PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012–2015
items: Unravelling the ontogeny of a Devonian early gnathostome, the “acanthodian” Triazeugacanthus affinis (eastern Canada)
items: Immunofluorescence characterization of spinal cord dorsal horn microglia and astrocytes in horses
items: Genome-wide identification and expression profile analysis of CCH gene family in Populus
items: New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae)
items: Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
items: Inferring microevolution from museum collections and resampling: lessons learned from Cepaea
items: Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies
items: Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity
items: Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides

Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012–2015
type: item
type: AcademicArticle
description: Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants and young children worldwide. To investigate the RSV burden in Thailand over four consecutive years (January 2012 to December 2015), we screened 3,306 samples obtained from children ≤5 years old with acute respiratory tract infection using semi-nested reverse-transcription polymerase chain reaction (RT-PCR). In all, 8.4% (277/3,306) of the specimens tested positive for RSV, most of which appeared in the rainy months of July to November. We then genotyped RSV by sequencing the G glycoprotein gene and performed phylogenetic analysis to determine the RSV antigenic subgroup. The majority (57.4%, 159/277) of the RSV belonged to subgroup A (RSV-A), of which NA1 genotype was the most common in 2012 while ON1 genotype became prevalent the following year. Among samples tested positive for RSV-B subgroup B (RSV-B) (42.6%, 118/277), most were genotype BA9 (92.6%, 87/94) with some BA10 and BA-C. Predicted amino acid sequence from the partial G region showed highly conserved N-linked glycosylation site at residue N237 among all RSV-A ON1 strains (68/68), and at residues N296 (86/87) and N310 (87/87) among RSV-B BA9 strains. Positive selection of key residues combined with notable sequence variations on the G gene contributed to the continued circulation of this rapidly evolving virus.
format: application/pdf
format: text/html
creator: Ilada Thongpan
creator: John Mauleekoonphairoj
creator: Preeyaporn Vichiwattana
creator: Sumeth Korkong
creator: Rujipat Wasitthankasem
creator: Sompong Vongpunsawad
creator: Yong Poovorawan
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.3970
publisher: PeerJ Inc.
rights: © 2017 Thongpan et al.
abstract: Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants and young children worldwide. To investigate the RSV burden in Thailand over four consecutive years (January 2012 to December 2015), we screened 3,306 samples obtained from children ≤5 years old with acute respiratory tract infection using semi-nested reverse-transcription polymerase chain reaction (RT-PCR). In all, 8.4% (277/3,306) of the specimens tested positive for RSV, most of which appeared in the rainy months of July to November. We then genotyped RSV by sequencing the G glycoprotein gene and performed phylogenetic analysis to determine the RSV antigenic subgroup. The majority (57.4%, 159/277) of the RSV belonged to subgroup A (RSV-A), of which NA1 genotype was the most common in 2012 while ON1 genotype became prevalent the following year. Among samples tested positive for RSV-B subgroup B (RSV-B) (42.6%, 118/277), most were genotype BA9 (92.6%, 87/94) with some BA10 and BA-C. Predicted amino acid sequence from the partial G region showed highly conserved N-linked glycosylation site at residue N237 among all RSV-A ON1 strains (68/68), and at residues N296 (86/87) and N310 (87/87) among RSV-B BA9 strains. Positive selection of key residues combined with notable sequence variations on the G gene contributed to the continued circulation of this rapidly evolving virus.
bibliographic citation: Thongpan et al. (2017) Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012–2015. PeerJ 5:e3970 https://doi.org/10.7717/peerj.3970
date submitted: 2017-08-18
date accepted: 2017-10-09
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thongpan
  given name: Ilada
author list: Agent
  family name: Mauleekoonphairoj
  given name: John
author list: Agent
  family name: Vichiwattana
  given name: Preeyaporn
author list: Agent
  family name: Korkong
  given name: Sumeth
author list: Agent
  family name: Wasitthankasem
  given name: Rujipat
author list: Agent
  family name: Vongpunsawad
  given name: Sompong
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.3970
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Thongpan et al.
attribution name: Thongpan et al.

