PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Temperature alters the shape of predator–prey cycles through effects on underlying mechanisms
items: The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods
items: Alveolar soft-part sarcoma (ASPS) resembles a mesenchymal stromal progenitor: evidence from meta-analysis of transcriptomic data
items: Bird-window collisions: different fall and winter risk and protective factors
items: The common personal behavior and preventive measures among 42 uninfected travelers from the Hubei province, China during COVID-19 outbreak: a cross-sectional survey in Macao SAR, China
items: Shape of attachment structures in parasitic isopodan crustaceans: the influence of attachment site and ontogeny
items: Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean
items: Identification of hydatidosis-related modules and key regulatory genes
items: How caged salmon respond to waves depends on time of day and currents
items: Parents know best: transgenerational predator recognition through parental effects

Temperature alters the shape of predator–prey cycles through effects on underlying mechanisms
type: item
type: AcademicArticle
description: Background Predicting the effects of climate warming on the dynamics of ecological systems requires understanding how temperature influences birth rates, death rates and the strength of species interactions. The temperature dependance of these processes—which are the underlying mechanisms of ecological dynamics—is often thought to be exponential or unimodal, generally supported by short-term experiments. However, ecological dynamics unfold over many generations. Our goal was to empirically document shifts in predator–prey cycles over the full range of temperatures that can possibly support a predator–prey system and then to uncover the effect of temperature on the underlying mechanisms driving those changes. Methods We measured the population dynamics of the Didinium-Paramecium predator–prey system across a wide range of temperatures to reveal systematic changes in the dynamics of the system. We then used ordinary differential equation fitting to estimate parameters of a model describing the dynamics, and used these estimates to assess the long-term temperature dependance of all the underlying mechanisms. Results We found that predator–prey cycles shrank in state space from colder to hotter temperatures and that both cycle period and amplitude varied with temperature. Model parameters showed mostly unimodal responses to temperature, with one parameter (predator mortality) increasing monotonically with temperature and one parameter (predator conversion efficiency) invariant with temperature. Our results indicate that temperature can have profound, systematic effects on ecological dynamics, and these can arise through diverse and simultaneous changes in multiple underlying mechanisms. Predicting the effects of temperature on ecological dynamics may require additional investigation into how the underlying drivers of population dynamics respond to temperature beyond a short-term, acute response.
format: application/pdf
format: text/html
creator: John P. DeLong
creator: Shelby Lyon
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.9377
publisher: PeerJ Inc.
rights: © 2020 DeLong and Lyon
abstract: Background Predicting the effects of climate warming on the dynamics of ecological systems requires understanding how temperature influences birth rates, death rates and the strength of species interactions. The temperature dependance of these processes—which are the underlying mechanisms of ecological dynamics—is often thought to be exponential or unimodal, generally supported by short-term experiments. However, ecological dynamics unfold over many generations. Our goal was to empirically document shifts in predator–prey cycles over the full range of temperatures that can possibly support a predator–prey system and then to uncover the effect of temperature on the underlying mechanisms driving those changes. Methods We measured the population dynamics of the Didinium-Paramecium predator–prey system across a wide range of temperatures to reveal systematic changes in the dynamics of the system. We then used ordinary differential equation fitting to estimate parameters of a model describing the dynamics, and used these estimates to assess the long-term temperature dependance of all the underlying mechanisms. Results We found that predator–prey cycles shrank in state space from colder to hotter temperatures and that both cycle period and amplitude varied with temperature. Model parameters showed mostly unimodal responses to temperature, with one parameter (predator mortality) increasing monotonically with temperature and one parameter (predator conversion efficiency) invariant with temperature. Our results indicate that temperature can have profound, systematic effects on ecological dynamics, and these can arise through diverse and simultaneous changes in multiple underlying mechanisms. Predicting the effects of temperature on ecological dynamics may require additional investigation into how the underlying drivers of population dynamics respond to temperature beyond a short-term, acute response.
bibliographic citation: DeLong et al. (2020) Temperature alters the shape of predator–prey cycles through effects on underlying mechanisms. PeerJ 8:e9377 https://doi.org/10.7717/peerj.9377
date submitted: 2020-01-15
date accepted: 2020-05-27
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeLong
  given name: John P.
