PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population
items: Genome-wide identification and characterization of WRKY gene family in Salix suchowensis
items: MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense
items: Testing the link between genome size and growth rate in maize
items: Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change
items: Platelet-rich concentrate in serum free medium enhances osteogenic differentiation of bone marrow-derived human mesenchymal stromal cells
items: Rhodopsin 7–The unusual Rhodopsin in Drosophila
items: Phylogeography by diffusion on a sphere: whole world phylogeography
items: Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees
items: A limitation of the Cognitive Reflection Test: familiarity

ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population
type: item
type: AcademicArticle
description: Background Left ventricular hypertrophy (LVH) is a marker of pediatric hypertension and predicts development of cardiovascular events. Electrocardiography (ECG) screening is used in pediatrics to detect LVH thanks to major accessibility, reproducibility and easy to use compared to transthoracic echocardiography (TTE), that remains the standard technique. Several diseases were previously investigated, but no data exists regarding our study population. The aim of our study was to evaluate the relationship between electrocardiographic and echocardiographic criteria of LVH in normotensive African children. Methods We studied 313 children (mean age 7,8 ± 3 yo), in north-Madagascar. They underwent ECG and TTE. Sokolow-Lyon index was calculated to identify ECG-LVH (>35 mm). Left ventricle mass (LVM) with TTE was calculated and indexed by height2.7 (LVMI2.7) and weight (LVMIw). We report the prevalence of TTE-LVH using three methods: (1) calculating percentiles age- and sex- specific with values >95th percentile identifying LVH; (2) LVMI2.7 >51 g/m2.7; (3) LVMIw >3.4 g/weight. Results 40 (13%) children showed LVMI values >95th percentile, 24 children (8%) an LVMI2.7 >51 g/m2.7 while 19 children (6%) an LVMIw >3.4 g/kg. LVH-ECG by Sokolow-Lyon index was present in five, three and three children respectively, with poor values of sensitivity (ranging from 13 to 16%), positive predictive value (from 11 to 18%) and high values of specificity (up to 92%). The effects of anthropometrics parameters on Sokolow-Lyon were analyzed and showed poor correlation. Conclusion ECG is a poor screening test for detecting LVH in children. In clinical practice, TTE remains the only tool to be used to exclude LVH.
format: application/pdf
format: text/html
creator: Giuseppe Di Gioia
creator: Antonio Creta
creator: Cosimo Marco Campanale
creator: Mario Fittipaldi
creator: Riccardo Giorgino
creator: Fabio Quintarelli
creator: Umberto Satriano
creator: Alessandro Cruciani
creator: Vincenzo Antinolfi
creator: Stefano Di Berardino
creator: Davide Costanzo
creator: Ranieri Bettini
creator: Giuseppe Mangiameli
creator: Marco Caricato
creator: Giovanni Mottini
subject: Cardiology
subject: Epidemiology
subject: Pediatrics
description: doi:10.7717/peerj.2439
publisher: PeerJ Inc.
rights: © 2016 Di Gioia et al.
abstract: Background Left ventricular hypertrophy (LVH) is a marker of pediatric hypertension and predicts development of cardiovascular events. Electrocardiography (ECG) screening is used in pediatrics to detect LVH thanks to major accessibility, reproducibility and easy to use compared to transthoracic echocardiography (TTE), that remains the standard technique. Several diseases were previously investigated, but no data exists regarding our study population. The aim of our study was to evaluate the relationship between electrocardiographic and echocardiographic criteria of LVH in normotensive African children. Methods We studied 313 children (mean age 7,8 ± 3 yo), in north-Madagascar. They underwent ECG and TTE. Sokolow-Lyon index was calculated to identify ECG-LVH (>35 mm). Left ventricle mass (LVM) with TTE was calculated and indexed by height2.7 (LVMI2.7) and weight (LVMIw). We report the prevalence of TTE-LVH using three methods: (1) calculating percentiles age- and sex- specific with values >95th percentile identifying LVH; (2) LVMI2.7 >51 g/m2.7; (3) LVMIw >3.4 g/weight. Results 40 (13%) children showed LVMI values >95th percentile, 24 children (8%) an LVMI2.7 >51 g/m2.7 while 19 children (6%) an LVMIw >3.4 g/kg. LVH-ECG by Sokolow-Lyon index was present in five, three and three children respectively, with poor values of sensitivity (ranging from 13 to 16%), positive predictive value (from 11 to 18%) and high values of specificity (up to 92%). The effects of anthropometrics parameters on Sokolow-Lyon were analyzed and showed poor correlation. Conclusion ECG is a poor screening test for detecting LVH in children. In clinical practice, TTE remains the only tool to be used to exclude LVH.