Unravelling the ontogeny of a Devonian early gnathostome, the “acanthodian” Triazeugacanthus affinis (eastern Canada)
type: item
type: AcademicArticle
description: The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian “acanthodian” Triazeugacanthus affinis, from the Miguasha Fossil-Fish Lagerstätte, is identified as one of the best known early vertebrate fossilised ontogenies given the exceptional preservation, the large size range, and the abundance of specimens. Morphological, morphometric, histological and chemical data are gathered on a growth series of Triazeugacanthus ranging from 4 to 52 mm in total length. The developmental trajectory of this Devonian “acanthodian” is characteristic of fishes showing a direct development with alternating steps and thresholds. Larvae show no squamation but a progressive appearance of cartilaginous neurocranial and vertebral elements, and appendicular elements, whereas juveniles progress in terms of ossification and squamation. The presence of cartilaginous and bony tissues, discriminated on histological and chemical signatures, shows a progressive mineralisation of neurocranial and vertebral elements. Comparison among different body proportions for larvae, juveniles and adults suggest allometric growth in juveniles. Because of the phylogenetic position of “acanthodians”, Triazeugacanthus ontogeny informs us about deep time developmental conditions in gnathostomes.
format: application/pdf
format: text/html
creator: Marion Chevrinais
creator: Jean-Yves Sire
creator: Richard Cloutier
subject: Developmental Biology
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.3969
publisher: PeerJ Inc.
rights: © 2017 Chevrinais et al.
abstract: The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian “acanthodian” Triazeugacanthus affinis, from the Miguasha Fossil-Fish Lagerstätte, is identified as one of the best known early vertebrate fossilised ontogenies given the exceptional preservation, the large size range, and the abundance of specimens. Morphological, morphometric, histological and chemical data are gathered on a growth series of Triazeugacanthus ranging from 4 to 52 mm in total length. The developmental trajectory of this Devonian “acanthodian” is characteristic of fishes showing a direct development with alternating steps and thresholds. Larvae show no squamation but a progressive appearance of cartilaginous neurocranial and vertebral elements, and appendicular elements, whereas juveniles progress in terms of ossification and squamation. The presence of cartilaginous and bony tissues, discriminated on histological and chemical signatures, shows a progressive mineralisation of neurocranial and vertebral elements. Comparison among different body proportions for larvae, juveniles and adults suggest allometric growth in juveniles. Because of the phylogenetic position of “acanthodians”, Triazeugacanthus ontogeny informs us about deep time developmental conditions in gnathostomes.
bibliographic citation: Chevrinais et al. (2017) Unravelling the ontogeny of a Devonian early gnathostome, the “acanthodian” Triazeugacanthus affinis (eastern Canada). PeerJ 5:e3969 https://doi.org/10.7717/peerj.3969
date submitted: 2017-08-01
date accepted: 2017-10-08
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chevrinais
  given name: Marion
author list: Agent
  family name: Sire
  given name: Jean-Yves
author list: Agent
  family name: Cloutier
  given name: Richard
doi: 10.7717/peerj.3969
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Chevrinais et al.
attribution name: Chevrinais et al.

