PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users
items: Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback
items: Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays
items: Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
items: Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation
items: Subcellular compartmentalization of the plant antioxidant system: an integrated overview
items: The chemotactic swimming behavior of bird schistosome miracidia in the presence of compatible and incompatible snail hosts
items: Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy
items: Light dependent courtship behavior in Drosophila simulans and D. melanogaster
items: Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China

The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users
type: item
type: AcademicArticle
description: Background Substitution can be defined as the consciously motivated choice to use one drug, either licit or illicit, instead of another, due to perceptions of cost, availability, safety, legality, substance characteristics, and substance attributions. Substitution represents a potential risk to drug users, mainly when substitutes are of higher potency and toxicity. This study offers a basic conceptualization of illicit substitution behavior and describes substitution patterns among users of two highly prevalent drugs of abuse—heroin and cannabis. Methods Here, 592 high-risk drug users undergoing pharmacological and psycho-social treatment were interviewed. Patients were asked questions about current drug use, lifetime substitution, and substitution patterns. Descriptive statistics, chi-square tests of independence, and multinomial logistic regressions were used to identify and test correlates of substitution patterns for heroin and cannabis. Results Of the 592 drug users interviewed, 448 subjects (75.7%) reported having substituted their preferred drug for another illicit substance. Interviews yielded a total of 275 substitution events reported by users of cannabis, and 351 substitution events reported by users of heroin. The most frequently reported substitution substances for responders who preferred heroin were illicit non-prescribed “street” methadone (35.9%), followed by oral and transdermal prescription opioids (17.7%). For responders who preferred cannabis, substitution for synthetic cannabinoid receptor agonists (33.5%) followed by alcohol (16.0%) were the most commonly reported. Age at onset–of–use (p < 0.005), population group (p = 0.008), and attending treatment for the first time (p = 0.026) were significantly associated with reported lifetime substitution. Past-year use of stimulants, heroin, hallucinogens, methylenedioxymethamphetamine (MDMA), and novel psychoactive substances were—at the 95% confidence level—also significantly associated with reported…
format: application/pdf
format: text/html
creator: Barak Shapira
creator: Paola Rosca
creator: Ronny Berkovitz
creator: Igor Gorjaltsan
creator: Yehuda Neumark
subject: Epidemiology
subject: Health Policy
subject: Pharmacology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9461
publisher: PeerJ Inc.
rights: © 2020 Shapira et al.
abstract: Background Substitution can be defined as the consciously motivated choice to use one drug, either licit or illicit, instead of another, due to perceptions of cost, availability, safety, legality, substance characteristics, and substance attributions. Substitution represents a potential risk to drug users, mainly when substitutes are of higher potency and toxicity. This study offers a basic conceptualization of illicit substitution behavior and describes substitution patterns among users of two highly prevalent drugs of abuse—heroin and cannabis. Methods Here, 592 high-risk drug users undergoing pharmacological and psycho-social treatment were interviewed. Patients were asked questions about current drug use, lifetime substitution, and substitution patterns. Descriptive statistics, chi-square tests of independence, and multinomial logistic regressions were used to identify and test correlates of substitution patterns for heroin and cannabis. Results Of the 592 drug users interviewed, 448 subjects (75.7%) reported having substituted their preferred drug for another illicit substance. Interviews yielded a total of 275 substitution events reported by users of cannabis, and 351 substitution events reported by users of heroin. The most frequently reported substitution substances for responders who preferred heroin were illicit non-prescribed “street” methadone (35.9%), followed by oral and transdermal prescription opioids (17.7%). For responders who preferred cannabis, substitution for synthetic cannabinoid receptor agonists (33.5%) followed by alcohol (16.0%) were the most commonly reported. Age at onset–of–use (p < 0.005), population group (p = 0.008), and attending treatment for the first time (p = 0.026) were significantly associated with reported lifetime substitution. Past-year use of stimulants, heroin, hallucinogens, methylenedioxymethamphetamine (MDMA), and novel psychoactive substances were—at the 95% confidence level—also significantly associated with reported…
bibliographic citation: Shapira et al. (2020) The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users. PeerJ 8:e9461 https://doi.org/10.7717/peerj.9461
date submitted: 2020-01-29
date accepted: 2020-06-10
issued: 2020-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shapira
  given name: Barak
author list: Agent
  family name: Rosca
  given name: Paola
author list: Agent
  family name: Berkovitz
  given name: Ronny
author list: Agent
  family name: Gorjaltsan
  given name: Igor
author list: Agent
  family name: Neumark
  given name: Yehuda
doi: 10.7717/peerj.9461
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-17
copyright: ©2020 Shapira et al.
attribution name: Shapira et al.

Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback
type: item
type: AcademicArticle
description: Anthropogenic eutrophication is altering aquatic environments by promoting primary production. This influences the population dynamics of consumers through bottom-up effects, but the underlying mechanisms and pathways are not always clear. To evaluate and mitigate effects of eutrophication on ecological communities, more research is needed on the underlying factors. Here we show that anthropogenic eutrophication increases population fecundity in the threespine stickleback (Gasterosteus aculeatus) by increasing the number of times females reproduce—lifetime fecundity—rather than instantaneous fecundity. When we exposed females to nutrient-enriched waters with enhanced algal growth, their interspawning interval shortened but the size of their egg clutches, or the size of their eggs, did not change. The shortening of the interspawning interval was probably caused by higher food intake, as algae growth promotes the growth of preferred prey populations. Enhanced female lifetime fecundity could increase offspring production and, hence, influence population dynamics. In support of this, earlier studies show that more offspring are emerging in habitats with denser algae growth. Thus, our results stress the importance of considering lifetime fecundity, in addition to instantaneous fecundity, when investigating the impact of human-induced eutrophication on population processes. At a broader level, our results highlight the importance of following individuals over longer time spans when evaluating the pathways and processes through which environmental changes influence individual fitness and population processes.
format: application/pdf
format: text/html
creator: Anne Saarinen
creator: Ulrika Candolin
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9521
publisher: PeerJ Inc.
rights: © 2020 Saarinen and Candolin
abstract: Anthropogenic eutrophication is altering aquatic environments by promoting primary production. This influences the population dynamics of consumers through bottom-up effects, but the underlying mechanisms and pathways are not always clear. To evaluate and mitigate effects of eutrophication on ecological communities, more research is needed on the underlying factors. Here we show that anthropogenic eutrophication increases population fecundity in the threespine stickleback (Gasterosteus aculeatus) by increasing the number of times females reproduce—lifetime fecundity—rather than instantaneous fecundity. When we exposed females to nutrient-enriched waters with enhanced algal growth, their interspawning interval shortened but the size of their egg clutches, or the size of their eggs, did not change. The shortening of the interspawning interval was probably caused by higher food intake, as algae growth promotes the growth of preferred prey populations. Enhanced female lifetime fecundity could increase offspring production and, hence, influence population dynamics. In support of this, earlier studies show that more offspring are emerging in habitats with denser algae growth. Thus, our results stress the importance of considering lifetime fecundity, in addition to instantaneous fecundity, when investigating the impact of human-induced eutrophication on population processes. At a broader level, our results highlight the importance of following individuals over longer time spans when evaluating the pathways and processes through which environmental changes influence individual fitness and population processes.
bibliographic citation: Saarinen et al. (2020) Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback. PeerJ 8:e9521 https://doi.org/10.7717/peerj.9521
date submitted: 2020-04-09
date accepted: 2020-06-19
issued: 2020-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saarinen
  given name: Anne
author list: Agent
  family name: Candolin
  given name: Ulrika
doi: 10.7717/peerj.9521
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-17
copyright: ©2020 Saarinen and Candolin
attribution name: Saarinen and Candolin

Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays
type: item
type: AcademicArticle
description: The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.
format: application/pdf
format: text/html
creator: Lidong Hao
creator: Shubing Shi
creator: Haibin Guo
creator: Ming Li
creator: Pan Hu
creator: Yadong Wei
creator: Yanfei Feng
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9551
publisher: PeerJ Inc.
rights: © 2020 Hao et al.
abstract: The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.
bibliographic citation: Hao et al. (2020) Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays. PeerJ 8:e9551 https://doi.org/10.7717/peerj.9551
date submitted: 2020-02-10
date accepted: 2020-06-24
issued: 2020-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Lidong
author list: Agent
  family name: Shi
  given name: Shubing
author list: Agent
  family name: Guo
  given name: Haibin
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Hu
  given name: Pan
author list: Agent
  family name: Wei
  given name: Yadong
author list: Agent
  family name: Feng
  given name: Yanfei
doi: 10.7717/peerj.9551
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-17
copyright: ©2020 Hao et al.
attribution name: Hao et al.

Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
type: item
type: AcademicArticle
description: Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.
format: application/pdf
format: text/html
creator: Arohi Parlikar
creator: Kishan Kalia
creator: Shruti Sinha
creator: Sucheta Patnaik
creator: Neeraj Sharma
creator: Sai Gayatri Vemuri
creator: Gaurav Sharma
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.9576
publisher: PeerJ Inc.
rights: © 2020 Parlikar et al.
abstract: Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.
bibliographic citation: Parlikar et al. (2020) Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2. PeerJ 8:e9576 https://doi.org/10.7717/peerj.9576
date submitted: 2020-04-29
date accepted: 2020-06-29
issued: 2020-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parlikar
  given name: Arohi
author list: Agent
  family name: Kalia
  given name: Kishan
author list: Agent
  family name: Sinha
  given name: Shruti
author list: Agent
  family name: Patnaik
  given name: Sucheta
author list: Agent
  family name: Sharma
  given name: Neeraj
author list: Agent
  family name: Vemuri
  given name: Sai Gayatri
author list: Agent
  family name: Sharma
  given name: Gaurav
doi: 10.7717/peerj.9576
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-17
copyright: © 2020 Parlikar et al.
attribution name: Parlikar et al.

Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation
type: item
type: AcademicArticle
description: Metagenome studies have provided us with insights into the complex interactions of microorganisms with their environments and hosts. Few studies have focused on microalgae-associated metagenomes, and no study has addressed aquatic microalgae and their bacterial communities in open pond raceways (OPRs). This study explored the possibility of using microalgal biomasses from OPRs for biodiesel and biofertilizer production. The fatty acid profiles of the biomasses and the physical and chemical properties of derived fuels were evaluated. In addition, the phenotype-based environmental adaptation ability of soybean plants was assessed. The growth rate, biomass, and lipid productivity of microalgae were also examined during mass cultivation from April to November 2017. Metagenomics analysis using MiSeq identified ∼127 eukaryotic phylotypes following mass cultivation with (OPR 1) or without (OPR 3) a semitransparent film. Of these, ∼80 phylotypes were found in both OPRs, while 23 and 24 phylotypes were identified in OPRs 1 and 3, respectively. The phylotypes belonged to various genera, such as Desmodesmus, Pseudopediastrum, Tetradesmus, and Chlorella, of which, the dominant microalgal species was Desmodesmus sp. On average, OPRs 1 and 3 produced ∼8.6 and 9.9 g m−2 d−1 (0.307 and 0.309 DW L−1) of total biomass, respectively, of which 14.0 and 13.3 wt% respectively, was lipid content. Fatty acid profiling revealed that total saturated fatty acids (mainly C16:0) of biodiesel obtained from the microalgal biomasses in OPRs 1 and 3 were 34.93% and 32.85%, respectively; total monounsaturated fatty acids (C16:1 and C18:1) were 32.40% and 31.64%, respectively; and polyunsaturated fatty acids (including C18:3) were 32.68% and 35.50%, respectively. Fuel properties determined by empirical equations were within the limits of biodiesel standards ASTM D6751 and EN 14214. Culture solutions with or without microalgal biomasses enhanced the environmental adaptation ability of soybean plants, …
format: application/pdf
format: text/html
creator: Seung-Woo Jo
creator: Jeong-Mi Do
creator: Ho Na
creator: Ji Won Hong
creator: Il-Sup Kim
creator: Ho-Sung Yoon
subject: Biodiversity
subject: Freshwater Biology
description: doi:10.7717/peerj.9418
publisher: PeerJ Inc.
rights: © 2020 Jo et al.