author list: Agent
  family name: Lyon
  given name: Shelby
doi: 10.7717/peerj.9377
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: © 2020 DeLong and Lyon
attribution name: DeLong and Lyon

The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods
type: item
type: AcademicArticle
description: Color is an essential clue for intra- and interspecies communication, playing a role in selection and speciation. Coloration can be based on nanostructures and pigments; carotenoids and carotenoproteins are among the most widespread pigments in animals. Over 350 species and subspecies of amphipods (Crustacea: Amphipoda) endemic to Lake Baikal exhibit an impressive variability of colors and coloration patterns, including intraspecific color morphs. However, the mechanisms forming this diversity are underexplored, as while the carotenoid composition of several transparent, green, and red species was investigated, there have been no reports on the corresponding carotenoid-binding proteins. In this work, we analyze the coloration of two brightly colored Baikal amphipods characterized by intraspecific color variability, Eulimnogammarus cyaneus and E. vittatus. We showed that the color of either species is defined by the level of putative carotenoid-binding proteins similar to the pheromone/odorant-binding protein family, as the concentration of these putative crustacyanin analogs was higher in blue or teal-colored animals than in the orange- or yellow-colored ones. At the same time, the color did not depend on the total carotenoid content, as it was similar between animals of contrasting color morphs. By exploring the diversity of these sequences within a larger phylogeny of invertebrate crustacyanins, we show that amphipods lack orthologs of the well-studied crustacyanins A and C, even though they possess some crustacyanin-like sequences. The analysis of expression levels in E. cyaneus showed that the transcripts encoding crustacyanin analogs had much higher expression than the crustacyanin-like sequences, suggesting that the former indeed contribute to the color of these brightly colored animals. The crustacyanin analogs seem to act in a similar way to the well-studied crustacyanins in body color formation, but the details of their action are still to be revealed.
format: application/pdf
format: text/html
creator: Polina Drozdova
creator: Alexandra Saranchina
creator: Mariya Morgunova
creator: Alena Kizenko
creator: Yulia Lubyaga
creator: Boris Baduev
creator: Maxim Timofeyev
subject: Biochemistry
subject: Evolutionary Studies
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9387
publisher: PeerJ Inc.
rights: © 2020 Drozdova et al.
abstract: Color is an essential clue for intra- and interspecies communication, playing a role in selection and speciation. Coloration can be based on nanostructures and pigments; carotenoids and carotenoproteins are among the most widespread pigments in animals. Over 350 species and subspecies of amphipods (Crustacea: Amphipoda) endemic to Lake Baikal exhibit an impressive variability of colors and coloration patterns, including intraspecific color morphs. However, the mechanisms forming this diversity are underexplored, as while the carotenoid composition of several transparent, green, and red species was investigated, there have been no reports on the corresponding carotenoid-binding proteins. In this work, we analyze the coloration of two brightly colored Baikal amphipods characterized by intraspecific color variability, Eulimnogammarus cyaneus and E. vittatus. We showed that the color of either species is defined by the level of putative carotenoid-binding proteins similar to the pheromone/odorant-binding protein family, as the concentration of these putative crustacyanin analogs was higher in blue or teal-colored animals than in the orange- or yellow-colored ones. At the same time, the color did not depend on the total carotenoid content, as it was similar between animals of contrasting color morphs. By exploring the diversity of these sequences within a larger phylogeny of invertebrate crustacyanins, we show that amphipods lack orthologs of the well-studied crustacyanins A and C, even though they possess some crustacyanin-like sequences. The analysis of expression levels in E. cyaneus showed that the transcripts encoding crustacyanin analogs had much higher expression than the crustacyanin-like sequences, suggesting that the former indeed contribute to the color of these brightly colored animals. The crustacyanin analogs seem to act in a similar way to the well-studied crustacyanins in body color formation, but the details of their action are still to be revealed.
bibliographic citation: Drozdova et al. (2020) The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods. PeerJ 8:e9387 https://doi.org/10.7717/peerj.9387
date submitted: 2020-01-15
date accepted: 2020-05-28
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Drozdova
  given name: Polina
author list: Agent
  family name: Saranchina
  given name: Alexandra
author list: Agent
  family name: Morgunova
  given name: Mariya
author list: Agent
  family name: Kizenko
  given name: Alena
author list: Agent
  family name: Lubyaga
  given name: Yulia
author list: Agent
  family name: Baduev
  given name: Boris
author list: Agent
  family name: Timofeyev
  given name: Maxim
doi: 10.7717/peerj.9387
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Drozdova et al.
attribution name: Drozdova et al.

