PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine
items: lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes
items: Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744
items: Revealing biases in the sampling of ecological interaction networks
items: Nutrient availability induces community shifts in seagrass meadows grazed by turtles
items: The reproductive system of the male and oviparous female of a model organism—the pea aphid, Acyrthosiphon pisum (Hemiptera, Aphididae)
items: Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions
items: Winter bird-window collisions: mitigation success, risk factors, and implementation challenges
items: Serine protease inhibitors and human wellbeing interplay: new insights for old friends
items: Post-fledging habitat use in a declining songbird

The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine
type: item
type: AcademicArticle
description: The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
format: application/pdf
format: text/html
creator: Douglass S. Rovinsky
creator: Alistair R. Evans
creator: Justin W. Adams
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.7457
publisher: PeerJ Inc.
rights: © 2019 Rovinsky et al.
abstract: The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
bibliographic citation: Rovinsky et al. (2019) The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine. PeerJ 7:e7457 https://doi.org/10.7717/peerj.7457
date submitted: 2019-03-27
date accepted: 2019-07-10
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rovinsky
  given name: Douglass S.
author list: Agent
  family name: Evans
  given name: Alistair R.
author list: Agent
  family name: Adams
  given name: Justin W.
doi: 10.7717/peerj.7457
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Rovinsky et al.
attribution name: Rovinsky et al.

lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes
type: item
type: AcademicArticle
description: Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.
format: application/pdf
format: text/html
creator: Haibin Zhang
creator: Cheng Chen
creator: Yinghong Cui
creator: Yuqing Li
creator: Zhaojun Wang
creator: Xinzhan Mao
creator: Pengcheng Dou
creator: Yihan Li
creator: Chi Ma
subject: Genetics
subject: Genomics
subject: Orthopedics
subject: Ethical Issues
description: doi:10.7717/peerj.7491
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.
bibliographic citation: Zhang et al. (2019) lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes. PeerJ 7:e7491 https://doi.org/10.7717/peerj.7491
date submitted: 2018-05-28
date accepted: 2019-07-16
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haibin
author list: Agent
  family name: Chen
  given name: Cheng
author list: Agent
  family name: Cui
  given name: Yinghong
author list: Agent
  family name: Li
  given name: Yuqing
author list: Agent
  family name: Wang
  given name: Zhaojun
author list: Agent
  family name: Mao
  given name: Xinzhan
author list: Agent
  family name: Dou
  given name: Pengcheng
author list: Agent
  family name: Li
  given name: Yihan
author list: Agent
  family name: Ma
  given name: Chi
doi: 10.7717/peerj.7491
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744
type: item
type: AcademicArticle
description: Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds.
format: application/pdf
format: text/html
creator: Krisztina Pesti
creator: Peter Lukacs
creator: Arpad Mike
subject: Biophysics
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.7542
publisher: PeerJ Inc.
rights: © 2019 Pesti et al.
abstract: Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds.
bibliographic citation: Pesti et al. (2019) Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744. PeerJ 7:e7542 https://doi.org/10.7717/peerj.7542
date submitted: 2019-03-05
date accepted: 2019-07-24
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pesti
  given name: Krisztina
author list: Agent
  family name: Lukacs
  given name: Peter
author list: Agent
  family name: Mike
  given name: Arpad
doi: 10.7717/peerj.7542
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: ©2019 Pesti et al.
attribution name: Pesti et al.

Revealing biases in the sampling of ecological interaction networks
type: item
type: AcademicArticle
description: The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling b…
format: application/pdf
format: text/html
creator: Marcus A.M. de Aguiar
creator: Erica A. Newman
creator: Mathias M. Pires
creator: Justin D. Yeakel
creator: Carl Boettiger
creator: Laura A. Burkle
creator: Dominique Gravel
creator: Paulo R. Guimarães
creator: James L. O’Donnell
creator: Timothée Poisot
creator: Marie-Josée Fortin
creator: David H. Hembry
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Mathematical Biology
subject: Data Science
description: doi:10.7717/peerj.7566
publisher: PeerJ Inc.
rights: © 2019 de Aguiar et al.
