PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Functional modularity in lake-dwelling characin fishes of Mexico
items: The Dark Cube: dark character profiles and OCEAN
items: Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?
items: Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees
items: Selected nutritional habits of teenagers associated with overweight and obesity
items: The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data
items: MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations
items: Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
items: Human agency beliefs influence behaviour during virtual social interactions
items: Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands

Functional modularity in lake-dwelling characin fishes of Mexico
type: item
type: AcademicArticle
description: Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi.
format: application/pdf
format: text/html
creator: Claudia Patricia Ornelas-García
creator: Amando Bautista
creator: Fabian Herder
creator: Ignacio Doadrio
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.3851
publisher: PeerJ Inc.
rights: © 2017 Ornelas-García et al.
abstract: Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi.
bibliographic citation: Ornelas-García et al. (2017) Functional modularity in lake-dwelling characin fishes of Mexico. PeerJ 5:e3851 https://doi.org/10.7717/peerj.3851
date submitted: 2017-05-20
date accepted: 2017-09-05
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ornelas-García
  given name: Claudia Patricia
author list: Agent
  family name: Bautista
  given name: Amando
author list: Agent
  family name: Herder
  given name: Fabian
author list: Agent
  family name: Doadrio
  given name: Ignacio
doi: 10.7717/peerj.3851
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Ornelas-García et al.
attribution name: Ornelas-García et al.

The Dark Cube: dark character profiles and OCEAN
type: item
type: AcademicArticle
description: Background The Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger’s biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships). Method Participants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP “maleficent”, MNp “manipulative narcissistic”, MnP “anti-social”, Mnp “Machiavellian”, mNP “psychopathic narcissistic”, mNp “narcissistic”, mnP “psychopathic”, and mnp “benevolent”. Results High narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp). Conclusions We suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relatio…
format: application/pdf
format: text/html
creator: Danilo Garcia
creator: Fernando R. González Moraga
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3845
publisher: PeerJ Inc.
rights: © 2017 Garcia and González Moraga
abstract: Background The Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger’s biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships). Method Participants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP “maleficent”, MNp “manipulative narcissistic”, MnP “anti-social”, Mnp “Machiavellian”, mNP “psychopathic narcissistic”, mNp “narcissistic”, mnP “psychopathic”, and mnp “benevolent”. Results High narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp). Conclusions We suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relatio…
bibliographic citation: Garcia et al. (2017) The Dark Cube: dark character profiles and OCEAN. PeerJ 5:e3845 https://doi.org/10.7717/peerj.3845
date submitted: 2016-07-19
date accepted: 2017-09-02
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia
  given name: Danilo
author list: Agent
  family name: González Moraga
  given name: Fernando R.
doi: 10.7717/peerj.3845
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Garcia and González Moraga
attribution name: Garcia and González Moraga

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?
type: item
type: AcademicArticle
description: The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
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creator: Manuel Pimentel
creator: Marcial Escudero
creator: Elvira Sahuquillo
creator: Miguel Ángel Minaya
creator: Pilar Catalán
subject: Biodiversity
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.3815
publisher: PeerJ Inc.
rights: © 2017 Pimentel et al.
abstract: The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
bibliographic citation: Pimentel et al. (2017) Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?. PeerJ 5:e3815 https://doi.org/10.7717/peerj.3815
date submitted: 2017-06-27
date accepted: 2017-08-26
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pimentel
  given name: Manuel
author list: Agent
  family name: Escudero
  given name: Marcial
author list: Agent
  family name: Sahuquillo
  given name: Elvira
author list: Agent
  family name: Minaya
  given name: Miguel Ángel
author list: Agent
  family name: Catalán
  given name: Pilar
doi: 10.7717/peerj.3815
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Pimentel et al.
attribution name: Pimentel et al.

Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees
type: item
type: AcademicArticle
description: Modern human technological culture depends on social learning. A widespread assumption for chimpanzee tool-use cultures is that they, too, are dependent on social learning. However, we provide evidence to suggest that individual learning, rather than social learning, is the driver behind determining the form of these behaviours within and across individuals. Low-fidelity social learning instead merely facilitates the reinnovation of these behaviours, and thus helps homogenise the behaviour across chimpanzees, creating the population-wide patterns observed in the wild (what here we call “socially mediated serial reinnovations”). This is the main prediction of the Zone of Latent Solutions (ZLS) hypothesis. This study directly tested the ZLS hypothesis on algae scooping, a wild chimpanzee tool-use behaviour. We provided naïve chimpanzees (n = 14, Mage = 31.33, SD = 10.09) with ecologically relevant materials of the wild behaviour but, crucially, without revealing any information on the behavioural form required to accomplish this task. This study found that naïve chimpanzees expressed the same behavioural form as their wild counterparts, suggesting that, as the ZLS theory predicts, individual learning is the driver behind the frequency of this behavioural form. As more behaviours are being found to be within chimpanzee’s ZLS, this hypothesis now provides a parsimonious explanation for chimpanzee tool cultures.
format: application/pdf
format: text/html
creator: Elisa Bandini
creator: Claudio Tennie
subject: Animal Behavior
subject: Evolutionary Studies
description: doi:10.7717/peerj.3814
publisher: PeerJ Inc.
rights: © 2017 Bandini and Tennie
abstract: Modern human technological culture depends on social learning. A widespread assumption for chimpanzee tool-use cultures is that they, too, are dependent on social learning. However, we provide evidence to suggest that individual learning, rather than social learning, is the driver behind determining the form of these behaviours within and across individuals. Low-fidelity social learning instead merely facilitates the reinnovation of these behaviours, and thus helps homogenise the behaviour across chimpanzees, creating the population-wide patterns observed in the wild (what here we call “socially mediated serial reinnovations”). This is the main prediction of the Zone of Latent Solutions (ZLS) hypothesis. This study directly tested the ZLS hypothesis on algae scooping, a wild chimpanzee tool-use behaviour. We provided naïve chimpanzees (n = 14, Mage = 31.33, SD = 10.09) with ecologically relevant materials of the wild behaviour but, crucially, without revealing any information on the behavioural form required to accomplish this task. This study found that naïve chimpanzees expressed the same behavioural form as their wild counterparts, suggesting that, as the ZLS theory predicts, individual learning is the driver behind the frequency of this behavioural form. As more behaviours are being found to be within chimpanzee’s ZLS, this hypothesis now provides a parsimonious explanation for chimpanzee tool cultures.
bibliographic citation: Bandini et al. (2017) Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees. PeerJ 5:e3814 https://doi.org/10.7717/peerj.3814
date submitted: 2017-04-04
date accepted: 2017-08-26
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bandini
  given name: Elisa
author list: Agent
  family name: Tennie
  given name: Claudio
doi: 10.7717/peerj.3814
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Bandini and Tennie
attribution name: Bandini and Tennie