Immunofluorescence characterization of spinal cord dorsal horn microglia and astrocytes in horses
type: item
type: AcademicArticle
description: The role of glial cells in pain modulation has recently gathered attention. The objective of this study was to determine healthy spinal microglia and astrocyte morphology and disposition in equine spinal cord dorsal horns using Iba-1 and GFAP/Cx-43 immunofluorescence labeling, respectively. Five adult horses without visible wounds or gait alterations were selected. Spinal cord segments were obtained post-mortem for immunohistochemical and immunocolocalization assays. Immunodetection of spinal cord dorsal horn astrocytes was done using a polyclonal goat antibody raised against Glial Fibrillary Acidic Protein (GFAP) and a polyclonal rabbit antibody against Connexin 43 (Cx-43). For immunodetection of spinal cord dorsal horn microglia, a polyclonal rabbit antibody against a synthetic peptide corresponding to the C-terminus of ionized calcium-binding adaptor molecule 1 (Iba-1) was used. Epifluorescence and confocal images were obtained for the morphological and organizational analysis. Evaluation of shape, area, cell diameter, cell process length and thickness was performed on dorsal horn microglia and astrocyte. Morphologically, an amoeboid spherical shape with a mean cell area of 92.4 + 34 µm2 (in lamina I, II and III) was found in horse microglial cells, located primarily in laminae I, II and III. Astrocyte primary stem branches (and cellular bodies to a much lesser extent) are mainly detected using GFAP. Thus, double GFAP/Cx-43 immunolabeling was needed in order to accurately characterize the morphology, dimension and cell density of astrocytes in horses. Horse and rodent astrocytes seem to have similar dimensions and localization. Horse astrocyte cells have an average diameter of 56 + 14 µm, with a main process length of 28 + 8 µm, and thickness of 1.4 + 0.3 µm, mainly situated in laminae I, II and III. Additionally, a close association between end-point astrocyte processes and microglial cell bodies was found. These results are the first characterization of cell mo…
format: application/pdf
format: text/html
creator: Constanza Stefania Meneses
creator: Heine Yacob Müller
creator: Daniel Eduardo Herzberg
creator: Benjamín Uberti
creator: Hedie Almagro Bustamante
creator: Marianne Patricia Werner
subject: Anesthesiology and Pain Management
subject: Molecular Biology
subject: Neuroscience
subject: Veterinary Medicine
description: doi:10.7717/peerj.3965
publisher: PeerJ Inc.
rights: © 2017 Meneses et al.
abstract: The role of glial cells in pain modulation has recently gathered attention. The objective of this study was to determine healthy spinal microglia and astrocyte morphology and disposition in equine spinal cord dorsal horns using Iba-1 and GFAP/Cx-43 immunofluorescence labeling, respectively. Five adult horses without visible wounds or gait alterations were selected. Spinal cord segments were obtained post-mortem for immunohistochemical and immunocolocalization assays. Immunodetection of spinal cord dorsal horn astrocytes was done using a polyclonal goat antibody raised against Glial Fibrillary Acidic Protein (GFAP) and a polyclonal rabbit antibody against Connexin 43 (Cx-43). For immunodetection of spinal cord dorsal horn microglia, a polyclonal rabbit antibody against a synthetic peptide corresponding to the C-terminus of ionized calcium-binding adaptor molecule 1 (Iba-1) was used. Epifluorescence and confocal images were obtained for the morphological and organizational analysis. Evaluation of shape, area, cell diameter, cell process length and thickness was performed on dorsal horn microglia and astrocyte. Morphologically, an amoeboid spherical shape with a mean cell area of 92.4 + 34 µm2 (in lamina I, II and III) was found in horse microglial cells, located primarily in laminae I, II and III. Astrocyte primary stem branches (and cellular bodies to a much lesser extent) are mainly detected using GFAP. Thus, double GFAP/Cx-43 immunolabeling was needed in order to accurately characterize the morphology, dimension and cell density of astrocytes in horses. Horse and rodent astrocytes seem to have similar dimensions and localization. Horse astrocyte cells have an average diameter of 56 + 14 µm, with a main process length of 28 + 8 µm, and thickness of 1.4 + 0.3 µm, mainly situated in laminae I, II and III. Additionally, a close association between end-point astrocyte processes and microglial cell bodies was found. These results are the first characterization of cell mo…
bibliographic citation: Meneses et al. (2017) Immunofluorescence characterization of spinal cord dorsal horn microglia and astrocytes in horses. PeerJ 5:e3965 https://doi.org/10.7717/peerj.3965
date submitted: 2017-06-29
date accepted: 2017-10-06
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meneses
  given name: Constanza Stefania
author list: Agent
  family name: Müller
  given name: Heine Yacob
author list: Agent
  family name: Herzberg
  given name: Daniel Eduardo
author list: Agent
  family name: Uberti
  given name: Benjamín
author list: Agent
  family name: Bustamante
  given name: Hedie Almagro
author list: Agent
  family name: Werner
  given name: Marianne Patricia
doi: 10.7717/peerj.3965
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Meneses et al.
attribution name: Meneses et al.