Alveolar soft-part sarcoma (ASPS) resembles a mesenchymal stromal progenitor: evidence from meta-analysis of transcriptomic data
type: item
type: AcademicArticle
description: Alveolar soft-part sarcoma (ASPS) is an extremely rare malignancy characterized by the unbalanced translocation der(17)t(X;17)(p11;q25). This translocation generates a fusion protein, ASPL-TFE3, that drives pathogenesis through aberrant transcriptional activity. Although considerable progress has been made in identifying ASPS therapeutic vulnerabilities (e.g., MET inhibitors), basic research efforts are hampered by the lack of appropriate in vitro reagents with which to study the disease. In this report, previously unmined microarray data for the ASPS cell line, ASPS-1, was analyzed relative to the NCI sarcoma cell line panel. These data were combined with meta-analysis of pre-existing ASPS patient microarray and RNA-seq data to derive a platform-independent ASPS transcriptome. Results demonstrated that ASPS-1, in the context of the NCI sarcoma cell panel, had some similarities to normal mesenchymal cells and connective tissue sarcomas. The cell line was characterized by high relative expression of transcripts such as CRYAB, MT1G, GCSAML, and SV2B. Notably, ASPS-1 lacked mRNA expression of myogenesis-related factors MYF5, MYF6, MYOD1, MYOG, PAX3, and PAX7. Furthermore, ASPS-1 had a predicted mRNA surfaceome resembling an undifferentiated mesenchymal stromal cell through expression of GPNMB, CD9 (TSPAN29), CD26 (DPP4), CD49C (ITGA3), CD54 (ICAM1), CD63 (TSPAN30), CD68 (SCARD1), CD130 (IL6ST), CD146 (MCAM), CD147 (BSG), CD151 (SFA-1), CD166 (ALCAM), CD222 (IGF2R), CD230 (PRP), CD236 (GPC), CD243 (ABCB1), and CD325 (CDHN). Subsequent re-analysis of ASPS patient data generated a consensus expression profile with considerable overlap between studies. In common with ASPS-1, elevated expression was noted for CTSK, DPP4, GPNMB, INHBE, LOXL4, PSG9, SLC20A1, STS, SULT1C2, SV2B, and UPP1. Transcripts over-expressed only in ASPS patient samples included ABCB5, CYP17A1, HIF1A, MDK, P4HB, PRL, and PSAP. These observations are consistent with that expected for a mesenchymal progen…
format: application/pdf
format: text/html
creator: Luke H. Stockwin
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.9394
publisher: PeerJ Inc.
rights: © 2020 Stockwin
abstract: Alveolar soft-part sarcoma (ASPS) is an extremely rare malignancy characterized by the unbalanced translocation der(17)t(X;17)(p11;q25). This translocation generates a fusion protein, ASPL-TFE3, that drives pathogenesis through aberrant transcriptional activity. Although considerable progress has been made in identifying ASPS therapeutic vulnerabilities (e.g., MET inhibitors), basic research efforts are hampered by the lack of appropriate in vitro reagents with which to study the disease. In this report, previously unmined microarray data for the ASPS cell line, ASPS-1, was analyzed relative to the NCI sarcoma cell line panel. These data were combined with meta-analysis of pre-existing ASPS patient microarray and RNA-seq data to derive a platform-independent ASPS transcriptome. Results demonstrated that ASPS-1, in the context of the NCI sarcoma cell panel, had some similarities to normal mesenchymal cells and connective tissue sarcomas. The cell line was characterized by high relative expression of transcripts such as CRYAB, MT1G, GCSAML, and SV2B. Notably, ASPS-1 lacked mRNA expression of myogenesis-related factors MYF5, MYF6, MYOD1, MYOG, PAX3, and PAX7. Furthermore, ASPS-1 had a predicted mRNA surfaceome resembling an undifferentiated mesenchymal stromal cell through expression of GPNMB, CD9 (TSPAN29), CD26 (DPP4), CD49C (ITGA3), CD54 (ICAM1), CD63 (TSPAN30), CD68 (SCARD1), CD130 (IL6ST), CD146 (MCAM), CD147 (BSG), CD151 (SFA-1), CD166 (ALCAM), CD222 (IGF2R), CD230 (PRP), CD236 (GPC), CD243 (ABCB1), and CD325 (CDHN). Subsequent re-analysis of ASPS patient data generated a consensus expression profile with considerable overlap between studies. In common with ASPS-1, elevated expression was noted for CTSK, DPP4, GPNMB, INHBE, LOXL4, PSG9, SLC20A1, STS, SULT1C2, SV2B, and UPP1. Transcripts over-expressed only in ASPS patient samples included ABCB5, CYP17A1, HIF1A, MDK, P4HB, PRL, and PSAP. These observations are consistent with that expected for a mesenchymal progen…
bibliographic citation: Stockwin (2020) Alveolar soft-part sarcoma (ASPS) resembles a mesenchymal stromal progenitor: evidence from meta-analysis of transcriptomic data. PeerJ 8:e9394 https://doi.org/10.7717/peerj.9394
date submitted: 2020-04-16
date accepted: 2020-05-29
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stockwin
  given name: Luke H.