bibliographic citation: Di Gioia et al. (2016) ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population. PeerJ 4:e2439 https://doi.org/10.7717/peerj.2439
date submitted: 2016-05-02
date accepted: 2016-08-13
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Di Gioia
  given name: Giuseppe
author list: Agent
  family name: Creta
  given name: Antonio
author list: Agent
  family name: Campanale
  given name: Cosimo Marco
author list: Agent
  family name: Fittipaldi
  given name: Mario
author list: Agent
  family name: Giorgino
  given name: Riccardo
author list: Agent
  family name: Quintarelli
  given name: Fabio
author list: Agent
  family name: Satriano
  given name: Umberto
author list: Agent
  family name: Cruciani
  given name: Alessandro
author list: Agent
  family name: Antinolfi
  given name: Vincenzo
author list: Agent
  family name: Di Berardino
  given name: Stefano
author list: Agent
  family name: Costanzo
  given name: Davide
author list: Agent
  family name: Bettini
  given name: Ranieri
author list: Agent
  family name: Mangiameli
  given name: Giuseppe
author list: Agent
  family name: Caricato
  given name: Marco
author list: Agent
  family name: Mottini
  given name: Giovanni
doi: 10.7717/peerj.2439
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Di Gioia et al.
attribution name: Di Gioia et al.

Genome-wide identification and characterization of WRKY gene family in Salix suchowensis
type: item
type: AcademicArticle
description: WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of thi…
format: application/pdf
format: text/html
creator: Changwei Bi
creator: Yiqing Xu
creator: Qiaolin Ye
creator: Tongming Yin
creator: Ning Ye
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2437
publisher: PeerJ Inc.
rights: © 2016 Bi et al.
abstract: WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of thi…
bibliographic citation: Bi et al. (2016) Genome-wide identification and characterization of WRKY gene family in Salix suchowensis. PeerJ 4:e2437 https://doi.org/10.7717/peerj.2437
date submitted: 2016-06-24
date accepted: 2016-08-13
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bi
  given name: Changwei
author list: Agent
  family name: Xu
  given name: Yiqing
author list: Agent
  family name: Ye
  given name: Qiaolin
author list: Agent
  family name: Yin
  given name: Tongming
author list: Agent
  family name: Ye
  given name: Ning
doi: 10.7717/peerj.2437
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: © 2016 Bi et al.
attribution name: Bi et al.

MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense
type: item
type: AcademicArticle
description: Many methylotrophs, microorganisms that consume carbon compounds lacking carbon–carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulator MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Lastly, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.
format: application/pdf
format: text/html
creator: Frances Chu
creator: David A.C. Beck
creator: Mary E. Lidstrom
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.2435
publisher: PeerJ Inc.
rights: © 2016 Chu et al.
abstract: Many methylotrophs, microorganisms that consume carbon compounds lacking carbon–carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulator MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Lastly, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.
bibliographic citation: Chu et al. (2016) MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense. PeerJ 4:e2435 https://doi.org/10.7717/peerj.2435
date submitted: 2016-05-25
date accepted: 2016-08-12
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chu
  given name: Frances
author list: Agent
  family name: Beck
  given name: David A.C.
author list: Agent
  family name: Lidstrom
  given name: Mary E.
doi: 10.7717/peerj.2435
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Chu et al.
attribution name: Chu et al.