Genome-wide identification and expression profile analysis of CCH gene family in Populus
type: item
type: AcademicArticle
description: Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.
format: application/pdf
format: text/html
creator: Zhiru Xu
creator: Liying Gao
creator: Mengquan Tang
creator: Chunpu Qu
creator: Jiahuan Huang
creator: Qi Wang
creator: Chuanping Yang
creator: Guanjun Liu
creator: Chengjun Yang
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3962
publisher: PeerJ Inc.
rights: © 2017 Xu et al.
abstract: Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.
bibliographic citation: Xu et al. (2017) Genome-wide identification and expression profile analysis of CCH gene family in Populus. PeerJ 5:e3962 https://doi.org/10.7717/peerj.3962
date submitted: 2017-07-24
date accepted: 2017-10-05
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Zhiru
author list: Agent
  family name: Gao
  given name: Liying
author list: Agent
  family name: Tang
  given name: Mengquan
author list: Agent
  family name: Qu
  given name: Chunpu
author list: Agent
  family name: Huang
  given name: Jiahuan
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Yang
  given name: Chuanping
author list: Agent
  family name: Liu
  given name: Guanjun
author list: Agent
  family name: Yang
  given name: Chengjun
doi: 10.7717/peerj.3962
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Xu et al.
attribution name: Xu et al.

New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae)
type: item
type: AcademicArticle
description: Two new species of the caddisfly genus Cernotina Ross, 1938 (Polycentropodidae) are described from the lowland Amazon basin of Ecuador, Cernotina tiputini, new species, and Cernotina waorani, new species. These represent the first new species described from this region. We also record from Ecuador for the first time Cernotina hastilis Flint, previously known from Tobago, and present new Ecuadorian locality records for C. cygnea Flint, and C. lobisomem Santos & Nessimian. The homology of the intermediate appendage of the male genitalia of this genus is established. The region surveyed is under severe environmental threat from logging, mining, and crude oil extraction, making the description of the biodiversity of the region imperative.
format: application/pdf
format: text/html
creator: Lucas M. Camargos
creator: Blanca Ríos-Touma
creator: Ralph W. Holzenthal
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.3960
publisher: PeerJ Inc.
rights: © 2017 Camargos et al.
abstract: Two new species of the caddisfly genus Cernotina Ross, 1938 (Polycentropodidae) are described from the lowland Amazon basin of Ecuador, Cernotina tiputini, new species, and Cernotina waorani, new species. These represent the first new species described from this region. We also record from Ecuador for the first time Cernotina hastilis Flint, previously known from Tobago, and present new Ecuadorian locality records for C. cygnea Flint, and C. lobisomem Santos & Nessimian. The homology of the intermediate appendage of the male genitalia of this genus is established. The region surveyed is under severe environmental threat from logging, mining, and crude oil extraction, making the description of the biodiversity of the region imperative.
bibliographic citation: Camargos et al. (2017) New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae). PeerJ 5:e3960 https://doi.org/10.7717/peerj.3960
date submitted: 2017-08-29
date accepted: 2017-10-05
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Camargos
  given name: Lucas M.
author list: Agent
  family name: Ríos-Touma
  given name: Blanca
author list: Agent
  family name: Holzenthal
  given name: Ralph W.
doi: 10.7717/peerj.3960
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Camargos et al.
attribution name: Camargos et al.