doi: 10.7717/peerj.9394
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Stockwin
attribution name: Stockwin

Bird-window collisions: different fall and winter risk and protective factors
type: item
type: AcademicArticle
description: Background To reduce bird fatalities from millions of window collisions each year in North America, it is important to understand how design and landscape elements relate to collision risk. The current study extends prior research that found that buildings near ornamental pear trees (Prunus calleryana) and buildings with mirrored windows significantly increased odds of collisions among eight buildings on the University of Utah campus in winter. The previous study found bird-friendly glass was not related to collision risk, although only one fatality occurred at two buildings with ORNILUX® ultraviolet (UV) or fritted windows. We reasoned that extending data collection to include fall might provide a better test of efficacy. We tested the following three hypotheses: (1) Buildings with mirrored windows would experience more collisions, replicating the original study; (2) the addition of fall migration data would reveal fewer collisions at the buildings with bird-friendly windows; (3) the danger of pear tree proximity would be heightened in winter, when fruit is ripe enough to appeal to frugivores, especially the Cedar Waxwings (Bombycilla cedrorum) that frequent these trees. Methods Trained observers monitored buildings three times per week in Fall (September 12 to October 27, 2019) and Winter (October 29, 2019 to January 24, 2020). Collisions were photographed and documented in the iNaturalist University of Utah Bird Window Collision Project. Results There were 39 total collisions, from 0 to 14 per building.Using generalized estimating equations, buildings near pear trees had 3.33-fold increased odds, mirrored windows had 5.92-fold increased odds, and bird-friendly windows had an 84% lower odds (Odds ratio = 0.16) of bird window collisions when analyzed separately; all were statistically significant (p < 0.01). A test of all possible combinations of risk and protective factors revealed that the best fit model included pear trees (odds = 2.31) and mirrored windows (odd…
format: application/pdf
format: text/html
creator: Barbara B. Brown
creator: Lia Hunter
creator: Sabrina Santos
subject: Animal Behavior
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.9401
publisher: PeerJ Inc.
rights: © 2020 Brown et al.
abstract: Background To reduce bird fatalities from millions of window collisions each year in North America, it is important to understand how design and landscape elements relate to collision risk. The current study extends prior research that found that buildings near ornamental pear trees (Prunus calleryana) and buildings with mirrored windows significantly increased odds of collisions among eight buildings on the University of Utah campus in winter. The previous study found bird-friendly glass was not related to collision risk, although only one fatality occurred at two buildings with ORNILUX® ultraviolet (UV) or fritted windows. We reasoned that extending data collection to include fall might provide a better test of efficacy. We tested the following three hypotheses: (1) Buildings with mirrored windows would experience more collisions, replicating the original study; (2) the addition of fall migration data would reveal fewer collisions at the buildings with bird-friendly windows; (3) the danger of pear tree proximity would be heightened in winter, when fruit is ripe enough to appeal to frugivores, especially the Cedar Waxwings (Bombycilla cedrorum) that frequent these trees. Methods Trained observers monitored buildings three times per week in Fall (September 12 to October 27, 2019) and Winter (October 29, 2019 to January 24, 2020). Collisions were photographed and documented in the iNaturalist University of Utah Bird Window Collision Project. Results There were 39 total collisions, from 0 to 14 per building.Using generalized estimating equations, buildings near pear trees had 3.33-fold increased odds, mirrored windows had 5.92-fold increased odds, and bird-friendly windows had an 84% lower odds (Odds ratio = 0.16) of bird window collisions when analyzed separately; all were statistically significant (p < 0.01). A test of all possible combinations of risk and protective factors revealed that the best fit model included pear trees (odds = 2.31) and mirrored windows (odd…
bibliographic citation: Brown et al. (2020) Bird-window collisions: different fall and winter risk and protective factors. PeerJ 8:e9401 https://doi.org/10.7717/peerj.9401
date submitted: 2020-04-01
date accepted: 2020-06-01
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Barbara B.
author list: Agent
  family name: Hunter
  given name: Lia
author list: Agent
  family name: Santos
  given name: Sabrina
doi: 10.7717/peerj.9401
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Brown et al.
attribution name: Brown et al.

The common personal behavior and preventive measures among 42 uninfected travelers from the Hubei province, China during COVID-19 outbreak: a cross-sectional survey in Macao SAR, China
type: item
type: AcademicArticle
description: Background The novel coronavirus diseases 2019 (COVID-19) caused over 1.7 million confirmed cases and cumulative mortality up to over 110,000 deaths worldwide as of 14 April 2020. A total of 57 Macao citizens were obligated to stay in Hubei province, China, where the highest COVID-19 prevalence was noted in the country and a “lockdown” policy was implemented for outbreak control for more than one month. They were escorted from Wuhan City to Macao via a chartered airplane organized by Macao SAR government and received quarantine for 14 days with none of the individual being diagnosed with COVID-19 by serial RNA tests from the nasopharyngeal specimens and sera antibodies. It was crucial to identify common characteristics among these 57 uninfected individuals. Methods A questionnaire survey was conducted to extract information such as behavior, change of habits and preventive measures. Results A total of 42 effective questionnaires were analyzed after exclusion of 14 infants and children with age under fifteen as ineligible for the survey and missing of one questionnaire, with a response rate of 97.7% (42 out of 43). The proportion of female composed more than 70% of this group of returners. The main reason for visiting Hubei in 88.1% of respondents was to visit relatives. Over 88% of respondents did not participate in high-risk activities due to mobility restriction. All (100%) denied contact with suspected or confirmed COVID-19 cases. Comparison of personal hygiene habits before and during disease outbreak showed a significant increase in practice including wearing a mask when outdoor (16.7% and 95.2%, P < 0.001) and often wash hands with soap or liquid soap (85.7% and 100%, P = 0.031).