Testing the link between genome size and growth rate in maize
type: item
type: AcademicArticle
description: Little is known about the factors driving within species Genome Size (GS) variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax) as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27). However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.
format: application/pdf
format: text/html
creator: Maud I. Tenaillon
creator: Domenica Manicacci
creator: Stéphane D. Nicolas
creator: Francois Tardieu
creator: Claude Welcker
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.2408
publisher: PeerJ Inc.
rights: © 2016 Tenaillon et al.
abstract: Little is known about the factors driving within species Genome Size (GS) variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax) as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27). However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.
bibliographic citation: Tenaillon et al. (2016) Testing the link between genome size and growth rate in maize. PeerJ 4:e2408 https://doi.org/10.7717/peerj.2408
date submitted: 2016-05-26
date accepted: 2016-08-04
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tenaillon
  given name: Maud I.
author list: Agent
  family name: Manicacci
  given name: Domenica
author list: Agent
  family name: Nicolas
  given name: Stéphane D.
author list: Agent
  family name: Tardieu
  given name: Francois
author list: Agent
  family name: Welcker
  given name: Claude
doi: 10.7717/peerj.2408
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Tenaillon et al.
attribution name: Tenaillon et al.

Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change
type: item
type: AcademicArticle
description: Background Faunal change is a basic and fundamental element in ecology, biogeography, and conservation biology, yet vanishingly few detailed studies have documented such changes rigorously over decadal time scales. This study responds to that gap in knowledge, providing a detailed analysis of Digital Accessible Knowledge of the birds of Mexico, designed to marshal DAK to identify sites that were sampled and inventoried rigorously prior to the beginning of major global climate change (1980). Methods We accumulated DAK records for Mexican birds from all relevant online biodiversity data portals. After extensive cleaning steps, we calculated completeness indices for each 0.05° pixel across the country; we also detected ‘hotspots’ of sampling, and calculated completeness indices for these broader areas as well. Sites were designated as well-sampled if they had completeness indices above 80% and >200 associated DAK records. Results We identified 100 individual pixels and 20 broader ‘hotspots’ of sampling that were demonstrably well-inventoried prior to 1980. These sites are catalogued and documented to promote and enable resurvey efforts that can document events of avifaunal change (and non-change) across the country on decadal time scales. Conclusions Development of repeated surveys for many sites across Mexico, and particularly for sites for which historical surveys document their avifaunas prior to major climate change processes, would pay rich rewards in information about distributional dynamics of Mexican birds.
format: application/pdf
format: text/html
creator: A. Townsend Peterson
creator: Adolfo G. Navarro-Sigüenza
creator: Enrique Martínez-Meyer
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.2362
publisher: PeerJ Inc.
rights: © 2016 Peterson et al.
abstract: Background Faunal change is a basic and fundamental element in ecology, biogeography, and conservation biology, yet vanishingly few detailed studies have documented such changes rigorously over decadal time scales. This study responds to that gap in knowledge, providing a detailed analysis of Digital Accessible Knowledge of the birds of Mexico, designed to marshal DAK to identify sites that were sampled and inventoried rigorously prior to the beginning of major global climate change (1980). Methods We accumulated DAK records for Mexican birds from all relevant online biodiversity data portals. After extensive cleaning steps, we calculated completeness indices for each 0.05° pixel across the country; we also detected ‘hotspots’ of sampling, and calculated completeness indices for these broader areas as well. Sites were designated as well-sampled if they had completeness indices above 80% and >200 associated DAK records. Results We identified 100 individual pixels and 20 broader ‘hotspots’ of sampling that were demonstrably well-inventoried prior to 1980. These sites are catalogued and documented to promote and enable resurvey efforts that can document events of avifaunal change (and non-change) across the country on decadal time scales. Conclusions Development of repeated surveys for many sites across Mexico, and particularly for sites for which historical surveys document their avifaunas prior to major climate change processes, would pay rich rewards in information about distributional dynamics of Mexican birds.