Selected nutritional habits of teenagers associated with overweight and obesity
type: item
type: AcademicArticle
description: Introduction A balanced diet is at the heart of healthy growth and development of children and youth, whereas inappropriate eating habits considerably influence the incidence of disorders connected with nutrition, including overweight and obesity. This paper aims at studying nutritional factors of 18-year-old secondary school youth in the urban environment and their effect on the incidence of overweight and obesity. Materials and methods The survey was conducted among 1,999 secondary school students chosen at random. The research tool consisted an original survey questionnaire. The measurements of respondents’ height and body mass provided data for calculating the body mass index. Results and conclusion The percentage of youth with deficient body mass was estimated at 8.4%. The percentage of normal weight students in the surveyed group was estimated at 77.6%. Overweight and obesity characterized 14.0% of the total number. As many as 21.8% of overweight and obese respondents would eat one or two meals as opposed to 16.8% of normal weight students. Three-fourths of the surveyed students would eat breakfast regardless of their nutritional habits. Lunch is eaten by 52.9% of normal weight 18-year-olds and 46.1% of overweight and obese students. The analysis of mealtimes suggests that overweight and obese students would have their breakfast and dinner at later hours than the rest of the surveyed. More than half of the participating students failed to eat lunch (53.9%), and one in four students within this group resigned from supper. Girls would eat fruit and vegetables more frequently than boys several times a day. The percentage of persons in the surveyed groups who would eat fast foods on a daily basis was similar regardless of their nutritional status. Sweetened carbonated beverages would be drunk more often by overweight and obese boys (81.2%) as compared with boys with proper body mass (75.8%). The same type of beverages would be popular with two-thirds of girls, and…
format: application/pdf
format: text/html
creator: Magdalena Zalewska
creator: Elżbieta Maciorkowska
subject: Nutrition
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.3681
publisher: PeerJ Inc.
rights: © 2017 Zalewska and Maciorkowska
abstract: Introduction A balanced diet is at the heart of healthy growth and development of children and youth, whereas inappropriate eating habits considerably influence the incidence of disorders connected with nutrition, including overweight and obesity. This paper aims at studying nutritional factors of 18-year-old secondary school youth in the urban environment and their effect on the incidence of overweight and obesity. Materials and methods The survey was conducted among 1,999 secondary school students chosen at random. The research tool consisted an original survey questionnaire. The measurements of respondents’ height and body mass provided data for calculating the body mass index. Results and conclusion The percentage of youth with deficient body mass was estimated at 8.4%. The percentage of normal weight students in the surveyed group was estimated at 77.6%. Overweight and obesity characterized 14.0% of the total number. As many as 21.8% of overweight and obese respondents would eat one or two meals as opposed to 16.8% of normal weight students. Three-fourths of the surveyed students would eat breakfast regardless of their nutritional habits. Lunch is eaten by 52.9% of normal weight 18-year-olds and 46.1% of overweight and obese students. The analysis of mealtimes suggests that overweight and obese students would have their breakfast and dinner at later hours than the rest of the surveyed. More than half of the participating students failed to eat lunch (53.9%), and one in four students within this group resigned from supper. Girls would eat fruit and vegetables more frequently than boys several times a day. The percentage of persons in the surveyed groups who would eat fast foods on a daily basis was similar regardless of their nutritional status. Sweetened carbonated beverages would be drunk more often by overweight and obese boys (81.2%) as compared with boys with proper body mass (75.8%). The same type of beverages would be popular with two-thirds of girls, and…
bibliographic citation: Zalewska et al. (2017) Selected nutritional habits of teenagers associated with overweight and obesity. PeerJ 5:e3681 https://doi.org/10.7717/peerj.3681
date submitted: 2017-01-13
date accepted: 2017-07-22
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zalewska
  given name: Magdalena
author list: Agent
  family name: Maciorkowska
  given name: Elżbieta
doi: 10.7717/peerj.3681
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: © 2017 Zalewska and Maciorkowska
attribution name: Zalewska and Maciorkowska

The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data
type: item
type: AcademicArticle
description: The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, with Hemisquilla as the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies.
format: application/pdf
format: text/html
creator: Cara Van Der Wal
creator: Shane T. Ahyong
creator: Simon Y.W. Ho
creator: Nathan Lo
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.3844
publisher: PeerJ Inc.
rights: © 2017 Van Der Wal et al.
abstract: The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, with Hemisquilla as the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies.
bibliographic citation: Van Der Wal et al. (2017) The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data. PeerJ 5:e3844 https://doi.org/10.7717/peerj.3844
date submitted: 2017-07-25
date accepted: 2017-09-02
issued: 2017-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Van Der Wal
  given name: Cara
author list: Agent
  family name: Ahyong
  given name: Shane T.
author list: Agent
  family name: Ho
  given name: Simon Y.W.
author list: Agent
  family name: Lo
  given name: Nathan
doi: 10.7717/peerj.3844
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-21
copyright: ©2017 Van Der Wal et al.
attribution name: Van Der Wal et al.

MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations
type: item
type: AcademicArticle
description: Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.
format: application/pdf
format: text/html
creator: Nela Nikolic
creator: Zrinka Didara
creator: Isabella Moll
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.3830
publisher: PeerJ Inc.
rights: © 2017 Nikolic et al.
abstract: Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.
bibliographic citation: Nikolic et al. (2017) MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ 5:e3830 https://doi.org/10.7717/peerj.3830
date submitted: 2017-05-23
date accepted: 2017-08-29
issued: 2017-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nikolic
  given name: Nela
author list: Agent
  family name: Didara
  given name: Zrinka
author list: Agent
  family name: Moll
  given name: Isabella
doi: 10.7717/peerj.3830
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-21
copyright: ©2017 Nikolic et al.
attribution name: Nikolic et al.

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
type: item
type: AcademicArticle
description: Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically develo…
format: application/pdf
format: text/html
creator: Simon Roux
creator: Joanne B. Emerson
creator: Emiley A. Eloe-Fadrosh
creator: Matthew B. Sullivan
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3817
publisher: PeerJ Inc.
rights: © 2017 Roux et al.
abstract: Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically develo…
bibliographic citation: Roux et al. (2017) Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ 5:e3817 https://doi.org/10.7717/peerj.3817
date submitted: 2017-06-24
date accepted: 2017-08-26
issued: 2017-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roux
  given name: Simon
author list: Agent
  family name: Emerson
  given name: Joanne B.
author list: Agent
  family name: Eloe-Fadrosh
  given name: Emiley A.
author list: Agent
  family name: Sullivan
  given name: Matthew B.
doi: 10.7717/peerj.3817
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-21
copyright: ©2017 Roux et al.
attribution name: Roux et al.