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
type: item
type: AcademicArticle
description: Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.
format: application/pdf
format: text/html
creator: Ara S. Winter
creator: Jennifer J.M. Hathaway
creator: Jason C. Kimble
creator: Debbie C. Buecher
creator: Ernest W. Valdez
creator: Andrea Porras-Alfaro
creator: Jesse M. Young
creator: Kaitlyn J.H. Read
creator: Diana E. Northup
subject: Biogeography
subject: Bioinformatics
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.3944
publisher: PeerJ Inc.
rights: © 2017
abstract: Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.
bibliographic citation: Winter et al. (2017) Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits. PeerJ 5:e3944 https://doi.org/10.7717/peerj.3944
date submitted: 2016-10-10
date accepted: 2017-09-28
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Winter
  given name: Ara S.
author list: Agent
  family name: Hathaway
  given name: Jennifer J.M.
author list: Agent
  family name: Kimble
  given name: Jason C.
author list: Agent
  family name: Buecher
  given name: Debbie C.
author list: Agent
  family name: Valdez
  given name: Ernest W.
author list: Agent
  family name: Porras-Alfaro
  given name: Andrea
author list: Agent
  family name: Young
  given name: Jesse M.
author list: Agent
  family name: Read
  given name: Kaitlyn J.H.
author list: Agent
  family name: Northup
  given name: Diana E.
doi: 10.7717/peerj.3944
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27

Inferring microevolution from museum collections and resampling: lessons learned from Cepaea
type: item
type: AcademicArticle
description: Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.
format: application/pdf
format: text/html
creator: Małgorzata Ożgo
creator: Thor-Seng Liew
creator: Nicole B. Webster
creator: Menno Schilthuizen
subject: Environmental Impacts
subject: Environmental Sciences
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3938
publisher: PeerJ Inc.
rights: © 2017 Ożgo et al.
abstract: Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.
bibliographic citation: Ożgo et al. (2017) Inferring microevolution from museum collections and resampling: lessons learned from Cepaea. PeerJ 5:e3938 https://doi.org/10.7717/peerj.3938
date submitted: 2016-07-19
date accepted: 2017-09-26
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ożgo
  given name: Małgorzata
author list: Agent
  family name: Liew
  given name: Thor-Seng
author list: Agent
  family name: Webster
  given name: Nicole B.
author list: Agent
  family name: Schilthuizen
  given name: Menno
doi: 10.7717/peerj.3938
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Ożgo et al.
attribution name: Ożgo et al.

Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies
type: item
type: AcademicArticle
description: Bone marrow stimulation may be applied to regenerate focal cartilage defects, but generally results in transient clinical improvement and formation of fibrocartilage rather than hyaline cartilage. Tissue engineering and regenerative medicine strive to develop new solutions to regenerate hyaline cartilage tissue. This systematic review and meta-analysis provides a comprehensive overview of current literature and assesses the efficacy of articular cartilage regeneration by implantation of cell-laden versus cell-free biomaterials in the knee and ankle joint in animals after bone marrow stimulation. PubMed and EMBASE (via OvidSP) were systematically searched using tissue engineering, cartilage and animals search strategies. Included were primary studies in which cellular and acellular biomaterials were implanted after applying bone marrow stimulation in the knee or ankle joint in healthy animals. Study characteristics were tabulated and outcome data were collected for meta-analysis for studies applying semi-quantitative histology as outcome measure (117 studies). Cartilage regeneration was expressed on an absolute 0–100% scale and random effects meta-analyses were performed. Implantation of cellular biomaterials significantly improved cartilage regeneration by 18.6% compared to acellular biomaterials. No significant differences were found between biomaterials loaded with stem cells and those loaded with somatic cells. Culture conditions of cells did not affect cartilage regeneration. Cartilage formation was reduced with adipose-derived stem cells compared to other cell types, but still improved compared to acellular scaffolds. Assessment of the risk of bias was impaired due to incomplete reporting for most studies. Implantation of cellular biomaterials improves cartilage regeneration compared to acellular biomaterials.