bibliographic citation: Peterson et al. (2016) Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change. PeerJ 4:e2362 https://doi.org/10.7717/peerj.2362
date submitted: 2016-06-14
date accepted: 2016-07-23
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: A. Townsend
author list: Agent
  family name: Navarro-Sigüenza
  given name: Adolfo G.
author list: Agent
  family name: Martínez-Meyer
  given name: Enrique
doi: 10.7717/peerj.2362
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Peterson et al.
attribution name: Peterson et al.

Platelet-rich concentrate in serum free medium enhances osteogenic differentiation of bone marrow-derived human mesenchymal stromal cells
type: item
type: AcademicArticle
description: Previous studies have shown that platelet concentrates used in conjunction with appropriate growth media enhance osteogenic differentiation of human mesenchymal stromal cells (hMSCs). However, their potential in inducing osteogenesis of hMSCs when cultured in serum free medium has not been explored. Furthermore, the resulting osteogenic molecular signatures of the hMSCs have not been compared to standard osteogenic medium. We studied the effect of infrequent supplementation (8-day interval) of 15% non-activated platelet-rich concentrate (PRC) in serum free medium on hMSCs proliferation and differentiation throughout a course of 24 days, and compared the effect with those cultured in a standard osteogenic medium (OM). Cell proliferation was analyzed by alamar blue assay. Gene expression of osteogenic markers (Runx2, Collagen1, Alkaline Phosphatase, Bone morphogenetic protein 2, Osteopontin, Osteocalcin, Osteonectin) were analyzed using Q-PCR. Immunocytochemical staining for osteocalcin, osteopontin and transcription factor Runx2 were done at 8, 16 and 24 days. Biochemical assays for the expression of ALP and osteocalcin were also performed at these time-points. Osteogenic differentiation was further confirmed qualitatively by Alizarin Red S staining that was quantified using cetylpyridinium chloride. Results showed that PRC supplemented in serum free medium enhanced hMSC proliferation, which peaked at day 16. The temporal pattern of gene expression of hMSCs under the influence of PRC was comparable to that of the osteogenic media, but at a greater extent at specific time points. Immunocytochemical staining revealed stronger staining for Runx2 in the PRC-treated group compared to OM, while the staining for Osteocalcin and Osteopontin were comparable in both groups. ALP activity and Osteocalcin/DNA level were higher in the PRC group. Cells in the PRC group had similar level of bone mineralization as those cultured in OM, as reflected by the intensity of Alizarin red st…
format: application/pdf
format: text/html
creator: Shani Samuel
creator: Raja Elina Ahmad
creator: Thamil Selvee Ramasamy
creator: Puvanan Karunanithi
creator: Sangeetha Vasudevaraj Naveen
creator: Malliga Raman Murali
creator: Azlina A. Abbas
creator: Tunku Kamarul
subject: Cell Biology
subject: Orthopedics
subject: Translational Medicine
description: doi:10.7717/peerj.2347
publisher: PeerJ Inc.
rights: © 2016 Samuel et al.