Human agency beliefs influence behaviour during virtual social interactions
type: item
type: AcademicArticle
description: In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an “intentional stance” by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants’ behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative “joint attention” game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other’s eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm (“Computer” condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room (“Human” condition). Those in the “Human” condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the “Computer” condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application’s goals.
format: application/pdf
format: text/html
creator: Nathan Caruana
creator: Dean Spirou
creator: Jon Brock
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
description: doi:10.7717/peerj.3819
publisher: PeerJ Inc.
rights: © 2017 Caruana et al.
abstract: In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an “intentional stance” by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants’ behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative “joint attention” game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other’s eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm (“Computer” condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room (“Human” condition). Those in the “Human” condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the “Computer” condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application’s goals.
bibliographic citation: Caruana et al. (2017) Human agency beliefs influence behaviour during virtual social interactions. PeerJ 5:e3819 https://doi.org/10.7717/peerj.3819
date submitted: 2017-06-10
date accepted: 2017-08-28
issued: 2017-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caruana
  given name: Nathan
author list: Agent
  family name: Spirou
  given name: Dean
author list: Agent
  family name: Brock
  given name: Jon
doi: 10.7717/peerj.3819
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-20
copyright: ©2017 Caruana et al.
attribution name: Caruana et al.

Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands
type: item
type: AcademicArticle
description: With 600 described species, the ant genus Tetramorium represents one of the most species-rich ant radiations. However, much work remains to fully document the hyperdiversity of this remarkable group. Tetramorium, while globally distributed, is thought to have originated in the Afrotropics and is particularly diverse in the Old World. Here, we focus attention on the Tetramorium fauna of India, a region of high biodiversity value and interest for conservation. We overview Tetramorium diversity in India by providing a species list, accounts of all species groups present, an illustrated identification key to Indian Tetramorium species groups and notes on the Indian Tetramorium fauna. Further, we describe two new species, Tetramorium krishnani sp. n. and Tetramorium jarawa sp. n. from the Andaman Islands archipelago and embed them into currently recognized Tetramorium tonganum and Tetramorium inglebyi species groups. We also provide illustrated species level keys for these groups. Along with detailed species descriptions and high-resolution montage images of types, we provide 3D cybertypes of the new species derived from X-ray micro-computed tomography.
format: application/pdf
format: text/html
creator: Gaurav Agavekar
creator: Francisco Hita Garcia
creator: Evan P. Economo
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.3800
publisher: PeerJ Inc.
rights: © 2017 Agavekar et al.
abstract: With 600 described species, the ant genus Tetramorium represents one of the most species-rich ant radiations. However, much work remains to fully document the hyperdiversity of this remarkable group. Tetramorium, while globally distributed, is thought to have originated in the Afrotropics and is particularly diverse in the Old World. Here, we focus attention on the Tetramorium fauna of India, a region of high biodiversity value and interest for conservation. We overview Tetramorium diversity in India by providing a species list, accounts of all species groups present, an illustrated identification key to Indian Tetramorium species groups and notes on the Indian Tetramorium fauna. Further, we describe two new species, Tetramorium krishnani sp. n. and Tetramorium jarawa sp. n. from the Andaman Islands archipelago and embed them into currently recognized Tetramorium tonganum and Tetramorium inglebyi species groups. We also provide illustrated species level keys for these groups. Along with detailed species descriptions and high-resolution montage images of types, we provide 3D cybertypes of the new species derived from X-ray micro-computed tomography.
bibliographic citation: Agavekar et al. (2017) Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands. PeerJ 5:e3800 https://doi.org/10.7717/peerj.3800
date submitted: 2017-06-30
date accepted: 2017-08-22
issued: 2017-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Agavekar
  given name: Gaurav
author list: Agent
  family name: Hita Garcia
  given name: Francisco
author list: Agent
  family name: Economo
  given name: Evan P.
doi: 10.7717/peerj.3800
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-20
copyright: © 2017 Agavekar et al.
attribution name: Agavekar et al.

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