PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
items: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
items: Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
items: Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
items: Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
items: Familiarity with visual stimuli boosts recency bias in macaques
items: Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry
items: Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns
items: Introducing a new tool to navigate, understand and use International Codes of Nomenclature
items: Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction

Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
type: item
type: AcademicArticle
description: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
format: application/pdf
format: text/html
creator: Kyle K. Biggar
creator: Jing Zhang
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8144
publisher: PeerJ Inc.
rights: © 2019 Biggar et al.
abstract: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
bibliographic citation: Biggar et al. (2019) Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia. PeerJ 7:e8144 https://doi.org/10.7717/peerj.8144
date submitted: 2019-05-21
date accepted: 2019-11-01
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biggar
  given name: Kyle K.
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.8144
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Biggar et al.
attribution name: Biggar et al.

Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
type: item
type: AcademicArticle
description: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
format: application/pdf
format: text/html
creator: Xin Hu
creator: Lili Zhu
creator: Yi Zhang
creator: Li Xu
creator: Na Li
creator: Xingguo Zhang
creator: Yu Pan
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7929
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
bibliographic citation: Hu et al. (2019) Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.). PeerJ 7:e7929 https://doi.org/10.7717/peerj.7929
date submitted: 2019-05-09
date accepted: 2019-09-20
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Xin
author list: Agent
  family name: Zhu
  given name: Lili
author list: Agent
  family name: Zhang
  given name: Yi
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Zhang
  given name: Xingguo
author list: Agent
  family name: Pan
  given name: Yu
doi: 10.7717/peerj.7929
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Hu et al.
attribution name: Hu et al.

Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
type: item
type: AcademicArticle
description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
format: application/pdf
format: text/html
creator: Siuli Mitra
creator: Vaishnavi Kunteepuram
creator: Klaus-Peter Koepfli
creator: Neha Mehra
creator: Wajeeda Tabasum
creator: Ara Sreenivas
creator: Ajay Gaur
subject: Conservation Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.8033
publisher: PeerJ Inc.
rights: © 2019 Mitra et al.
abstract: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
bibliographic citation: Mitra et al. (2019) Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications. PeerJ 7:e8033 https://doi.org/10.7717/peerj.8033
date submitted: 2019-02-07
date accepted: 2019-10-14
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitra
  given name: Siuli
author list: Agent
  family name: Kunteepuram
  given name: Vaishnavi
author list: Agent
  family name: Koepfli
  given name: Klaus-Peter
author list: Agent
  family name: Mehra
  given name: Neha
author list: Agent
  family name: Tabasum
  given name: Wajeeda
author list: Agent
  family name: Sreenivas
  given name: Ara
author list: Agent
  family name: Gaur
  given name: Ajay
doi: 10.7717/peerj.8033
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Mitra et al.
attribution name: Mitra et al.

Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
type: item
type: AcademicArticle
description: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number o…
format: application/pdf
format: text/html
creator: Neil S. Cobb
creator: Lawrence F. Gall
creator: Jennifer M. Zaspel
creator: Nicolas J. Dowdy
creator: Lindsie M. McCabe
creator: Akito Y. Kawahara
subject: Biodiversity
subject: Entomology
description: doi:10.7717/peerj.8086
publisher: PeerJ Inc.
rights: © 2019 Cobb et al.
abstract: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number o…
bibliographic citation: Cobb et al. (2019) Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 7:e8086 https://doi.org/10.7717/peerj.8086
date submitted: 2019-08-02
date accepted: 2019-10-23
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cobb
  given name: Neil S.
author list: Agent
  family name: Gall
  given name: Lawrence F.
author list: Agent
  family name: Zaspel
  given name: Jennifer M.
author list: Agent
  family name: Dowdy
  given name: Nicolas J.
author list: Agent
  family name: McCabe
  given name: Lindsie M.
author list: Agent
  family name: Kawahara
  given name: Akito Y.
doi: 10.7717/peerj.8086
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Cobb et al.
attribution name: Cobb et al.

Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
type: item
type: AcademicArticle
description: Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to susp…
format: application/pdf
format: text/html
creator: Eva Cuesta
creator: Jorge M. Lobo
subject: Biophysics
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.8104
publisher: PeerJ Inc.
rights: © 2019 Cuesta and Lobo
abstract: Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to susp…
bibliographic citation: Cuesta et al. (2019) Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference. PeerJ 7:e8104 https://doi.org/10.7717/peerj.8104
date submitted: 2019-06-14
date accepted: 2019-10-25
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuesta
  given name: Eva
author list: Agent
  family name: Lobo
  given name: Jorge M.
doi: 10.7717/peerj.8104
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: © 2019 Cuesta and Lobo
attribution name: Cuesta and Lobo