abstract: Previous studies have shown that platelet concentrates used in conjunction with appropriate growth media enhance osteogenic differentiation of human mesenchymal stromal cells (hMSCs). However, their potential in inducing osteogenesis of hMSCs when cultured in serum free medium has not been explored. Furthermore, the resulting osteogenic molecular signatures of the hMSCs have not been compared to standard osteogenic medium. We studied the effect of infrequent supplementation (8-day interval) of 15% non-activated platelet-rich concentrate (PRC) in serum free medium on hMSCs proliferation and differentiation throughout a course of 24 days, and compared the effect with those cultured in a standard osteogenic medium (OM). Cell proliferation was analyzed by alamar blue assay. Gene expression of osteogenic markers (Runx2, Collagen1, Alkaline Phosphatase, Bone morphogenetic protein 2, Osteopontin, Osteocalcin, Osteonectin) were analyzed using Q-PCR. Immunocytochemical staining for osteocalcin, osteopontin and transcription factor Runx2 were done at 8, 16 and 24 days. Biochemical assays for the expression of ALP and osteocalcin were also performed at these time-points. Osteogenic differentiation was further confirmed qualitatively by Alizarin Red S staining that was quantified using cetylpyridinium chloride. Results showed that PRC supplemented in serum free medium enhanced hMSC proliferation, which peaked at day 16. The temporal pattern of gene expression of hMSCs under the influence of PRC was comparable to that of the osteogenic media, but at a greater extent at specific time points. Immunocytochemical staining revealed stronger staining for Runx2 in the PRC-treated group compared to OM, while the staining for Osteocalcin and Osteopontin were comparable in both groups. ALP activity and Osteocalcin/DNA level were higher in the PRC group. Cells in the PRC group had similar level of bone mineralization as those cultured in OM, as reflected by the intensity of Alizarin red st…
bibliographic citation: Samuel et al. (2016) Platelet-rich concentrate in serum free medium enhances osteogenic differentiation of bone marrow-derived human mesenchymal stromal cells. PeerJ 4:e2347 https://doi.org/10.7717/peerj.2347
date submitted: 2016-03-08
date accepted: 2016-07-19
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Samuel
  given name: Shani
author list: Agent
  family name: Ahmad
  given name: Raja Elina
author list: Agent
  family name: Ramasamy
  given name: Thamil Selvee
author list: Agent
  family name: Karunanithi
  given name: Puvanan
author list: Agent
  family name: Naveen
  given name: Sangeetha Vasudevaraj
author list: Agent
  family name: Murali
  given name: Malliga Raman
author list: Agent
  family name: Abbas
  given name: Azlina A.
author list: Agent
  family name: Kamarul
  given name: Tunku
doi: 10.7717/peerj.2347
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Samuel et al.
attribution name: Samuel et al.

Rhodopsin 7–The unusual Rhodopsin in Drosophila
type: item
type: AcademicArticle
description: Rhodopsins are the major photopigments in the fruit fly Drosophila melanogaster. Drosophila express six well-characterized Rhodopsins (Rh1–Rh6) with distinct absorption maxima and expression pattern. In 2000, when the Drosophila genome was published, a novel Rhodopsin gene was discovered: Rhodopsin 7 (Rh7). Rh7 is highly conserved among the Drosophila genus and is also found in other arthropods. Phylogenetic trees based on protein sequences suggest that the seven Drosophila Rhodopsins cluster in three different groups. While Rh1, Rh2 and Rh6 form a “vertebrate-melanopsin-type”–cluster, and Rh3, Rh4 and Rh5 form an “insect-type”-Rhodopsin cluster, Rh7 seem to form its own cluster. Although Rh7 has nearly all important features of a functional Rhodopsin, it differs from other Rhodopsins in its genomic and structural properties, suggesting it might have an overall different role than other known Rhodopsins.
format: application/pdf
format: text/html
creator: Pingkalai R. Senthilan
creator: Charlotte Helfrich-Förster
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.2427
publisher: PeerJ Inc.
