolerance. Eruca sativa (E. sativa) exhibits tolerance to abiotic stresses. However, thorough evaluation of its salt stress tolerance and screening for traits that could be reliably applied for salt tolerance needs to be studied. The current study was designed to characterize 25 E. sativa accessions, originating from diverse geographical regions of Pakistan, for the salt stress tolerance. Methods Salt stress (150 mM NaCl) was applied for 2 weeks to the plants at four leaf stage in hydroponics. Data of the following morpho-physiological traits were collected from control and treated plants of all the accessions: root length (RL), shoot length (SL), plant height (PH), leaf number (LN), leaf area (LA), fresh weight (FW), dry weight (DW), chlorophyl content (SPAD), electrolyte leakage (EL), relative water content (RWC), gas exchange parameters and mineral ion content. Salt tolerance was determined based on membership function value (MFV) of the tested traits. Results Compared with control, the salt-stressed group had significantly reduced mean SL, RL, PH, LN, LA, FW, DW and SPAD. NaCl treatment triggered a slight increase in EL in few accessions. Mean RWC of control and treated groups were not significantly different although few accessions exhibited variation in this trait. Salt stress caused a significant reduction in photosynthesis rate (PR), transpiration rate (TR) and stomatal conductance (SC) but intercellular CO2 (Ci) was not significantly different between control and treated groups. Compared with control, the salt-stressed plants accumulated significantly higher Na+, K+ and Ca2+ while significantly lower Mg2+. K+/Na+ ratio was significantly decreased in salt-stressed plants compared with control. Importantly, significant inter-accession variati…
bibliographic citation: Afsar et al. (2020) Evaluation of salt tolerance in Eruca sativa accessions based on morpho-physiological traits. PeerJ 8:e9749 https://doi.org/10.7717/peerj.9749
date submitted: 2020-05-20
date accepted: 2020-07-27
issued: 2020-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Afsar
  given name: Sadia
author list: Agent
  family name: Bibi
  given name: Gulnaz
author list: Agent
  family name: Ahmad
  given name: Raza
author list: Agent
  family name: Bilal
  given name: Muhammad
author list: Agent
  family name: Naqvi
  given name: Tatheer Alam
author list: Agent
  family name: Baig
  given name: Ayesha
author list: Agent
  family name: Shah
  given name: Mohammad Maroof
author list: Agent
  family name: Huang
  given name: Bangquan
author list: Agent
  family name: Hussain
  given name: Jamshaid
doi: 10.7717/peerj.9749
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-13
copyright: © 2020 Afsar et al.
attribution name: Afsar et al.

Prevalence of and risk factors associated with latent tuberculosis infection in a Latin American region
type: item
type: AcademicArticle
description: Tuberculosis (TB) represents a health problem in Colombia, and its control is focused on the search for contacts and treatment of TB cases underscoring the role of latent tuberculosis infection (LTBI) as a reservoir of Mycobacterium tuberculosis. The burden of LTBI in Colombia is unknown. We aimed to estimate the prevalence of LTBI and identify the associated risk factors. In this cross-sectional study, we recruited participants from four health care centers in Cali, Colombia. The participants were eligible if they were aged between 14 and 70 years, and all participants answered a survey evaluating their medical history and sociodemographic and lifestyle factors. LTBI status was based on tuberculin skin test (TST) positivity using two thresholds: ≥10 mm (TST-10) and ≥15 mm (TST-15). The magnitude of the associations between independent factors and dependent outcomes (LTBI status and TST induration) were evaluated by logistic regression and generalized linear models, respectively. A total of 589 individuals were included with TST positivity rates of 25.3% (TST-10) and 13.2% (TST-15). Logistic regression showed that being between age 40 and 69 years (OR = 7.28, 95% CI [1.62–32.7]), being male (OR = 1.71, 95% CI [1.04–2.84]), being employed (OR = 1.56, 95% CI [1.02–2.38]), and having a low intake of alcohol (OR = 2.40, 95% CI [1.13–5.11]) were risk factors for TST positivity, while living in the north zone (OR = 0.32, 95% CI [0.18–0.55]), living in the suburb zone (OR = 0.28, 95% CI [0.15–0.52]) and having a secondary education (OR = 0.49 95% CI [0.29–0.83]) lowered the risk of TST positivity. The generalized linear model showed that the previous predictors, as well as a low body mass index, had an effect on TST reaction size. The LTBI prevalence found in the population was moderate, reflecting the continuous transmission of M. tuberculosis. Social factors seem to play a decisive role in the risk of LTBI. Employed males, who are over 40 years of age, are overweight, ha…
format: application/pdf
format: text/html
creator: Javier Andrés Bustamante-Rengifo
creator: Luz Ángela González-Salazar
creator: Nicole Osorio-Certuche
creator: Yesica Bejarano-Lozano
creator: José Rafael Tovar Cuevas
creator: Miryam Astudillo-Hernández
creator: Maria del Pilar Crespo-Ortiz
subject: Microbiology
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.9429
publisher: PeerJ Inc.