abstract: Metagenome studies have provided us with insights into the complex interactions of microorganisms with their environments and hosts. Few studies have focused on microalgae-associated metagenomes, and no study has addressed aquatic microalgae and their bacterial communities in open pond raceways (OPRs). This study explored the possibility of using microalgal biomasses from OPRs for biodiesel and biofertilizer production. The fatty acid profiles of the biomasses and the physical and chemical properties of derived fuels were evaluated. In addition, the phenotype-based environmental adaptation ability of soybean plants was assessed. The growth rate, biomass, and lipid productivity of microalgae were also examined during mass cultivation from April to November 2017. Metagenomics analysis using MiSeq identified ∼127 eukaryotic phylotypes following mass cultivation with (OPR 1) or without (OPR 3) a semitransparent film. Of these, ∼80 phylotypes were found in both OPRs, while 23 and 24 phylotypes were identified in OPRs 1 and 3, respectively. The phylotypes belonged to various genera, such as Desmodesmus, Pseudopediastrum, Tetradesmus, and Chlorella, of which, the dominant microalgal species was Desmodesmus sp. On average, OPRs 1 and 3 produced ∼8.6 and 9.9 g m−2 d−1 (0.307 and 0.309 DW L−1) of total biomass, respectively, of which 14.0 and 13.3 wt% respectively, was lipid content. Fatty acid profiling revealed that total saturated fatty acids (mainly C16:0) of biodiesel obtained from the microalgal biomasses in OPRs 1 and 3 were 34.93% and 32.85%, respectively; total monounsaturated fatty acids (C16:1 and C18:1) were 32.40% and 31.64%, respectively; and polyunsaturated fatty acids (including C18:3) were 32.68% and 35.50%, respectively. Fuel properties determined by empirical equations were within the limits of biodiesel standards ASTM D6751 and EN 14214. Culture solutions with or without microalgal biomasses enhanced the environmental adaptation ability of soybean plants, …
bibliographic citation: Jo et al. (2020) Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation. PeerJ 8:e9418 https://doi.org/10.7717/peerj.9418
date submitted: 2019-10-28
date accepted: 2020-06-03
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jo
  given name: Seung-Woo
author list: Agent
  family name: Do
  given name: Jeong-Mi
author list: Agent
  family name: Na
  given name: Ho
author list: Agent
  family name: Hong
  given name: Ji Won
author list: Agent
  family name: Kim
  given name: Il-Sup
author list: Agent
  family name: Yoon
  given name: Ho-Sung
doi: 10.7717/peerj.9418
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: ©2020 Jo et al.
attribution name: Jo et al.

Subcellular compartmentalization of the plant antioxidant system: an integrated overview
type: item
type: AcademicArticle
description: The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.
format: application/pdf
format: text/html
creator: Aleksandr Bobrovskikh
creator: Ulyana Zubairova
creator: Alexey Kolodkin
creator: Alexey Doroshkov
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9451
publisher: PeerJ Inc.
rights: © 2020 Bobrovskikh et al.
abstract: The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.
bibliographic citation: Bobrovskikh et al. (2020) Subcellular compartmentalization of the plant antioxidant system: an integrated overview. PeerJ 8:e9451 https://doi.org/10.7717/peerj.9451
date submitted: 2020-04-08
date accepted: 2020-06-09
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bobrovskikh
  given name: Aleksandr
author list: Agent
  family name: Zubairova
  given name: Ulyana
author list: Agent
  family name: Kolodkin
  given name: Alexey
author list: Agent
  family name: Doroshkov
  given name: Alexey
doi: 10.7717/peerj.9451
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 Bobrovskikh et al.
attribution name: Bobrovskikh et al.

The chemotactic swimming behavior of bird schistosome miracidia in the presence of compatible and incompatible snail hosts
type: item
type: AcademicArticle
description: No effective method has yet been developed to prevent the threat posed by the emerging disease—cercarial dermatitis (swimmer’s itch), caused by infective cercariae of bird schistosomes (Digenea: Schistosomatidae). In our previous studies, the New Zealand mud snail—Potamopyrgus antipodarum (Gray, 1853; Gastropoda, Tateidae)—was used as a barrier between the miracidia of Trichobilharzia regenti and the target snails Radix balthica. Since the presence of non-indigenous snails reduced the parasite prevalence under laboratory conditions, we posed three new research questions: (1) Do bird schistosomes show totally perfect efficacy for chemotactic swimming behavior? (2) Do the larvae respond to substances emitted by incompatible snail species? (3) Do the excretory-secretory products of incompatible snail species interfere with the search for a compatible snail host? The experiments were carried out in choice-chambers for the miracidia of T. regenti and T. szidati. The arms of the chambers, depending on the variant, were filled with water conditioned by P. antipodarum, water conditioned by lymnaeid hosts, and dechlorinated tap water. Miracidia of both bird schistosome species chose more frequently the water conditioned by snails—including the water conditioned by the incompatible lymnaeid host and the alien species, P. antipodarum. However, species-specific differences were noticed in the behavior of miracidia. T. regenti remained more often inside the base arm rather than in the arm filled with water conditioned by P. antipodarum or the control arm. T. szidati, however, usually left the base arm and moved to the arm filled with water conditioned by P. antipodarum. In conclusion, the non-host snail excretory-secretory products may interfere with the snail host-finding behavior of bird schistosome miracidia and therefore they may reduce the risk of swimmer’s itch.