rights: © 2016 Senthilan & Helfrich-Förster
abstract: Rhodopsins are the major photopigments in the fruit fly Drosophila melanogaster. Drosophila express six well-characterized Rhodopsins (Rh1–Rh6) with distinct absorption maxima and expression pattern. In 2000, when the Drosophila genome was published, a novel Rhodopsin gene was discovered: Rhodopsin 7 (Rh7). Rh7 is highly conserved among the Drosophila genus and is also found in other arthropods. Phylogenetic trees based on protein sequences suggest that the seven Drosophila Rhodopsins cluster in three different groups. While Rh1, Rh2 and Rh6 form a “vertebrate-melanopsin-type”–cluster, and Rh3, Rh4 and Rh5 form an “insect-type”-Rhodopsin cluster, Rh7 seem to form its own cluster. Although Rh7 has nearly all important features of a functional Rhodopsin, it differs from other Rhodopsins in its genomic and structural properties, suggesting it might have an overall different role than other known Rhodopsins.
bibliographic citation: Senthilan et al. (2016) Rhodopsin 7–The unusual Rhodopsin in Drosophila. PeerJ 4:e2427 https://doi.org/10.7717/peerj.2427
date submitted: 2016-05-24
date accepted: 2016-08-11
issued: 2016-09-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Senthilan
  given name: Pingkalai R.
author list: Agent
  family name: Helfrich-Förster
  given name: Charlotte
doi: 10.7717/peerj.2427
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-06
copyright: © 2016 Senthilan & Helfrich-Förster
attribution name: Senthilan & Helfrich-Förster

Phylogeography by diffusion on a sphere: whole world phylogeography
type: item
type: AcademicArticle
description: Background Techniques for reconstructing geographical history along a phylogeny can answer many questions of interest about the geographical origins of species. Bayesian models based on the assumption that taxa move through a diffusion process have found many applications. However, these methods rely on diffusion processes on a plane, and do not take the spherical nature of our planet in account. Performing an analysis that covers the whole world thus does not take in account the distortions caused by projections like the Mercator projection. Results In this paper, we introduce a Bayesian phylogeographical method based on diffusion on a sphere. When the area where taxa are sampled from is small, a sphere can be approximated by a plane and the model results in the same inferences as with models using diffusion on a plane. For taxa sampled from the whole world, we obtain substantial differences. We present an efficient algorithm for performing inference in a Markov Chain Monte Carlo (MCMC) algorithm, and show applications to small and large samples areas. We compare results between planar and spherical diffusion in a simulation study and apply the method by inferring the origin of Hepatitis B based on sequences sampled from Eurasia and Africa. Conclusions We describe a framework for performing phylogeographical inference, which is suitable when the distortion introduced by map projections is large, but works well on a smaller scale as well. The framework allows sampling tips from regions, which is useful when the exact sample location is unknown, and placing prior information on locations of clades in the tree. The method is implemented in the GEO_SPHERE package in BEAST 2, which is open source licensed under LGPL and allows joint tree and geography inference under a wide range of models.
format: application/pdf
format: text/html
creator: Remco Bouckaert
subject: Biogeography
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.2406
publisher: PeerJ Inc.
rights: © 2016 Bouckaert
abstract: Background Techniques for reconstructing geographical history along a phylogeny can answer many questions of interest about the geographical origins of species. Bayesian models based on the assumption that taxa move through a diffusion process have found many applications. However, these methods rely on diffusion processes on a plane, and do not take the spherical nature of our planet in account. Performing an analysis that covers the whole world thus does not take in account the distortions caused by projections like the Mercator projection. Results In this paper, we introduce a Bayesian phylogeographical method based on diffusion on a sphere. When the area where taxa are sampled from is small, a sphere can be approximated by a plane and the model results in the same inferences as with models using diffusion on a plane. For taxa sampled from the whole world, we obtain substantial differences. We present an efficient algorithm for performing inference in a Markov Chain Monte Carlo (MCMC) algorithm, and show applications to small and large samples areas. We compare results between planar and spherical diffusion in a simulation study and apply the method by inferring the origin of Hepatitis B based on sequences sampled from Eurasia and Africa. Conclusions We describe a framework for performing phylogeographical inference, which is suitable when the distortion introduced by map projections is large, but works well on a smaller scale as well. The framework allows sampling tips from regions, which is useful when the exact sample location is unknown, and placing prior information on locations of clades in the tree. The method is implemented in the GEO_SPHERE package in BEAST 2, which is open source licensed under LGPL and allows joint tree and geography inference under a wide range of models.