rights: © 2020 Bustamante-Rengifo et al.
abstract: Tuberculosis (TB) represents a health problem in Colombia, and its control is focused on the search for contacts and treatment of TB cases underscoring the role of latent tuberculosis infection (LTBI) as a reservoir of Mycobacterium tuberculosis. The burden of LTBI in Colombia is unknown. We aimed to estimate the prevalence of LTBI and identify the associated risk factors. In this cross-sectional study, we recruited participants from four health care centers in Cali, Colombia. The participants were eligible if they were aged between 14 and 70 years, and all participants answered a survey evaluating their medical history and sociodemographic and lifestyle factors. LTBI status was based on tuberculin skin test (TST) positivity using two thresholds: ≥10 mm (TST-10) and ≥15 mm (TST-15). The magnitude of the associations between independent factors and dependent outcomes (LTBI status and TST induration) were evaluated by logistic regression and generalized linear models, respectively. A total of 589 individuals were included with TST positivity rates of 25.3% (TST-10) and 13.2% (TST-15). Logistic regression showed that being between age 40 and 69 years (OR = 7.28, 95% CI [1.62–32.7]), being male (OR = 1.71, 95% CI [1.04–2.84]), being employed (OR = 1.56, 95% CI [1.02–2.38]), and having a low intake of alcohol (OR = 2.40, 95% CI [1.13–5.11]) were risk factors for TST positivity, while living in the north zone (OR = 0.32, 95% CI [0.18–0.55]), living in the suburb zone (OR = 0.28, 95% CI [0.15–0.52]) and having a secondary education (OR = 0.49 95% CI [0.29–0.83]) lowered the risk of TST positivity. The generalized linear model showed that the previous predictors, as well as a low body mass index, had an effect on TST reaction size. The LTBI prevalence found in the population was moderate, reflecting the continuous transmission of M. tuberculosis. Social factors seem to play a decisive role in the risk of LTBI. Employed males, who are over 40 years of age, are overweight, ha…
bibliographic citation: Bustamante-Rengifo et al. (2020) Prevalence of and risk factors associated with latent tuberculosis infection in a Latin American region. PeerJ 8:e9429 https://doi.org/10.7717/peerj.9429
date submitted: 2019-10-03
date accepted: 2020-06-06
issued: 2020-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bustamante-Rengifo
  given name: Javier Andrés
author list: Agent
  family name: González-Salazar
  given name: Luz Ángela
author list: Agent
  family name: Osorio-Certuche
  given name: Nicole
author list: Agent
  family name: Bejarano-Lozano
  given name: Yesica
author list: Agent
  family name: Tovar Cuevas
  given name: José Rafael
author list: Agent
  family name: Astudillo-Hernández
  given name: Miryam
author list: Agent
  family name: Crespo-Ortiz
  given name: Maria del Pilar
doi: 10.7717/peerj.9429
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-12
copyright: © 2020 Bustamante-Rengifo et al.
attribution name: Bustamante-Rengifo et al.

Perils and pitfalls of mixed-effects regression models in biology
type: item
type: AcademicArticle
description: Biological systems, at all scales of organisation from nucleic acids to ecosystems, are inherently complex and variable. Biologists therefore use statistical analyses to detect signal among this systemic noise. Statistical models infer trends, find functional relationships and detect differences that exist among groups or are caused by experimental manipulations. They also use statistical relationships to help predict uncertain futures. All branches of the biological sciences now embrace the possibilities of mixed-effects modelling and its flexible toolkit for partitioning noise and signal. The mixed-effects model is not, however, a panacea for poor experimental design, and should be used with caution when inferring or deducing the importance of both fixed and random effects. Here we describe a selection of the perils and pitfalls that are widespread in the biological literature, but can be avoided by careful reflection, modelling and model-checking. We focus on situations where incautious modelling risks exposure to these pitfalls and the drawing of incorrect conclusions. Our stance is that statements of significance, information content or credibility all have their place in biological research, as long as these statements are cautious and well-informed by checks on the validity of assumptions. Our intention is to reveal potential perils and pitfalls in mixed model estimation so that researchers can use these powerful approaches with greater awareness and confidence. Our examples are ecological, but translate easily to all branches of biology.
format: application/pdf
format: text/html
creator: Matthew J. Silk
creator: Xavier A. Harrison
creator: David J. Hodgson
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
subject: Statistics
description: doi:10.7717/peerj.9522
publisher: PeerJ Inc.
rights: © 2020 Silk et al.
