PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes
items: Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton
items: Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
items: Microbial communities in the reef water at Kham Island, lower Gulf of Thailand
items: Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations
items: Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization
items: Are extinction opinions extinct?
items: Quid est Clea helena? Evidence for a previously unrecognized radiation of assassin snails (Gastropoda: Buccinoidea: Nassariidae)
items: Atrial fibrillation and psychological factors: a systematic review
items: Ecological interactions and the Netflix problem

The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes
type: item
type: AcademicArticle
description: Background Hypoxia-inducible factor (HIF)-1 is involved in the regulation of hypoxic preconditioning in cardiomyocytes. Under hypoxic conditions, HIF-1α accumulates and is translocated to the nucleus, where it forms an active complex with HIF-1β and activates transcription of approximately 60 kinds of hypoxia-adaptive genes. Microtubules are hollow tubular structures in the cell that maintain cellular morphology and that transport substances. This study attempted to clarify the role of microtubule structure in the endonuclear aggregation of HIF-1α following hypoxic preconditioning of cardiomyocytes. Methods Primary rat cardiomyocytes were isolated and cultured. The cardiomyocyte culture system was used to establish a hypoxia model and a hypoxic preconditioning model. Interventions were performed on primary cardiomyocytes using a microtubule-depolymerizing agent and different concentrations of a microtubule stabilizer. The microtubule structure and the degree of HIF-1α nuclear aggregation were observed by confocal laser scanning microscopy. The expression of HIF-1α in the cytoplasm and nucleus was detected using Western blotting. Cardiomyocyte energy content, reflected by adenosine triphosphate/adenosine diphosphate (ATP/ADP), and key glycolytic enzymes were monitored by colorimetry and high-performance liquid chromatography (HPLC). Reactive oxygen species (ROS) production was also used to comprehensively assess whether microtubule stabilization can enhance the myocardial protective effect of hypoxic preconditioning. Results During prolonged hypoxia, it was found that the destruction of the microtubule network structure of cardiomyocytes was gradually aggravated. After this preconditioning, an abundance of HIF-1α was clustered in the nucleus. When the microtubules were depolymerized and hypoxia pretreatment was performed, HIF-1α clustering occurred around the nucleus, and HIF-1α nuclear expression was low. The levels of key glycolytic enzymes were significantly highe…
format: application/pdf
format: text/html
creator: Hai Guo
creator: Hong Zheng
creator: Jianjiang Wu
creator: Hai-ping Ma
creator: Jin Yu
creator: Maimaitili Yiliyaer
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Cell Biology
description: doi:10.7717/peerj.3662
publisher: PeerJ Inc.
rights: © 2017 Guo et al.
abstract: Background Hypoxia-inducible factor (HIF)-1 is involved in the regulation of hypoxic preconditioning in cardiomyocytes. Under hypoxic conditions, HIF-1α accumulates and is translocated to the nucleus, where it forms an active complex with HIF-1β and activates transcription of approximately 60 kinds of hypoxia-adaptive genes. Microtubules are hollow tubular structures in the cell that maintain cellular morphology and that transport substances. This study attempted to clarify the role of microtubule structure in the endonuclear aggregation of HIF-1α following hypoxic preconditioning of cardiomyocytes. Methods Primary rat cardiomyocytes were isolated and cultured. The cardiomyocyte culture system was used to establish a hypoxia model and a hypoxic preconditioning model. Interventions were performed on primary cardiomyocytes using a microtubule-depolymerizing agent and different concentrations of a microtubule stabilizer. The microtubule structure and the degree of HIF-1α nuclear aggregation were observed by confocal laser scanning microscopy. The expression of HIF-1α in the cytoplasm and nucleus was detected using Western blotting. Cardiomyocyte energy content, reflected by adenosine triphosphate/adenosine diphosphate (ATP/ADP), and key glycolytic enzymes were monitored by colorimetry and high-performance liquid chromatography (HPLC). Reactive oxygen species (ROS) production was also used to comprehensively assess whether microtubule stabilization can enhance the myocardial protective effect of hypoxic preconditioning. Results During prolonged hypoxia, it was found that the destruction of the microtubule network structure of cardiomyocytes was gradually aggravated. After this preconditioning, an abundance of HIF-1α was clustered in the nucleus. When the microtubules were depolymerized and hypoxia pretreatment was performed, HIF-1α clustering occurred around the nucleus, and HIF-1α nuclear expression was low. The levels of key glycolytic enzymes were significantly highe…
bibliographic citation: Guo et al. (2017) The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes. PeerJ 5:e3662 https://doi.org/10.7717/peerj.3662
date submitted: 2017-01-19
date accepted: 2017-07-18
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Hai
author list: Agent
  family name: Zheng
  given name: Hong
author list: Agent
  family name: Wu
  given name: Jianjiang
author list: Agent
  family name: Ma
  given name: Hai-ping
author list: Agent
  family name: Yu
  given name: Jin
author list: Agent
  family name: Yiliyaer
  given name: Maimaitili
doi: 10.7717/peerj.3662
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Guo et al.