bibliographic citation: Bouckaert (2016) Phylogeography by diffusion on a sphere: whole world phylogeography. PeerJ 4:e2406 https://doi.org/10.7717/peerj.2406
date submitted: 2016-04-19
date accepted: 2016-08-03
issued: 2016-09-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bouckaert
  given name: Remco
doi: 10.7717/peerj.2406
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-06
copyright: ©2016 Bouckaert
attribution name: Bouckaert

Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees
type: item
type: AcademicArticle
description: Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.
format: application/pdf
format: text/html
creator: Kyle Dexter
creator: Jérôme Chave
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.2402
publisher: PeerJ Inc.
rights: © 2016 Dexter and Chave
abstract: Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.
bibliographic citation: Dexter et al. (2016) Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees. PeerJ 4:e2402 https://doi.org/10.7717/peerj.2402
date submitted: 2016-05-13
date accepted: 2016-08-03
issued: 2016-09-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dexter
  given name: Kyle
author list: Agent
  family name: Chave
  given name: Jérôme
doi: 10.7717/peerj.2402
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-06
copyright: ©2016 Dexter and Chave
attribution name: Dexter and Chave

A limitation of the Cognitive Reflection Test: familiarity
type: item
type: AcademicArticle
description: The Cognitive Reflection Test (CRT; Frederick, 2005) is a frequently used measure of cognitive vs. intuitive reflection. It is also a frequently found entertaining ‘test’ on the Internet. In a large age-stratified community-based sample (N = 2,272), we analyzed the impact of having already performed the CRT or any similar task in the past. Indeed, we found that 44% of participants had experiences with these tasks, which was reflected in higher CRT scores (Cohen’s d = 0.41). Furthermore, experienced participants were different from naïve participants in regard to their socio-demographics (younger, higher educated, fewer siblings, more likely single or in a relationship than married, having no children). The best predictors of a high CRT score were the highest educational qualification (4.62% explained variance) followed by the experience with the task (3.06%). Therefore, we suggest using more recent multi-item CRTs with newer items and a more elaborated test construction.
format: application/pdf
format: text/html
creator: Stefan Stieger
creator: Ulf-Dietrich Reips
subject: Neuroscience
subject: Pharmacology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2395
publisher: PeerJ Inc.
rights: © 2016 Stieger & Reips
abstract: The Cognitive Reflection Test (CRT; Frederick, 2005) is a frequently used measure of cognitive vs. intuitive reflection. It is also a frequently found entertaining ‘test’ on the Internet. In a large age-stratified community-based sample (N = 2,272), we analyzed the impact of having already performed the CRT or any similar task in the past. Indeed, we found that 44% of participants had experiences with these tasks, which was reflected in higher CRT scores (Cohen’s d = 0.41). Furthermore, experienced participants were different from naïve participants in regard to their socio-demographics (younger, higher educated, fewer siblings, more likely single or in a relationship than married, having no children). The best predictors of a high CRT score were the highest educational qualification (4.62% explained variance) followed by the experience with the task (3.06%). Therefore, we suggest using more recent multi-item CRTs with newer items and a more elaborated test construction.
bibliographic citation: Stieger et al. (2016) A limitation of the Cognitive Reflection Test: familiarity. PeerJ 4:e2395 https://doi.org/10.7717/peerj.2395
date submitted: 2016-06-10
date accepted: 2016-08-02
issued: 2016-09-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stieger
  given name: Stefan
author list: Agent
  family name: Reips
  given name: Ulf-Dietrich
doi: 10.7717/peerj.2395
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-06
copyright: © 2016 Stieger & Reips
attribution name: Stieger & Reips

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