abstract: Biological systems, at all scales of organisation from nucleic acids to ecosystems, are inherently complex and variable. Biologists therefore use statistical analyses to detect signal among this systemic noise. Statistical models infer trends, find functional relationships and detect differences that exist among groups or are caused by experimental manipulations. They also use statistical relationships to help predict uncertain futures. All branches of the biological sciences now embrace the possibilities of mixed-effects modelling and its flexible toolkit for partitioning noise and signal. The mixed-effects model is not, however, a panacea for poor experimental design, and should be used with caution when inferring or deducing the importance of both fixed and random effects. Here we describe a selection of the perils and pitfalls that are widespread in the biological literature, but can be avoided by careful reflection, modelling and model-checking. We focus on situations where incautious modelling risks exposure to these pitfalls and the drawing of incorrect conclusions. Our stance is that statements of significance, information content or credibility all have their place in biological research, as long as these statements are cautious and well-informed by checks on the validity of assumptions. Our intention is to reveal potential perils and pitfalls in mixed model estimation so that researchers can use these powerful approaches with greater awareness and confidence. Our examples are ecological, but translate easily to all branches of biology.
bibliographic citation: Silk et al. (2020) Perils and pitfalls of mixed-effects regression models in biology. PeerJ 8:e9522 https://doi.org/10.7717/peerj.9522
date submitted: 2020-04-01
date accepted: 2020-06-20
issued: 2020-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silk
  given name: Matthew J.
author list: Agent
  family name: Harrison
  given name: Xavier A.
author list: Agent
  family name: Hodgson
  given name: David J.
doi: 10.7717/peerj.9522
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-12
copyright: © 2020 Silk et al.
attribution name: Silk et al.

Nectar robbing in the trainbearers (Lesbia, Trochilidae)
type: item
type: AcademicArticle
description: Many flower visitors engage in floral larceny, a suite of so-called ’illegitimate’ visits in which foragers take nectar without providing pollination services. The data on prevalence of illegitimate visits among hummingbirds, as well as the total proportion of foraging and diet that such visits comprise is broadly lacking. Here, we report the occurrence of nectar larceny in the two currently recognized species of trainbearers and analyze the proportion of plant visits categorized by mode of interaction as: robbing, theft, and/or pollination. We augment our original field observations using a trove of data from citizen science databases. Although it is difficult to distinguish primary vs. secondary robbing and theft vs. pollination, we conservatively estimate that ca. 40% of the recorded nectar foraging visits involve nectar robbing. Males appear to engage in robbing marginally more than females, but further studies are necessary to confidently examine the multi-way interactions among sex, species, mode of visitation, and other factors. Our results also indicate that the suggested relationship between serrations on bill tomia and traits such as nectar robbing or territorial defense may be complicated. We discuss the significance of these findings in the context of recent developments in study of nectar foraging, larceny, and pollination from both avian and plant perspectives.
format: application/pdf
format: text/html
creator: Boris Igić
creator: Ivory Nguyen
creator: Phillip B. Fenberg
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.9561
publisher: PeerJ Inc.
rights: © 2020 Igić et al.
abstract: Many flower visitors engage in floral larceny, a suite of so-called ’illegitimate’ visits in which foragers take nectar without providing pollination services. The data on prevalence of illegitimate visits among hummingbirds, as well as the total proportion of foraging and diet that such visits comprise is broadly lacking. Here, we report the occurrence of nectar larceny in the two currently recognized species of trainbearers and analyze the proportion of plant visits categorized by mode of interaction as: robbing, theft, and/or pollination. We augment our original field observations using a trove of data from citizen science databases. Although it is difficult to distinguish primary vs. secondary robbing and theft vs. pollination, we conservatively estimate that ca. 40% of the recorded nectar foraging visits involve nectar robbing. Males appear to engage in robbing marginally more than females, but further studies are necessary to confidently examine the multi-way interactions among sex, species, mode of visitation, and other factors. Our results also indicate that the suggested relationship between serrations on bill tomia and traits such as nectar robbing or territorial defense may be complicated. We discuss the significance of these findings in the context of recent developments in study of nectar foraging, larceny, and pollination from both avian and plant perspectives.
bibliographic citation: Igić et al. (2020) Nectar robbing in the trainbearers (Lesbia, Trochilidae). PeerJ 8:e9561 https://doi.org/10.7717/peerj.9561
date submitted: 2020-03-03
date accepted: 2020-06-25
issued: 2020-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Igić
  given name: Boris
author list: Agent
  family name: Nguyen
  given name: Ivory
author list: Agent
  family name: Fenberg
  given name: Phillip B.
doi: 10.7717/peerj.9561
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-12
copyright: © 2020 Igić et al.
attribution name: Igić et al.

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