attribution name: Guo et al.

Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton
type: item
type: AcademicArticle
description: Calcineurin B-like (CBL) proteins, as calcium sensors, play pivotal roles in plant responses to diverse abiotic stresses and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, knowledge about functions and evolution of CBLs in Gossypium plants is scarce. Here, we conducted a genome-wide survey and identified 13, 13 and 22 CBL genes in the progenitor diploid Gossypium arboreum and Gossypium raimondii, and the cultivated allotetraploid Gossypium hirsutum, respectively. Analysis of physical properties, chromosomal locations, conserved domains and phylogeny indicated rather conserved nature of CBLs among the three Gossypium species. Moreover, these CBLs have closer genetic evolutionary relationship with the CBLs from cocoa than with those from other plants. Most CBL genes underwent evolution under purifying selection in the three Gossypium plants. Additionally, nearly all G. hirsutum CBL (GhCBL) genes were expressed in the root, stem, leaf, flower and fiber. Many GhCBLs were preferentially expressed in the flower while several GhCBLs were mainly expressed in roots. Expression patterns of GhCBL genes in response to potassium deficiency were also studied. The expression of most GhCBLs were moderately induced in roots after treatments with low-potassium stress. Yeast two-hybrid experiments indicated that GhCBL1-2, GhCBL1-3, GhCBL4-4, GhCBL8, GhCBL9 and GhCBL10-3 interacted with GhCIPK23, respectively. Our results provided a comprehensive view of the CBLs and valuable information for researchers to further investigate the roles and functional mechanisms of the CBLs in Gossypium.
format: application/pdf
format: text/html
creator: Tingting Lu
creator: Gaofeng Zhang
creator: Lirong Sun
creator: Ji Wang
creator: Fushun Hao
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3653
publisher: PeerJ Inc.
rights: © 2017 Lu et al.
abstract: Calcineurin B-like (CBL) proteins, as calcium sensors, play pivotal roles in plant responses to diverse abiotic stresses and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, knowledge about functions and evolution of CBLs in Gossypium plants is scarce. Here, we conducted a genome-wide survey and identified 13, 13 and 22 CBL genes in the progenitor diploid Gossypium arboreum and Gossypium raimondii, and the cultivated allotetraploid Gossypium hirsutum, respectively. Analysis of physical properties, chromosomal locations, conserved domains and phylogeny indicated rather conserved nature of CBLs among the three Gossypium species. Moreover, these CBLs have closer genetic evolutionary relationship with the CBLs from cocoa than with those from other plants. Most CBL genes underwent evolution under purifying selection in the three Gossypium plants. Additionally, nearly all G. hirsutum CBL (GhCBL) genes were expressed in the root, stem, leaf, flower and fiber. Many GhCBLs were preferentially expressed in the flower while several GhCBLs were mainly expressed in roots. Expression patterns of GhCBL genes in response to potassium deficiency were also studied. The expression of most GhCBLs were moderately induced in roots after treatments with low-potassium stress. Yeast two-hybrid experiments indicated that GhCBL1-2, GhCBL1-3, GhCBL4-4, GhCBL8, GhCBL9 and GhCBL10-3 interacted with GhCIPK23, respectively. Our results provided a comprehensive view of the CBLs and valuable information for researchers to further investigate the roles and functional mechanisms of the CBLs in Gossypium.