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format: text/html
creator: Chon Fu Lio
creator: Hou Hon Cheong
creator: Chin Ion Lei
creator: Iek Long Lo
creator: Lan Yao
creator: Chong Lam
creator: Iek Hou Leong
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.9428
publisher: PeerJ Inc.
rights: © 2020 Lio et al.
abstract: Background The novel coronavirus diseases 2019 (COVID-19) caused over 1.7 million confirmed cases and cumulative mortality up to over 110,000 deaths worldwide as of 14 April 2020. A total of 57 Macao citizens were obligated to stay in Hubei province, China, where the highest COVID-19 prevalence was noted in the country and a “lockdown” policy was implemented for outbreak control for more than one month. They were escorted from Wuhan City to Macao via a chartered airplane organized by Macao SAR government and received quarantine for 14 days with none of the individual being diagnosed with COVID-19 by serial RNA tests from the nasopharyngeal specimens and sera antibodies. It was crucial to identify common characteristics among these 57 uninfected individuals. Methods A questionnaire survey was conducted to extract information such as behavior, change of habits and preventive measures. Results A total of 42 effective questionnaires were analyzed after exclusion of 14 infants and children with age under fifteen as ineligible for the survey and missing of one questionnaire, with a response rate of 97.7% (42 out of 43). The proportion of female composed more than 70% of this group of returners. The main reason for visiting Hubei in 88.1% of respondents was to visit relatives. Over 88% of respondents did not participate in high-risk activities due to mobility restriction. All (100%) denied contact with suspected or confirmed COVID-19 cases. Comparison of personal hygiene habits before and during disease outbreak showed a significant increase in practice including wearing a mask when outdoor (16.7% and 95.2%, P < 0.001) and often wash hands with soap or liquid soap (85.7% and 100%, P = 0.031).
bibliographic citation: Lio et al. (2020) The common personal behavior and preventive measures among 42 uninfected travelers from the Hubei province, China during COVID-19 outbreak: a cross-sectional survey in Macao SAR, China. PeerJ 8:e9428 https://doi.org/10.7717/peerj.9428
date submitted: 2020-04-22
date accepted: 2020-06-06
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lio
  given name: Chon Fu
author list: Agent
  family name: Cheong
  given name: Hou Hon
author list: Agent
  family name: Lei
  given name: Chin Ion
author list: Agent
  family name: Lo
  given name: Iek Long
author list: Agent
  family name: Yao
  given name: Lan
author list: Agent
  family name: Lam
  given name: Chong
author list: Agent
  family name: Leong
  given name: Iek Hou
doi: 10.7717/peerj.9428
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: © 2020 Lio et al.
attribution name: Lio et al.

Shape of attachment structures in parasitic isopodan crustaceans: the influence of attachment site and ontogeny
type: item
type: AcademicArticle
description: Many fields of modern systematic biology are adult-centred. This is unfortunately also the case for Cymothoidae, an ingroup of parasitic forms of Isopoda, with fishes as hosts. Different ingroups of Cymothoidae have specialised appendages that enable their fish associated lifestyles, attaching to different sites on the body of the host. The extent to which these structures vary among species and in relation different sites of attachment, and between different ontogenetic stages, is explored here. This study presents the detailed descriptions, illustrations, comparisons, and analysis of a variety of attachment structures of 13 adult and immature specimens representing three major groups Ceratothoa, Elthusa and Anilocra, along with full focus, detailed photographs of all the examined life stages. The three groups exhibit different strategies attaching to mouth, gill and externally, respectively. A statistical representation of the morphology of the dactyli, used for attaching to the host, was performed. This included a critical comparison of 10 additional species documented in literature. This is the first comprehensive description and photographs of specialised appendage morphology of immatures of Ceratothoa, as well as the first detailed micrographs of embryonic stages of Cymothoidae, and the first lateral and ventral views of immature stages of the examined species. Immature specimens possess morphological characters that can be used to distinguish between different species, but cannot be accurately identified based on diagnostic characters of adults. Quantitative analysis indicates that ontogeny plays a major role in the shape of the attachment structures (e.g. dactyli).