format: application/pdf
format: text/html
creator: Michiel W. Pot
creator: Toin H. van Kuppevelt
creator: Veronica K. Gonzales
creator: Pieter Buma
creator: Joanna IntHout
creator: Rob B.M. de Vries
creator: Willeke F. Daamen
subject: Bioengineering
subject: Evidence Based Medicine
subject: Orthopedics
subject: Rheumatology
subject: Translational Medicine
description: doi:10.7717/peerj.3927
publisher: PeerJ Inc.
rights: © 2017 Pot et al.
abstract: Bone marrow stimulation may be applied to regenerate focal cartilage defects, but generally results in transient clinical improvement and formation of fibrocartilage rather than hyaline cartilage. Tissue engineering and regenerative medicine strive to develop new solutions to regenerate hyaline cartilage tissue. This systematic review and meta-analysis provides a comprehensive overview of current literature and assesses the efficacy of articular cartilage regeneration by implantation of cell-laden versus cell-free biomaterials in the knee and ankle joint in animals after bone marrow stimulation. PubMed and EMBASE (via OvidSP) were systematically searched using tissue engineering, cartilage and animals search strategies. Included were primary studies in which cellular and acellular biomaterials were implanted after applying bone marrow stimulation in the knee or ankle joint in healthy animals. Study characteristics were tabulated and outcome data were collected for meta-analysis for studies applying semi-quantitative histology as outcome measure (117 studies). Cartilage regeneration was expressed on an absolute 0–100% scale and random effects meta-analyses were performed. Implantation of cellular biomaterials significantly improved cartilage regeneration by 18.6% compared to acellular biomaterials. No significant differences were found between biomaterials loaded with stem cells and those loaded with somatic cells. Culture conditions of cells did not affect cartilage regeneration. Cartilage formation was reduced with adipose-derived stem cells compared to other cell types, but still improved compared to acellular scaffolds. Assessment of the risk of bias was impaired due to incomplete reporting for most studies. Implantation of cellular biomaterials improves cartilage regeneration compared to acellular biomaterials.
bibliographic citation: Pot et al. (2017) Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies. PeerJ 5:e3927 https://doi.org/10.7717/peerj.3927
date submitted: 2017-06-23
date accepted: 2017-09-25
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pot
  given name: Michiel W.
author list: Agent
  family name: van Kuppevelt
  given name: Toin H.
author list: Agent
  family name: Gonzales
  given name: Veronica K.
author list: Agent
  family name: Buma
  given name: Pieter
author list: Agent
  family name: IntHout
  given name: Joanna
author list: Agent
  family name: de Vries
  given name: Rob B.M.
author list: Agent
  family name: Daamen
  given name: Willeke F.
doi: 10.7717/peerj.3927
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Pot et al.
attribution name: Pot et al.

Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity
type: item
type: AcademicArticle
description: Background Biomineralization, e.g., in sea urchins or mollusks, includes the assembly of mesoscopic superstructures from inorganic crystalline components and biopolymers. The resulting mesocrystals inspire biophysicists and material scientists alike, because of their extraordinary physical properties. Current efforts to replicate mesocrystal synthesis in vitro require understanding the principles of their self-assembly in vivo. One question, not addressed so far, is whether intracellular crystals of proteins can assemble with biopolymers into functional mesocrystal-like structures. During our electron microscopy studies into Artemia franciscana (Crustacea: Branchiopoda), we found initial evidence of such proteinaceous mesostructures. Results EM preparations with high-pressure freezing and accelerated freeze substitution revealed an extraordinary intracellular source of mesostructured inclusions in both the cyto-and nucleoplasm of the epidermal lining of ovisacs of A. franciscana. Confocal reflection microscopy not only confirmed our finding; it also revealed reflective, light dispersing activity of these flake-like structures, their positioning and orientation with respect to the ovisac inside. Both the striation of alternating electron dense and electron-lucent components and the sharp edges of the flakes indicate self-assembly of material of yet unknown origin under supposed participation of crystallization. However, selected area electron diffraction could not verify the status of crystallization. Energy dispersive X-ray analysis measured a marked increase in nitrogen within the flake-like inclusion, and the almost complete absence of elements that are typically involved in inorganic crystallization. This rise in nitrogen could possibility be related to higher package density of proteins, achieved by mesostructure assembly. Conclusions The ovisac lining of A. franciscana is endowed with numerous mesostructured inclusions that have not been previously reported. We…
format: application/pdf
format: text/html
creator: Elena Hollergschwandtner
creator: Thomas Schwaha
creator: Josef Neumüller
creator: Ulrich Kaindl
creator: Daniela Gruber
creator: Margret Eckhard
creator: Michael Stöger-Pollach
creator: Siegfried Reipert
subject: Aquaculture, Fisheries and Fish Science
subject: Cell Biology
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.3923
publisher: PeerJ Inc.