bibliographic citation: Lu et al. (2017) Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PeerJ 5:e3653 https://doi.org/10.7717/peerj.3653
date submitted: 2017-04-25
date accepted: 2017-07-14
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Tingting
author list: Agent
  family name: Zhang
  given name: Gaofeng
author list: Agent
  family name: Sun
  given name: Lirong
author list: Agent
  family name: Wang
  given name: Ji
author list: Agent
  family name: Hao
  given name: Fushun
doi: 10.7717/peerj.3653
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Lu et al.
attribution name: Lu et al.

Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
type: item
type: AcademicArticle
description: Objective The trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might be a viable therapeutic approach. Decellularized TM scaffolds have previously been produced by ablating cells with suicide gene therapy or saponin, which risks incomplete cell removal or dissolution of the extracellular matrix, respectively. We hypothesized that improved trabecular meshwork cell ablation would result from freeze-thaw cycles compared to chemical treatment. Materials and Methods We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion within two hours of sacrifice. Intraocular pressure (IOP) was recorded continuously by a pressure transducer system. After 72 h of IOP stabilization, eight eyes were assigned to freeze-thaw (F) ablation (−80 °C × 2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The TM was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture media for 180 h. TM histology was assessed by hematoxylin and eosin staining. TM viability was evaluated by a calcein AM/propidium iodide (PI) assay. The TM extracellular matrix was stained with Picro Sirius Red. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with five degrees of freedom. Results F and S experienced a similar IOP reduction of 30% from baseline (P = 0.64). IOP reduction of about 30% occurred in F within 24 h and in S within 48 h. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis and Picro Sirius staining confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calce…
format: application/pdf
format: text/html
creator: Yalong Dang
creator: Susannah Waxman
creator: Chao Wang
creator: Adrianna Jensen
creator: Ralitsa T. Loewen
creator: Richard A. Bilonick
creator: Nils A. Loewen
subject: Bioengineering
subject: Biotechnology
subject: Ophthalmology
description: doi:10.7717/peerj.3629
publisher: PeerJ Inc.
rights: © 2017 Dang et al.
abstract: Objective The trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might be a viable therapeutic approach. Decellularized TM scaffolds have previously been produced by ablating cells with suicide gene therapy or saponin, which risks incomplete cell removal or dissolution of the extracellular matrix, respectively. We hypothesized that improved trabecular meshwork cell ablation would result from freeze-thaw cycles compared to chemical treatment. Materials and Methods We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion within two hours of sacrifice. Intraocular pressure (IOP) was recorded continuously by a pressure transducer system. After 72 h of IOP stabilization, eight eyes were assigned to freeze-thaw (F) ablation (−80 °C × 2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The TM was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture media for 180 h. TM histology was assessed by hematoxylin and eosin staining. TM viability was evaluated by a calcein AM/propidium iodide (PI) assay. The TM extracellular matrix was stained with Picro Sirius Red. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with five degrees of freedom. Results F and S experienced a similar IOP reduction of 30% from baseline (P = 0.64). IOP reduction of about 30% occurred in F within 24 h and in S within 48 h. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis and Picro Sirius staining confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calce…
bibliographic citation: Dang et al. (2017) Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model. PeerJ 5:e3629 https://doi.org/10.7717/peerj.3629
date submitted: 2017-02-07
date accepted: 2017-07-10
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dang
  given name: Yalong
author list: Agent
  family name: Waxman
  given name: Susannah
author list: Agent
  family name: Wang
  given name: Chao
author list: Agent
  family name: Jensen
  given name: Adrianna
author list: Agent
  family name: Loewen
  given name: Ralitsa T.
author list: Agent
  family name: Bilonick
  given name: Richard A.
author list: Agent
  family name: Loewen
  given name: Nils A.
doi: 10.7717/peerj.3629
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Dang et al.
attribution name: Dang et al.