format: application/pdf
format: text/html
creator: Serita van der Wal
creator: Joachim T. Haug
subject: Marine Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.9181
publisher: PeerJ Inc.
rights: © 2020 van der Wal and Haug
abstract: Many fields of modern systematic biology are adult-centred. This is unfortunately also the case for Cymothoidae, an ingroup of parasitic forms of Isopoda, with fishes as hosts. Different ingroups of Cymothoidae have specialised appendages that enable their fish associated lifestyles, attaching to different sites on the body of the host. The extent to which these structures vary among species and in relation different sites of attachment, and between different ontogenetic stages, is explored here. This study presents the detailed descriptions, illustrations, comparisons, and analysis of a variety of attachment structures of 13 adult and immature specimens representing three major groups Ceratothoa, Elthusa and Anilocra, along with full focus, detailed photographs of all the examined life stages. The three groups exhibit different strategies attaching to mouth, gill and externally, respectively. A statistical representation of the morphology of the dactyli, used for attaching to the host, was performed. This included a critical comparison of 10 additional species documented in literature. This is the first comprehensive description and photographs of specialised appendage morphology of immatures of Ceratothoa, as well as the first detailed micrographs of embryonic stages of Cymothoidae, and the first lateral and ventral views of immature stages of the examined species. Immature specimens possess morphological characters that can be used to distinguish between different species, but cannot be accurately identified based on diagnostic characters of adults. Quantitative analysis indicates that ontogeny plays a major role in the shape of the attachment structures (e.g. dactyli).
bibliographic citation: van der Wal et al. (2020) Shape of attachment structures in parasitic isopodan crustaceans: the influence of attachment site and ontogeny. PeerJ 8:e9181 https://doi.org/10.7717/peerj.9181
date submitted: 2019-12-27
date accepted: 2020-04-22
issued: 2020-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van der Wal
  given name: Serita
author list: Agent
  family name: Haug
  given name: Joachim T.
doi: 10.7717/peerj.9181
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-18
copyright: © 2020 van der Wal and Haug
attribution name: van der Wal and Haug

Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean
type: item
type: AcademicArticle
description: The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4–5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson–Crick base pairing: adenine–adenine in stem D of tRNATrp, uracil–uracil and adenine–cytosine in the acceptor arm of the tRNALys and cytosine–cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D str…
format: application/pdf
format: text/html
creator: Harvey Infante-Rojas
creator: Leonardo Marino-Ramirez
creator: Javier Hernández-Fernández
subject: Bioinformatics
subject: Conservation Biology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.9204
publisher: PeerJ Inc.
rights: © 2020
abstract: The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4–5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson–Crick base pairing: adenine–adenine in stem D of tRNATrp, uracil–uracil and adenine–cytosine in the acceptor arm of the tRNALys and cytosine–cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D str…
bibliographic citation: Infante-Rojas et al. (2020) Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean. PeerJ 8:e9204 https://doi.org/10.7717/peerj.9204
date submitted: 2019-11-15
date accepted: 2020-04-25
issued: 2020-06-18
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Infante-Rojas
  given name: Harvey
author list: Agent
  family name: Marino-Ramirez
  given name: Leonardo
author list: Agent
  family name: Hernández-Fernández
  given name: Javier
doi: 10.7717/peerj.9204
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-18

Identification of hydatidosis-related modules and key regulatory genes
type: item
type: AcademicArticle
description: Background Echinococcosis caused by larval of Echinococcus is prevalent all over the world. Although clinical experience showed that the presence of tapeworms could not be found in liver lesions, the repeated infection and aggravation of lesions still occur in the host. Here, this study constructed a multifactor-driven disease-related dysfunction network to explore the potential molecular pathogenesis mechanism in different hosts after E.multilocularis infection. Method First, iTRAQ sequencing was performed on human liver infected with E.multilocularis. Second, obtained microRNAs(miRNAs) expression profiles of humans and canine infected with Echinococcus from the GEO database. In addition, we also performed differential expression analysis, protein interaction network analysis, enrichment analysis, and crosstalk analysis to obtain genes and modules related to E.multilocularis infection. Pivot analysis is used to calculate the potential regulatory effects of multiple factors on the module and identify related non-coding RNAs(ncRNAs) and transcription factors(TFs). Finally, we screened the target genes of miRNAs of Echinococcus to further explore its infection mechanism. Results A total of 267 differentially expressed proteins from humans and 3,635 differentially expressed genes from canine were obtained. They participated in 16 human-related dysfunction modules and five canine-related dysfunction modules, respectively. Both human and canine dysfunction modules are significantly involved in BMP signaling pathway and TGF-beta signaling pathway. In addition, pivot analysis found that 1,129 ncRNAs and 110 TFs significantly regulated human dysfunction modules, 158 ncRNAs and nine TFs significantly regulated canine dysfunction modules. Surprisingly, the Echinococcus miR-184 plays a role in the pathogenicity regulation by targeting nine TFs and one ncRNA in humans. Similarly, miR-184 can also cause physiological dysfunction by regulating two transcription factors in canine.…
format: application/pdf
format: text/html
creator: Jijun Song
creator: Mingxin Song
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.9280
publisher: PeerJ Inc.