Familiarity with visual stimuli boosts recency bias in macaques
type: item
type: AcademicArticle
description: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
format: application/pdf
format: text/html
creator: Nicolas Brunet
creator: Bharathi Jagadeesh
subject: Animal Behavior
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8105
publisher: PeerJ Inc.
rights: © 2019 Brunet and Jagadeesh
abstract: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
bibliographic citation: Brunet et al. (2019) Familiarity with visual stimuli boosts recency bias in macaques. PeerJ 7:e8105 https://doi.org/10.7717/peerj.8105
date submitted: 2019-06-11
date accepted: 2019-10-26
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brunet
  given name: Nicolas
author list: Agent
  family name: Jagadeesh
  given name: Bharathi
doi: 10.7717/peerj.8105
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Brunet and Jagadeesh
attribution name: Brunet and Jagadeesh

Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry
type: item
type: AcademicArticle
description: Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
format: application/pdf
format: text/html
creator: Samir Meramo-Hurtado
creator: Kariana Moreno-Sader
creator: Ángel D. González-Delgado
subject: Green Chemistry
description: doi:10.7717/peerj.8113
publisher: PeerJ Inc.
rights: © 2019 Meramo-Hurtado et al.
abstract: Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
bibliographic citation: Meramo-Hurtado et al. (2019) Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry. PeerJ 7:e8113 https://doi.org/10.7717/peerj.8113
date submitted: 2019-05-21
date accepted: 2019-10-28
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meramo-Hurtado
  given name: Samir
author list: Agent
  family name: Moreno-Sader
  given name: Kariana
author list: Agent
  family name: González-Delgado
  given name: Ángel D.
doi: 10.7717/peerj.8113
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Meramo-Hurtado et al.
attribution name: Meramo-Hurtado et al.

Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns
type: item
type: AcademicArticle
description: Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than…
format: application/pdf
format: text/html
creator: Dana L.M. Campbell
creator: Emily J. Dickson
creator: Caroline Lee
subject: Agricultural Science
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.8122
publisher: PeerJ Inc.
rights: © 2019 Campbell et al.
abstract: Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than…
bibliographic citation: Campbell et al. (2019) Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns. PeerJ 7:e8122 https://doi.org/10.7717/peerj.8122
date submitted: 2019-09-04
date accepted: 2019-10-30
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campbell
  given name: Dana L.M.
author list: Agent
  family name: Dickson
  given name: Emily J.
author list: Agent
  family name: Lee
  given name: Caroline
doi: 10.7717/peerj.8122
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Campbell et al.
attribution name: Campbell et al.

Introducing a new tool to navigate, understand and use International Codes of Nomenclature
type: item
type: AcademicArticle
description: Background In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. Methods The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. Results The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. Discussion Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This …
format: application/pdf
format: text/html
creator: Evangelos Vlachos
subject: Taxonomy
subject: Zoology
subject: Computational Science
description: doi:10.7717/peerj.8127
publisher: PeerJ Inc.
rights: © 2019 Vlachos
abstract: Background In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. Methods The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. Results The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. Discussion Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This …
bibliographic citation: Vlachos (2019) Introducing a new tool to navigate, understand and use International Codes of Nomenclature. PeerJ 7:e8127 https://doi.org/10.7717/peerj.8127
date submitted: 2019-06-12
date accepted: 2019-10-30
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vlachos
  given name: Evangelos
doi: 10.7717/peerj.8127
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Vlachos
attribution name: Vlachos

Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction
type: item
type: AcademicArticle
description: Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.
format: application/pdf
format: text/html
creator: Kristina J.H. Kleinwort
creator: Stefanie M. Hauck
creator: Roxane L. Degroote
creator: Armin M. Scholz
creator: Christina Hölzel
creator: Erwin P. Maertlbauer
creator: Cornelia Deeg
subject: Food Science and Technology
subject: Microbiology
subject: Veterinary Medicine
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.8130
publisher: PeerJ Inc.
rights: © 2019 Kleinwort et al.
abstract: Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.
bibliographic citation: Kleinwort et al. (2019) Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction. PeerJ 7:e8130 https://doi.org/10.7717/peerj.8130
date submitted: 2019-08-14
date accepted: 2019-10-31
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kleinwort
  given name: Kristina J.H.
author list: Agent
  family name: Hauck
  given name: Stefanie M.
author list: Agent
  family name: Degroote
  given name: Roxane L.
author list: Agent
  family name: Scholz
  given name: Armin M.
author list: Agent
  family name: Hölzel
  given name: Christina
author list: Agent
  family name: Maertlbauer
  given name: Erwin P.
author list: Agent
  family name: Deeg
  given name: Cornelia
doi: 10.7717/peerj.8130
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: © 2019 Kleinwort et al.
attribution name: Kleinwort et al.

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