abstract: The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling b…
bibliographic citation: de Aguiar et al. (2019) Revealing biases in the sampling of ecological interaction networks. PeerJ 7:e7566 https://doi.org/10.7717/peerj.7566
date submitted: 2019-04-23
date accepted: 2019-07-29
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Aguiar
  given name: Marcus A.M.
author list: Agent
  family name: Newman
  given name: Erica A.
author list: Agent
  family name: Pires
  given name: Mathias M.
author list: Agent
  family name: Yeakel
  given name: Justin D.
author list: Agent
  family name: Boettiger
  given name: Carl
author list: Agent
  family name: Burkle
  given name: Laura A.
author list: Agent
  family name: Gravel
  given name: Dominique
author list: Agent
  family name: Guimarães
  given name: Paulo R.
author list: Agent
  family name: O’Donnell
  given name: James L.
author list: Agent
  family name: Poisot
  given name: Timothée
author list: Agent
  family name: Fortin
  given name: Marie-Josée
author list: Agent
  family name: Hembry
  given name: David H.
doi: 10.7717/peerj.7566
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 de Aguiar et al.
attribution name: de Aguiar et al.

Nutrient availability induces community shifts in seagrass meadows grazed by turtles
type: item
type: AcademicArticle
description: In the Caribbean, green turtles graze seagrass meadows dominated by Thalassia testudinum through rotational grazing, resulting in the creation of grazed and recovering (abandoned) patches surrounded by ungrazed seagrasses. We evaluated the seagrass community and its environment along a turtle grazing gradient; with the duration of (simulated) grazing as a proxy for the level of grazing pressure. The grazing levels consisted of Short-term (4 months clipping), Medium-term (8 months clipping), Long-term grazing (8 months of clipping in previously grazed areas), 8-months recovery of previously grazed patches, and ungrazed or unclipped patches as controls. We measured biomass and density of the seagrasses and rhizophytic algae, and changes in sediment parameters. Medium- and Long-term grazing promoted a shift in community species composition. At increasing grazing pressure, the total biomass of T. testudinum declined, whereas that of early-successional increased. Ammonium concentrations were highest in the patches of Medium-term (9.2 + 0.8 μM) and Long-term grazing levels (11.0 + 2.2 μM) and were lowest in the control areas (4.6 + 1.5 μM). T. testudinum is a late-successional species that maintains sediment nutrient concentrations at levels below the requirements of early-successional species when dominant. When the abundance of this species declines due to grazing, these resources become available, likely driving a shift in community composition toward a higher abundance of early-successional species.
format: application/pdf
format: text/html
creator: Isis Gabriela Martínez López
creator: Marloes van Den Akker
creator: Liene Walk
creator: Marieke M. van Katwijk
creator: Tjisse van Der Heide
creator: Brigitta I. van Tussenbroek
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.7570
publisher: PeerJ Inc.
rights: © 2019 Martínez López et al.
abstract: In the Caribbean, green turtles graze seagrass meadows dominated by Thalassia testudinum through rotational grazing, resulting in the creation of grazed and recovering (abandoned) patches surrounded by ungrazed seagrasses. We evaluated the seagrass community and its environment along a turtle grazing gradient; with the duration of (simulated) grazing as a proxy for the level of grazing pressure. The grazing levels consisted of Short-term (4 months clipping), Medium-term (8 months clipping), Long-term grazing (8 months of clipping in previously grazed areas), 8-months recovery of previously grazed patches, and ungrazed or unclipped patches as controls. We measured biomass and density of the seagrasses and rhizophytic algae, and changes in sediment parameters. Medium- and Long-term grazing promoted a shift in community species composition. At increasing grazing pressure, the total biomass of T. testudinum declined, whereas that of early-successional increased. Ammonium concentrations were highest in the patches of Medium-term (9.2 + 0.8 μM) and Long-term grazing levels (11.0 + 2.2 μM) and were lowest in the control areas (4.6 + 1.5 μM). T. testudinum is a late-successional species that maintains sediment nutrient concentrations at levels below the requirements of early-successional species when dominant. When the abundance of this species declines due to grazing, these resources become available, likely driving a shift in community composition toward a higher abundance of early-successional species.
bibliographic citation: Martínez López et al. (2019) Nutrient availability induces community shifts in seagrass meadows grazed by turtles. PeerJ 7:e7570 https://doi.org/10.7717/peerj.7570
date submitted: 2019-04-04
date accepted: 2019-07-29
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez López
  given name: Isis Gabriela
author list: Agent
  family name: van Den Akker
  given name: Marloes
author list: Agent
  family name: Walk
  given name: Liene
author list: Agent
  family name: van Katwijk
  given name: Marieke M.
author list: Agent
  family name: van Der Heide
  given name: Tjisse
author list: Agent
  family name: van Tussenbroek
  given name: Brigitta I.
doi: 10.7717/peerj.7570
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Martínez López et al.
attribution name: Martínez López et al.