Microbial communities in the reef water at Kham Island, lower Gulf of Thailand
type: item
type: AcademicArticle
description: Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and se…
format: application/pdf
format: text/html
creator: Naraporn Somboonna
creator: Alisa Wilantho
creator: Somchai Monanunsap
creator: Suchana Chavanich
creator: Sithichoke Tangphatsornruang
creator: Sissades Tongsima
subject: Biodiversity
subject: Marine Biology
subject: Microbiology
subject: Natural Resource Management
description: doi:10.7717/peerj.3625
publisher: PeerJ Inc.
rights: © 2017 Somboonna et al.
abstract: Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and se…
bibliographic citation: Somboonna et al. (2017) Microbial communities in the reef water at Kham Island, lower Gulf of Thailand. PeerJ 5:e3625 https://doi.org/10.7717/peerj.3625
date submitted: 2017-03-09
date accepted: 2017-07-08
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Somboonna
  given name: Naraporn
author list: Agent
  family name: Wilantho
  given name: Alisa
author list: Agent
  family name: Monanunsap
  given name: Somchai
author list: Agent
  family name: Chavanich
  given name: Suchana
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
author list: Agent
  family name: Tongsima
  given name: Sissades
doi: 10.7717/peerj.3625
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Somboonna et al.
attribution name: Somboonna et al.

Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations
type: item
type: AcademicArticle
description: Phylogeographic analyses of the gall fly Urophora cardui have in earlier studies based on allozymes and mtDNA identified small-scale, parapatrically diverged populations within an expanding Western Palearctic population. However, the low polymorphism of these markers prohibited an accurate delimitation of the evolutionary origin of the parapatric divergence. Urophora cardui from the Western Palearctic have been introduced into Canada as biological control agents of the host plant Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-, penta- and tetra-nucleotide repeat motifs and report a genotyping-by-sequencing SNP protocol. We test the markers for genetic variation among three parapatric U. cardui populations. Microsatellite variability (N = 59 individuals) was high: expected heterozygosity/locus/population (0.60–0.90), allele number/locus/population (5–21). One locus was alternatively sex-linked in males or females. Cross-species amplification in the sister species U. stylata was successful or partially successful for seven loci. For genotyping-by-sequencing (N = 18 individuals), different DNA extraction methods did not affect data quality. Depending on sequence sorting criteria, 1,177–2,347 unlinked SNPs and 1,750–4,469 parsimony informative sites were found in 3,514–5,767 loci recovered after paralog filtering. Both marker systems quantified the same population partitions with high probabilities. Many and highly differentiated loci in both marker systems indicate genome-wide diversification and genetically distinct populations.
format: application/pdf
format: text/html
creator: Jes Johannesen
creator: Armin G. Fabritzek
creator: Bettina Ebner
creator: Sven-Ernö Bikar
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.3582
publisher: PeerJ Inc.
rights: © 2017 Johannesen et al.
abstract: Phylogeographic analyses of the gall fly Urophora cardui have in earlier studies based on allozymes and mtDNA identified small-scale, parapatrically diverged populations within an expanding Western Palearctic population. However, the low polymorphism of these markers prohibited an accurate delimitation of the evolutionary origin of the parapatric divergence. Urophora cardui from the Western Palearctic have been introduced into Canada as biological control agents of the host plant Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-, penta- and tetra-nucleotide repeat motifs and report a genotyping-by-sequencing SNP protocol. We test the markers for genetic variation among three parapatric U. cardui populations. Microsatellite variability (N = 59 individuals) was high: expected heterozygosity/locus/population (0.60–0.90), allele number/locus/population (5–21). One locus was alternatively sex-linked in males or females. Cross-species amplification in the sister species U. stylata was successful or partially successful for seven loci. For genotyping-by-sequencing (N = 18 individuals), different DNA extraction methods did not affect data quality. Depending on sequence sorting criteria, 1,177–2,347 unlinked SNPs and 1,750–4,469 parsimony informative sites were found in 3,514–5,767 loci recovered after paralog filtering. Both marker systems quantified the same population partitions with high probabilities. Many and highly differentiated loci in both marker systems indicate genome-wide diversification and genetically distinct populations.