rights: © 2020 Song and Song
abstract: Background Echinococcosis caused by larval of Echinococcus is prevalent all over the world. Although clinical experience showed that the presence of tapeworms could not be found in liver lesions, the repeated infection and aggravation of lesions still occur in the host. Here, this study constructed a multifactor-driven disease-related dysfunction network to explore the potential molecular pathogenesis mechanism in different hosts after E.multilocularis infection. Method First, iTRAQ sequencing was performed on human liver infected with E.multilocularis. Second, obtained microRNAs(miRNAs) expression profiles of humans and canine infected with Echinococcus from the GEO database. In addition, we also performed differential expression analysis, protein interaction network analysis, enrichment analysis, and crosstalk analysis to obtain genes and modules related to E.multilocularis infection. Pivot analysis is used to calculate the potential regulatory effects of multiple factors on the module and identify related non-coding RNAs(ncRNAs) and transcription factors(TFs). Finally, we screened the target genes of miRNAs of Echinococcus to further explore its infection mechanism. Results A total of 267 differentially expressed proteins from humans and 3,635 differentially expressed genes from canine were obtained. They participated in 16 human-related dysfunction modules and five canine-related dysfunction modules, respectively. Both human and canine dysfunction modules are significantly involved in BMP signaling pathway and TGF-beta signaling pathway. In addition, pivot analysis found that 1,129 ncRNAs and 110 TFs significantly regulated human dysfunction modules, 158 ncRNAs and nine TFs significantly regulated canine dysfunction modules. Surprisingly, the Echinococcus miR-184 plays a role in the pathogenicity regulation by targeting nine TFs and one ncRNA in humans. Similarly, miR-184 can also cause physiological dysfunction by regulating two transcription factors in canine.…
bibliographic citation: Song et al. (2020) Identification of hydatidosis-related modules and key regulatory genes. PeerJ 8:e9280 https://doi.org/10.7717/peerj.9280
date submitted: 2019-12-03
date accepted: 2020-05-12
issued: 2020-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Jijun
author list: Agent
  family name: Song
  given name: Mingxin
doi: 10.7717/peerj.9280
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-18
copyright: ©2020 Song and Song
attribution name: Song and Song

How caged salmon respond to waves depends on time of day and currents
type: item
type: AcademicArticle
description: Disease, pest control, and environmental factors such as water quality and carrying capacity limit growth of salmon production in existing farm areas. One way to circumvent such problems is to move production into more exposed locations with greater water exchange. Farming in exposed locations is better for the environment, but may carry unforeseen costs for the fish in those farms. Currents may be too strong, and waves may be too large with a negative impact on growth and profit for farmers and on fish welfare. This study employed two major fish monitoring methods to determine the ability of Atlantic Salmon (Salmo salar) to cope with wavy conditions in exposed farms. Echosounders were used to determine vertical distribution and horizontal preference of fish during different wave and current conditions as well as times of day. Video cameras were used to monitor shoal cohesion, swimming effort, and fish prevalence in locations of interest. The results indicate complex interacting effects of wave parameters, currents, and time of day on fish behaviour and vertical distribution. During the day, hydrodynamic conditions had stronger effects on vertical distribution than during the night. In weak currents, fish generally moved further down in taller waves, but stronger currents generally caused fish to move upwards regardless of wave conditions. Long period waves had unpredictable effects on vertical distribution with fish sometimes seeking deeper water and other times moving up to shallower water. It is unclear how much the cage bottom restricted vertical distribution and whether movement upwards in the water columns was related to cage deformation. In extreme cases, waves can reach below the bottom of a salmon cage, preventing fish from moving below the waves and cage deformation could exacerbate this situation. Farmers ought to take into consideration the many interacting effects on salmon behaviour within a cage as well as the potential for cage deformation when they …
format: application/pdf
format: text/html
creator: Ása Johannesen
creator: Øystein Patursson
creator: Jóhannus Kristmundsson
creator: Signar Pæturssonur Dam
creator: Pascal Klebert
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.9313
publisher: PeerJ Inc.
rights: © 2020 Johannesen et al.