The reproductive system of the male and oviparous female of a model organism—the pea aphid, Acyrthosiphon pisum (Hemiptera, Aphididae)
type: item
type: AcademicArticle
description: The structure of the reproductive system of the sexual generation—males and oviparous females—of the pea aphid Acyrthosiphon pisum (Harris) (Hemiptera, Aphididae), a serious pest of cultivated plants of Fabaceae, was investigated. For the first time we describe the morphology, histology and ultrastructure of the reproductive system in both morphs of the sexual generation of aphids within one species, using light and fluorescent microscopy, as well as transmission and scanning electron microscopy. The results revealed that males have testes composed of three follicles fused by the upper ends of the vasa efferentia, the vasa deferentia run independently, the accessory glands are asymmetric and the ejaculatory duct shortened. Oviparous females have ovaries composed of seven ovarioles each. The lateral oviducts join to a short common oviduct connected with the unpaired spermatheca and paired accessory glands. Yolky eggs with an aggregation of symbiotic bacteria at the posterior pole are produced. Histologically, the components of genital tracts are broadly similar: the epithelial cells of the walls of the vasa deferentia and accessory glands of the male and oviparous female have secretory functions which correlate with the age of the studied morphs. We also found symbiotic bacteria within the vasa deferentia epithelial cells in males and within the cells of the lateral oviducts of females. Because the pea aphid is listed among the 14 species that are of the greatest economic importance, our results will be useful for managing aphid populations, protecting plants and ensuring global food security.
format: application/pdf
format: text/html
creator: Karina Wieczorek
creator: Mariusz Kanturski
creator: Cezary Sempruch
creator: Piotr Świątek
subject: Agricultural Science
subject: Entomology
subject: Histology
description: doi:10.7717/peerj.7573
publisher: PeerJ Inc.
rights: © 2019 Wieczorek et al.
abstract: The structure of the reproductive system of the sexual generation—males and oviparous females—of the pea aphid Acyrthosiphon pisum (Harris) (Hemiptera, Aphididae), a serious pest of cultivated plants of Fabaceae, was investigated. For the first time we describe the morphology, histology and ultrastructure of the reproductive system in both morphs of the sexual generation of aphids within one species, using light and fluorescent microscopy, as well as transmission and scanning electron microscopy. The results revealed that males have testes composed of three follicles fused by the upper ends of the vasa efferentia, the vasa deferentia run independently, the accessory glands are asymmetric and the ejaculatory duct shortened. Oviparous females have ovaries composed of seven ovarioles each. The lateral oviducts join to a short common oviduct connected with the unpaired spermatheca and paired accessory glands. Yolky eggs with an aggregation of symbiotic bacteria at the posterior pole are produced. Histologically, the components of genital tracts are broadly similar: the epithelial cells of the walls of the vasa deferentia and accessory glands of the male and oviparous female have secretory functions which correlate with the age of the studied morphs. We also found symbiotic bacteria within the vasa deferentia epithelial cells in males and within the cells of the lateral oviducts of females. Because the pea aphid is listed among the 14 species that are of the greatest economic importance, our results will be useful for managing aphid populations, protecting plants and ensuring global food security.
bibliographic citation: Wieczorek et al. (2019) The reproductive system of the male and oviparous female of a model organism—the pea aphid, Acyrthosiphon pisum (Hemiptera, Aphididae). PeerJ 7:e7573 https://doi.org/10.7717/peerj.7573
date submitted: 2019-04-18
date accepted: 2019-07-29
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wieczorek
  given name: Karina
author list: Agent
  family name: Kanturski
  given name: Mariusz
author list: Agent
  family name: Sempruch
  given name: Cezary
author list: Agent
  family name: Świątek
  given name: Piotr
doi: 10.7717/peerj.7573
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Wieczorek et al.
attribution name: Wieczorek et al.

Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions
type: item
type: AcademicArticle
description: Zooplankton exported from lentic systems provision lotic systems with easily captured, consumed, and assimilated prey items. Previous studies have demonstrated that the community composition of zooplankton exports (CCZE) vary over time, which introduces temporal differences in lotic resource availability (zooplankton prey) in downstream habitats. In the study presented here, we monitored variation in CCZE from a polymictic reservoir outfall in response to physical–chemical and atmospheric conditions bi-hourly over three different 24-h periods. Community composition of zooplankton export varied over the course of the day, and exports were most closely associated with wind directionality. Future studies of temporal variation in CCZE should incorporate wind conditions, especially in shallow systems where holomixis occurs frequently. Polymictic reservoirs are becoming increasingly common as the global pace of small dam construction quickens, making both the identification of factors influencing CCZE and the impact of zooplankton exports on local biodiversity and ecosystem function increasingly important to understand.
format: application/pdf
format: text/html
creator: Nathan Ruhl
creator: Desireé Haban
creator: Caitlyn Czajkowski
creator: Michael Grove
creator: Courtney E. Richmond
subject: Ecology
subject: Ecosystem Science
subject: Freshwater Biology
description: doi:10.7717/peerj.7611
publisher: PeerJ Inc.
rights: © 2019 Ruhl et al.
abstract: Zooplankton exported from lentic systems provision lotic systems with easily captured, consumed, and assimilated prey items. Previous studies have demonstrated that the community composition of zooplankton exports (CCZE) vary over time, which introduces temporal differences in lotic resource availability (zooplankton prey) in downstream habitats. In the study presented here, we monitored variation in CCZE from a polymictic reservoir outfall in response to physical–chemical and atmospheric conditions bi-hourly over three different 24-h periods. Community composition of zooplankton export varied over the course of the day, and exports were most closely associated with wind directionality. Future studies of temporal variation in CCZE should incorporate wind conditions, especially in shallow systems where holomixis occurs frequently. Polymictic reservoirs are becoming increasingly common as the global pace of small dam construction quickens, making both the identification of factors influencing CCZE and the impact of zooplankton exports on local biodiversity and ecosystem function increasingly important to understand.
bibliographic citation: Ruhl et al. (2019) Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions. PeerJ 7:e7611 https://doi.org/10.7717/peerj.7611
date submitted: 2019-04-24
date accepted: 2019-08-05
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruhl
  given name: Nathan
author list: Agent
  family name: Haban
  given name: Desireé
author list: Agent
  family name: Czajkowski
  given name: Caitlyn
author list: Agent
  family name: Grove
  given name: Michael
author list: Agent
  family name: Richmond
  given name: Courtney E.
doi: 10.7717/peerj.7611
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Ruhl et al.
attribution name: Ruhl et al.

Winter bird-window collisions: mitigation success, risk factors, and implementation challenges
type: item
type: AcademicArticle
description: Millions of birds die in bird-window collisions in the United States each year. In specialized test settings, researchers have developed methods to alter window designs to mitigate collisions. However, few published studies provide pretest and posttest evaluations of mitigation treatment areas and untreated control areas on existing buildings. We initially monitored bird-window collisions at a single building on the University of Utah campus in Salt Lake City, Utah, USA, during winter 1 (November 9, 2017–January 2, 2018). We found 15 bird-window collisions, most under a portion of the building with a mirrored façade. To test a mitigation treatment, we installed Feather Friendly® bird deterrent film on part of the mirrored façade after winter 1. The unmitigated areas of the same building served as a control area. We continued monitoring during the following winter 2 (November 15, 2018–January 12, 2019). The treated area collisions declined from seven before mitigation to two after mitigation, a 71% reduction. The control area had eight collisions at both times. Results of a generalized estimating equation yielded a significant area by season interaction effect (p = 0.03) and fewer collisions in the mitigated area than the control area at winter 2 (p = 0.03), supporting efficacy of the mitigation. In winter 2 we also expanded monitoring to eight total buildings to evaluate the risks of mirrored windows and proximity to fruiting pear trees (Prunus calleryana) and the benefits of bird-friendly glass. Bird-friendly glass, found on two buildings, included windows with permanent fritted dots or embedded ultraviolet patterns. We counted 22 collisions across the eight buildings. Mirrored windows and proximity to fruiting pear trees related to higher odds of bird-window collisions, based on separate generalized estimating equations. The best fit model included mirrored windows and pear trees. The two buildings with bird-friendly glass had only one collision, suggesting that t…
format: application/pdf
format: text/html
creator: Barbara B. Brown
creator: Erika Kusakabe
creator: Angelo Antonopoulos
creator: Sarah Siddoway
creator: Lisa Thompson
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.7620
publisher: PeerJ Inc.