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creator: Anna Marszewska
creator: Anna Cichy
creator: Jana Bulantová
creator: Petr Horák
creator: Elżbieta Żbikowska
subject: Animal Behavior
subject: Ecology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.9487
publisher: PeerJ Inc.
rights: © 2020 Marszewska et al.
abstract: No effective method has yet been developed to prevent the threat posed by the emerging disease—cercarial dermatitis (swimmer’s itch), caused by infective cercariae of bird schistosomes (Digenea: Schistosomatidae). In our previous studies, the New Zealand mud snail—Potamopyrgus antipodarum (Gray, 1853; Gastropoda, Tateidae)—was used as a barrier between the miracidia of Trichobilharzia regenti and the target snails Radix balthica. Since the presence of non-indigenous snails reduced the parasite prevalence under laboratory conditions, we posed three new research questions: (1) Do bird schistosomes show totally perfect efficacy for chemotactic swimming behavior? (2) Do the larvae respond to substances emitted by incompatible snail species? (3) Do the excretory-secretory products of incompatible snail species interfere with the search for a compatible snail host? The experiments were carried out in choice-chambers for the miracidia of T. regenti and T. szidati. The arms of the chambers, depending on the variant, were filled with water conditioned by P. antipodarum, water conditioned by lymnaeid hosts, and dechlorinated tap water. Miracidia of both bird schistosome species chose more frequently the water conditioned by snails—including the water conditioned by the incompatible lymnaeid host and the alien species, P. antipodarum. However, species-specific differences were noticed in the behavior of miracidia. T. regenti remained more often inside the base arm rather than in the arm filled with water conditioned by P. antipodarum or the control arm. T. szidati, however, usually left the base arm and moved to the arm filled with water conditioned by P. antipodarum. In conclusion, the non-host snail excretory-secretory products may interfere with the snail host-finding behavior of bird schistosome miracidia and therefore they may reduce the risk of swimmer’s itch.
bibliographic citation: Marszewska et al. (2020) The chemotactic swimming behavior of bird schistosome miracidia in the presence of compatible and incompatible snail hosts. PeerJ 8:e9487 https://doi.org/10.7717/peerj.9487
date submitted: 2020-03-23
date accepted: 2020-06-15
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marszewska
  given name: Anna
author list: Agent
  family name: Cichy
  given name: Anna
author list: Agent
  family name: Bulantová
  given name: Jana
author list: Agent
  family name: Horák
  given name: Petr
author list: Agent
  family name: Żbikowska
  given name: Elżbieta
doi: 10.7717/peerj.9487
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 Marszewska et al.
attribution name: Marszewska et al.

Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy
type: item
type: AcademicArticle
description: Specimens of the genus Loimia (Annelida, Terebellidae) deposited in the Marine Biological Museum of the Chinese Academy of Sciences (MBMCAS) together with materials newly collected from China seas were examined. Based on morphological comparisons and molecular analysis, some specimens collected from the coasts of Shandong province and Guangxi province were confirmed as two new Loimia species respectively (Loimia borealis sp. n. and Loimia macrobranchia sp. n.). Morphologically, L. borealis sp. n. is distinguished from previously known species of this genus by having seven equal sized ventral shields, with length five times the width; this species was retrieved as sister to the clades of Loimia arborea Moore, 1903 and Loimia bandera Hutchings, 1990 in the phylogenetic tree, which was reconstructed based on mitochondrial COI gene. Loimia macrobranchia sp. n. differs from congeners by the large size of its first pair of branchiae with a thick main stem and about 18 dendritic branches arranged in two levels. A key to identifying Loimia species found in Chinese seas is given.
format: application/pdf
format: text/html
creator: Weina Wang
creator: Jixing Sui
creator: Qi Kou
creator: Xin-Zheng Li
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9491
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Specimens of the genus Loimia (Annelida, Terebellidae) deposited in the Marine Biological Museum of the Chinese Academy of Sciences (MBMCAS) together with materials newly collected from China seas were examined. Based on morphological comparisons and molecular analysis, some specimens collected from the coasts of Shandong province and Guangxi province were confirmed as two new Loimia species respectively (Loimia borealis sp. n. and Loimia macrobranchia sp. n.). Morphologically, L. borealis sp. n. is distinguished from previously known species of this genus by having seven equal sized ventral shields, with length five times the width; this species was retrieved as sister to the clades of Loimia arborea Moore, 1903 and Loimia bandera Hutchings, 1990 in the phylogenetic tree, which was reconstructed based on mitochondrial COI gene. Loimia macrobranchia sp. n. differs from congeners by the large size of its first pair of branchiae with a thick main stem and about 18 dendritic branches arranged in two levels. A key to identifying Loimia species found in Chinese seas is given.