abstract: Disease, pest control, and environmental factors such as water quality and carrying capacity limit growth of salmon production in existing farm areas. One way to circumvent such problems is to move production into more exposed locations with greater water exchange. Farming in exposed locations is better for the environment, but may carry unforeseen costs for the fish in those farms. Currents may be too strong, and waves may be too large with a negative impact on growth and profit for farmers and on fish welfare. This study employed two major fish monitoring methods to determine the ability of Atlantic Salmon (Salmo salar) to cope with wavy conditions in exposed farms. Echosounders were used to determine vertical distribution and horizontal preference of fish during different wave and current conditions as well as times of day. Video cameras were used to monitor shoal cohesion, swimming effort, and fish prevalence in locations of interest. The results indicate complex interacting effects of wave parameters, currents, and time of day on fish behaviour and vertical distribution. During the day, hydrodynamic conditions had stronger effects on vertical distribution than during the night. In weak currents, fish generally moved further down in taller waves, but stronger currents generally caused fish to move upwards regardless of wave conditions. Long period waves had unpredictable effects on vertical distribution with fish sometimes seeking deeper water and other times moving up to shallower water. It is unclear how much the cage bottom restricted vertical distribution and whether movement upwards in the water columns was related to cage deformation. In extreme cases, waves can reach below the bottom of a salmon cage, preventing fish from moving below the waves and cage deformation could exacerbate this situation. Farmers ought to take into consideration the many interacting effects on salmon behaviour within a cage as well as the potential for cage deformation when they …
bibliographic citation: Johannesen et al. (2020) How caged salmon respond to waves depends on time of day and currents. PeerJ 8:e9313 https://doi.org/10.7717/peerj.9313
date submitted: 2020-01-21
date accepted: 2020-05-17
issued: 2020-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johannesen
  given name: Ása
author list: Agent
  family name: Patursson
  given name: Øystein
author list: Agent
  family name: Kristmundsson
  given name: Jóhannus
author list: Agent
  family name: Dam
  given name: Signar Pæturssonur
author list: Agent
  family name: Klebert
  given name: Pascal
doi: 10.7717/peerj.9313
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-18
copyright: ©2020 Johannesen et al.
attribution name: Johannesen et al.

Parents know best: transgenerational predator recognition through parental effects
type: item
type: AcademicArticle
description: In highly biodiverse systems, such as coral reefs, prey species are faced with predatory threats from numerous species. Recognition of predators can be innate, or learned, and can help increase the chance of survival. Research suggests that parental exposure to increased predatory threats can affect the development, behaviour, and ultimately, success of their offspring. Breeding pairs of damselfish (Acanthochromis polyacanthus) were subjected to one of three olfactory and visual treatments (predator, herbivore, or control), and their developing embryos were subsequently exposed to five different chemosensory cues. Offspring of parents assigned to the predator treatment exhibited a mean increase in heart rate two times greater than that of offspring from parents in herbivore or control treatments. This increased reaction to a parentally known predator odour suggests that predator-treated parents passed down relevant threat information to their offspring, via parental effects. This is the first time transgenerational recognition of a specific predator has been confirmed in any species. This phenomenon could influence predator-induced mortality rates and enable populations to adaptively respond to fluctuations in predator composition and environmental changes.
format: application/pdf
format: text/html
creator: Jennifer A. Atherton
creator: Mark I. McCormick
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.9340
publisher: PeerJ Inc.
rights: © 2020 Atherton and McCormick
abstract: In highly biodiverse systems, such as coral reefs, prey species are faced with predatory threats from numerous species. Recognition of predators can be innate, or learned, and can help increase the chance of survival. Research suggests that parental exposure to increased predatory threats can affect the development, behaviour, and ultimately, success of their offspring. Breeding pairs of damselfish (Acanthochromis polyacanthus) were subjected to one of three olfactory and visual treatments (predator, herbivore, or control), and their developing embryos were subsequently exposed to five different chemosensory cues. Offspring of parents assigned to the predator treatment exhibited a mean increase in heart rate two times greater than that of offspring from parents in herbivore or control treatments. This increased reaction to a parentally known predator odour suggests that predator-treated parents passed down relevant threat information to their offspring, via parental effects. This is the first time transgenerational recognition of a specific predator has been confirmed in any species. This phenomenon could influence predator-induced mortality rates and enable populations to adaptively respond to fluctuations in predator composition and environmental changes.
bibliographic citation: Atherton et al. (2020) Parents know best: transgenerational predator recognition through parental effects. PeerJ 8:e9340 https://doi.org/10.7717/peerj.9340
date submitted: 2019-10-14
date accepted: 2020-05-20
issued: 2020-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Atherton
  given name: Jennifer A.
author list: Agent
  family name: McCormick
  given name: Mark I.
doi: 10.7717/peerj.9340
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-18
copyright: ©2020 Atherton and McCormick
attribution name: Atherton and McCormick

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