rights: © 2019 Brown et al.
abstract: Millions of birds die in bird-window collisions in the United States each year. In specialized test settings, researchers have developed methods to alter window designs to mitigate collisions. However, few published studies provide pretest and posttest evaluations of mitigation treatment areas and untreated control areas on existing buildings. We initially monitored bird-window collisions at a single building on the University of Utah campus in Salt Lake City, Utah, USA, during winter 1 (November 9, 2017–January 2, 2018). We found 15 bird-window collisions, most under a portion of the building with a mirrored façade. To test a mitigation treatment, we installed Feather Friendly® bird deterrent film on part of the mirrored façade after winter 1. The unmitigated areas of the same building served as a control area. We continued monitoring during the following winter 2 (November 15, 2018–January 12, 2019). The treated area collisions declined from seven before mitigation to two after mitigation, a 71% reduction. The control area had eight collisions at both times. Results of a generalized estimating equation yielded a significant area by season interaction effect (p = 0.03) and fewer collisions in the mitigated area than the control area at winter 2 (p = 0.03), supporting efficacy of the mitigation. In winter 2 we also expanded monitoring to eight total buildings to evaluate the risks of mirrored windows and proximity to fruiting pear trees (Prunus calleryana) and the benefits of bird-friendly glass. Bird-friendly glass, found on two buildings, included windows with permanent fritted dots or embedded ultraviolet patterns. We counted 22 collisions across the eight buildings. Mirrored windows and proximity to fruiting pear trees related to higher odds of bird-window collisions, based on separate generalized estimating equations. The best fit model included mirrored windows and pear trees. The two buildings with bird-friendly glass had only one collision, suggesting that t…
bibliographic citation: Brown et al. (2019) Winter bird-window collisions: mitigation success, risk factors, and implementation challenges. PeerJ 7:e7620 https://doi.org/10.7717/peerj.7620
date submitted: 2019-05-10
date accepted: 2019-08-05
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Barbara B.
author list: Agent
  family name: Kusakabe
  given name: Erika
author list: Agent
  family name: Antonopoulos
  given name: Angelo
author list: Agent
  family name: Siddoway
  given name: Sarah
author list: Agent
  family name: Thompson
  given name: Lisa
doi: 10.7717/peerj.7620
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: ©2019 Brown et al.
attribution name: Brown et al.

Serine protease inhibitors and human wellbeing interplay: new insights for old friends
type: item
type: AcademicArticle
description: Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches.
format: application/pdf
format: text/html
creator: Héla Mkaouar
creator: Nizar Akermi
creator: Aicha Kriaa
creator: Anne-Laure Abraham
creator: Amin Jablaoui
creator: Souha Soussou
creator: Raja Mokdad-Gargouri
creator: Emmanuelle Maguin
creator: Moez Rhimi
subject: Microbiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.7224
publisher: PeerJ Inc.
rights: © 2019 Mkaouar et al.
abstract: Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches.
bibliographic citation: Mkaouar et al. (2019) Serine protease inhibitors and human wellbeing interplay: new insights for old friends. PeerJ 7:e7224 https://doi.org/10.7717/peerj.7224
date submitted: 2019-04-17
date accepted: 2019-05-31
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mkaouar
  given name: Héla
author list: Agent
  family name: Akermi
  given name: Nizar
author list: Agent
  family name: Kriaa
  given name: Aicha
author list: Agent
  family name: Abraham
  given name: Anne-Laure
author list: Agent
  family name: Jablaoui
  given name: Amin
author list: Agent
  family name: Soussou
  given name: Souha
author list: Agent
  family name: Mokdad-Gargouri
  given name: Raja
author list: Agent
  family name: Maguin
  given name: Emmanuelle
author list: Agent
  family name: Rhimi
  given name: Moez
doi: 10.7717/peerj.7224
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Mkaouar et al.
attribution name: Mkaouar et al.