rights: © 2017 Hollergschwandtner et al.
abstract: Background Biomineralization, e.g., in sea urchins or mollusks, includes the assembly of mesoscopic superstructures from inorganic crystalline components and biopolymers. The resulting mesocrystals inspire biophysicists and material scientists alike, because of their extraordinary physical properties. Current efforts to replicate mesocrystal synthesis in vitro require understanding the principles of their self-assembly in vivo. One question, not addressed so far, is whether intracellular crystals of proteins can assemble with biopolymers into functional mesocrystal-like structures. During our electron microscopy studies into Artemia franciscana (Crustacea: Branchiopoda), we found initial evidence of such proteinaceous mesostructures. Results EM preparations with high-pressure freezing and accelerated freeze substitution revealed an extraordinary intracellular source of mesostructured inclusions in both the cyto-and nucleoplasm of the epidermal lining of ovisacs of A. franciscana. Confocal reflection microscopy not only confirmed our finding; it also revealed reflective, light dispersing activity of these flake-like structures, their positioning and orientation with respect to the ovisac inside. Both the striation of alternating electron dense and electron-lucent components and the sharp edges of the flakes indicate self-assembly of material of yet unknown origin under supposed participation of crystallization. However, selected area electron diffraction could not verify the status of crystallization. Energy dispersive X-ray analysis measured a marked increase in nitrogen within the flake-like inclusion, and the almost complete absence of elements that are typically involved in inorganic crystallization. This rise in nitrogen could possibility be related to higher package density of proteins, achieved by mesostructure assembly. Conclusions The ovisac lining of A. franciscana is endowed with numerous mesostructured inclusions that have not been previously reported. We…
bibliographic citation: Hollergschwandtner et al. (2017) Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity. PeerJ 5:e3923 https://doi.org/10.7717/peerj.3923
date submitted: 2017-04-25
date accepted: 2017-09-23
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hollergschwandtner
  given name: Elena
author list: Agent
  family name: Schwaha
  given name: Thomas
author list: Agent
  family name: Neumüller
  given name: Josef
author list: Agent
  family name: Kaindl
  given name: Ulrich
author list: Agent
  family name: Gruber
  given name: Daniela
author list: Agent
  family name: Eckhard
  given name: Margret
author list: Agent
  family name: Stöger-Pollach
  given name: Michael
author list: Agent
  family name: Reipert
  given name: Siegfried
doi: 10.7717/peerj.3923
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Hollergschwandtner et al.
attribution name: Hollergschwandtner et al.

Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides
type: item
type: AcademicArticle
description: Background Studies directed at understanding the demography and population dynamics of corals are relatively scarce. This limits our understanding of both the dynamics of coral populations and our capacity to develop management and conservation initiatives directed at conserving such ecosystems. Methods From 2012 to 2014, we collected data on the growth, survival, and recruitment rates of two common Caribbean coral species, the stress-tolerant Orbicella annularis and the weedy Porites astreoides. A set of size-based population matrix model was developed for two localities in Northeastern Puerto Rico and used to estimate population growth rates (λ) and determine the life cycle transition(s) that contribute the most to spatiotemporal differences in λs. The model was parameterized by following the fate of 100 colonies of each species at the two sites for two years. Results Our data indicate that spatial variability in vital rates of both species was higher than temporal variability. During the first year, populations of O. annularis exhibited λs below equilibrium at Carlos Rosario (0.817) and Palomino (0.694), followed by a considerable decline at both sites during the second year (0.700 and 0.667). Populations of P. astreoides showed higher λs than O. annularis during the first census period at Carlos Rosario (0.898) and Palomino (0.894) with a decline at one of the sites (0.681 and 0.893) during the second census period. Colony fate in both species exhibited a significant interaction with respect to location but not to time (G2 = 20.96; df = 3 for O. annularis and G2 = 9.55; df = 3 for P. astreoides). Discussion The similar variability of λs as well as the similar survival rates for both species during the two-year census period (2012–2014) show similar variability on demographic patterns in space and time. Our results suggest that location rather than time is important for the resiliency in coral colonies. Also, P. astreoides will show higher resistance to disturban…
format: application/pdf
format: text/html
creator: Francisco J. Soto-Santiago
creator: Alex Mercado-Molina
creator: Koralis Reyes-Maldonado
creator: Yaileen Vélez
creator: Claudia P. Ruiz-Díaz
creator: Alberto Sabat
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3906
publisher: PeerJ Inc.
rights: © 2017 Soto-Santiago et al.
abstract: Background Studies directed at understanding the demography and population dynamics of corals are relatively scarce. This limits our understanding of both the dynamics of coral populations and our capacity to develop management and conservation initiatives directed at conserving such ecosystems. Methods From 2012 to 2014, we collected data on the growth, survival, and recruitment rates of two common Caribbean coral species, the stress-tolerant Orbicella annularis and the weedy Porites astreoides. A set of size-based population matrix model was developed for two localities in Northeastern Puerto Rico and used to estimate population growth rates (λ) and determine the life cycle transition(s) that contribute the most to spatiotemporal differences in λs. The model was parameterized by following the fate of 100 colonies of each species at the two sites for two years. Results Our data indicate that spatial variability in vital rates of both species was higher than temporal variability. During the first year, populations of O. annularis exhibited λs below equilibrium at Carlos Rosario (0.817) and Palomino (0.694), followed by a considerable decline at both sites during the second year (0.700 and 0.667). Populations of P. astreoides showed higher λs than O. annularis during the first census period at Carlos Rosario (0.898) and Palomino (0.894) with a decline at one of the sites (0.681 and 0.893) during the second census period. Colony fate in both species exhibited a significant interaction with respect to location but not to time (G2 = 20.96; df = 3 for O. annularis and G2 = 9.55; df = 3 for P. astreoides). Discussion The similar variability of λs as well as the similar survival rates for both species during the two-year census period (2012–2014) show similar variability on demographic patterns in space and time. Our results suggest that location rather than time is important for the resiliency in coral colonies. Also, P. astreoides will show higher resistance to disturban…
bibliographic citation: Soto-Santiago et al. (2017) Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides. PeerJ 5:e3906 https://doi.org/10.7717/peerj.3906
date submitted: 2017-06-29
date accepted: 2017-09-19
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soto-Santiago
  given name: Francisco J.
author list: Agent
  family name: Mercado-Molina
  given name: Alex
author list: Agent
  family name: Reyes-Maldonado
  given name: Koralis
author list: Agent
  family name: Vélez
  given name: Yaileen
author list: Agent
  family name: Ruiz-Díaz
  given name: Claudia P.
author list: Agent
  family name: Sabat
  given name: Alberto
doi: 10.7717/peerj.3906
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: © 2017 Soto-Santiago et al.
attribution name: Soto-Santiago et al.

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