bibliographic citation: Wang et al. (2020) Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy. PeerJ 8:e9491 https://doi.org/10.7717/peerj.9491
date submitted: 2019-12-21
date accepted: 2020-06-16
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Weina
author list: Agent
  family name: Sui
  given name: Jixing
author list: Agent
  family name: Kou
  given name: Qi
author list: Agent
  family name: Li
  given name: Xin-Zheng
doi: 10.7717/peerj.9491
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Light dependent courtship behavior in Drosophila simulans and D. melanogaster
type: item
type: AcademicArticle
description: Differences in courtship signals and perception are well-known among Drosophila species. One such described difference is the dependency on light, and thus presumably vision, for copulation success. Many studies have described a difference in light-dependent copulation success between D. melanogaster and D. simulans, identifying D. simulans as a light-dependent species, and D. melanogaster as a light-independent one. However, many of these studies use assays of varying design and few strains to represent the entire species. Here, we attempt to better characterize this purported difference using 11 strains of each species, paired by collection location, in behavioral assays conducted at two different exposure times. We show that, while there is a species-wide difference in magnitude of light-dependent copulation success, D. melanogaster copulation success is, on average, still impaired in the dark at both exposure times we measured. Additionally, there is significant variation in strain-specific ability to copulate in the dark in both species across two different exposure times. We find that this variation correlates strongly with longitude in D. melanogaster, but not in D. simulans. We hypothesize that differences in species history and demography may explain behavioral variation. Finally, we use courtship assays to show that light-dependent copulation success in one D. simulans strain is driven in part by both males and females. We discuss potential differences in courtship signals and/or signal importance between these species and potential for further comparative studies for functional characterization.
format: application/pdf
format: text/html
creator: Michael P. Shahandeh
creator: Cameryn Brock
creator: Thomas L. Turner
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.9499
publisher: PeerJ Inc.
rights: © 2020 Shahandeh et al.
abstract: Differences in courtship signals and perception are well-known among Drosophila species. One such described difference is the dependency on light, and thus presumably vision, for copulation success. Many studies have described a difference in light-dependent copulation success between D. melanogaster and D. simulans, identifying D. simulans as a light-dependent species, and D. melanogaster as a light-independent one. However, many of these studies use assays of varying design and few strains to represent the entire species. Here, we attempt to better characterize this purported difference using 11 strains of each species, paired by collection location, in behavioral assays conducted at two different exposure times. We show that, while there is a species-wide difference in magnitude of light-dependent copulation success, D. melanogaster copulation success is, on average, still impaired in the dark at both exposure times we measured. Additionally, there is significant variation in strain-specific ability to copulate in the dark in both species across two different exposure times. We find that this variation correlates strongly with longitude in D. melanogaster, but not in D. simulans. We hypothesize that differences in species history and demography may explain behavioral variation. Finally, we use courtship assays to show that light-dependent copulation success in one D. simulans strain is driven in part by both males and females. We discuss potential differences in courtship signals and/or signal importance between these species and potential for further comparative studies for functional characterization.
bibliographic citation: Shahandeh et al. (2020) Light dependent courtship behavior in Drosophila simulans and D. melanogaster. PeerJ 8:e9499 https://doi.org/10.7717/peerj.9499
date submitted: 2019-11-12
date accepted: 2020-06-17
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shahandeh
  given name: Michael P.
author list: Agent
  family name: Brock
  given name: Cameryn
author list: Agent
  family name: Turner
  given name: Thomas L.
doi: 10.7717/peerj.9499
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: ©2020 Shahandeh et al.
attribution name: Shahandeh et al.

Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China
type: item
type: AcademicArticle
description: Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.
format: application/pdf
format: text/html
creator: Xiaojuan Chen
creator: Da He
creator: Lianfeng Zhou
creator: Yankun Cao
creator: Zhanjing Li
subject: Biodiversity
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.9500
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.
bibliographic citation: Chen et al. (2020) Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China. PeerJ 8:e9500 https://doi.org/10.7717/peerj.9500
date submitted: 2019-11-29
date accepted: 2020-06-17
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaojuan
author list: Agent
  family name: He
  given name: Da
author list: Agent
  family name: Zhou
  given name: Lianfeng
author list: Agent
  family name: Cao
  given name: Yankun
author list: Agent
  family name: Li
  given name: Zhanjing
doi: 10.7717/peerj.9500
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 Chen et al.
attribution name: Chen et al.

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