Post-fledging habitat use in a declining songbird
type: item
type: AcademicArticle
description: Background Fledglings of many mature forest-dependent Neotropical songbirds move from mature forest habitats into areas of thick vegetation such as regenerating clearcuts. The Cerulean Warbler (Setophaga cerulea), a Neotropical migratory songbird, is a species of conservation concern across its range and it is listed as endangered in Indiana. This species has declined faster than any other species of wood-warbler in North America. Most prior research on Cerulean Warblers has examined the breeding biology, but there are no data on habitat use by fledgling Cerulean Warblers. Our research aimed to determine where fledgling Cerulean Warblers dispersed after they left their nest, but before they migrated to their wintering grounds. Methods Since 2007, Cerulean Warbler breeding populations have been monitored in Yellowwood and Morgan–Monroe state forests in southern Indiana as part of a 100-year study called the Hardwood Ecosystem Experiment. To identify habitats used by fledgling Cerulean Warblers, we captured by hand or mist-nets, adult and juvenile Cerulean Warblers once young had fledged from a nest. We attached radio-transmitters to individuals and tracked each bird daily using radio-telemetry. Radio-telemetry data were collected from May to July 2015–2017, and microhabitat data on fledgling locations and random locations were collected during the same years in the month of July. Results Fledgling presence, when compared to random non-use sites, was positively correlated to presence of grapevines, greater vertical vegetation density, and greater ground and canopy cover. Fledgling presence was negatively correlated with white oak abundance, aspect, basal area, and the abundance of mature trees that Cerulean Warbler adults use for nesting. Conclusions Our study is the first to demonstrate that Cerulean Warbler fledglings occupy habitats that are characterized by specific habitat components. Fledgling sites were located in areas with high vegetation density, such as clu…
format: application/pdf
format: text/html
creator: Clayton D. Delancey
creator: Kamal Islam
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7358
publisher: PeerJ Inc.
rights: © 2019 Delancey and Islam
abstract: Background Fledglings of many mature forest-dependent Neotropical songbirds move from mature forest habitats into areas of thick vegetation such as regenerating clearcuts. The Cerulean Warbler (Setophaga cerulea), a Neotropical migratory songbird, is a species of conservation concern across its range and it is listed as endangered in Indiana. This species has declined faster than any other species of wood-warbler in North America. Most prior research on Cerulean Warblers has examined the breeding biology, but there are no data on habitat use by fledgling Cerulean Warblers. Our research aimed to determine where fledgling Cerulean Warblers dispersed after they left their nest, but before they migrated to their wintering grounds. Methods Since 2007, Cerulean Warbler breeding populations have been monitored in Yellowwood and Morgan–Monroe state forests in southern Indiana as part of a 100-year study called the Hardwood Ecosystem Experiment. To identify habitats used by fledgling Cerulean Warblers, we captured by hand or mist-nets, adult and juvenile Cerulean Warblers once young had fledged from a nest. We attached radio-transmitters to individuals and tracked each bird daily using radio-telemetry. Radio-telemetry data were collected from May to July 2015–2017, and microhabitat data on fledgling locations and random locations were collected during the same years in the month of July. Results Fledgling presence, when compared to random non-use sites, was positively correlated to presence of grapevines, greater vertical vegetation density, and greater ground and canopy cover. Fledgling presence was negatively correlated with white oak abundance, aspect, basal area, and the abundance of mature trees that Cerulean Warbler adults use for nesting. Conclusions Our study is the first to demonstrate that Cerulean Warbler fledglings occupy habitats that are characterized by specific habitat components. Fledgling sites were located in areas with high vegetation density, such as clu…
bibliographic citation: Delancey et al. (2019) Post-fledging habitat use in a declining songbird. PeerJ 7:e7358 https://doi.org/10.7717/peerj.7358
date submitted: 2019-02-13
date accepted: 2019-06-26
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delancey
  given name: Clayton D.
author list: Agent
  family name: Islam
  given name: Kamal
doi: 10.7717/peerj.7358
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Delancey and Islam
attribution name: Delancey and Islam

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