bibliographic citation: Johannesen et al. (2017) Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations. PeerJ 5:e3582 https://doi.org/10.7717/peerj.3582
date submitted: 2017-03-09
date accepted: 2017-06-25
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johannesen
  given name: Jes
author list: Agent
  family name: Fabritzek
  given name: Armin G.
author list: Agent
  family name: Ebner
  given name: Bettina
author list: Agent
  family name: Bikar
  given name: Sven-Ernö
doi: 10.7717/peerj.3582
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Johannesen et al.
attribution name: Johannesen et al.

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization
type: item
type: AcademicArticle
description: Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C. solstitialis had been reported to be diploid (2n = 2x = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C. solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C. solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.
format: application/pdf
format: text/html
creator: Ramona-Elena Irimia
creator: Daniel Montesinos
creator: Özkan Eren
creator: Christopher J. Lortie
creator: Kristine French
creator: Lohengrin A. Cavieres
creator: Gastón J. Sotes
creator: José L. Hierro
creator: Andreia Jorge
creator: João Loureiro
subject: Biogeography
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.3531
publisher: PeerJ Inc.
rights: © 2017 Irimia et al.
abstract: Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C. solstitialis had been reported to be diploid (2n = 2x = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C. solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C. solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.
bibliographic citation: Irimia et al. (2017) Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization. PeerJ 5:e3531 https://doi.org/10.7717/peerj.3531
date submitted: 2017-04-25
date accepted: 2017-06-12
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Irimia
  given name: Ramona-Elena
author list: Agent
  family name: Montesinos
  given name: Daniel
author list: Agent
  family name: Eren
  given name: Özkan
author list: Agent
  family name: Lortie
  given name: Christopher J.
author list: Agent
  family name: French
  given name: Kristine
author list: Agent
  family name: Cavieres
  given name: Lohengrin A.
author list: Agent
  family name: Sotes
  given name: Gastón J.
author list: Agent
  family name: Hierro
  given name: José L.
author list: Agent
  family name: Jorge
  given name: Andreia
author list: Agent
  family name: Loureiro
  given name: João
doi: 10.7717/peerj.3531
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Irimia et al.
attribution name: Irimia et al.

Are extinction opinions extinct?
type: item
type: AcademicArticle
description: Extinction models vary in the information they require, the simplest considering the rate of certain sightings only. More complicated methods include uncertain sightings and allow for variation in the reliability of uncertain sightings. Generally extinction models require expert opinion, either as a prior belief that a species is extinct, or to establish the quality of a sighting record, or both. Is this subjectivity necessary? We present two models to explore whether the individual quality of sightings, judged by experts, is strongly informative of the probability of extinction: the ‘quality breakpoint method’ and the ‘quality as variance method’. For the first method we use the Barbary lion as an exemplar. For the second method we use the Barbary lion, Alaotra grebe, Jamaican petrel and Pohnpei starling as exemplars. The ‘quality breakpoint method’ uses certain and uncertain sighting records, and the quality of uncertain records, to establish whether a change point in the rate of sightings can be established using a simultaneous Bayesian optimisation with a non-informative prior. For the Barbary lion, there is a change in subjective quality of sightings around 1930. Unexpectedly sighting quality increases after this date. This suggests that including quality scores from experts can lead to irregular effects and may not offer reliable results. As an alternative, we use quality as a measure of variance around the sightings, not a change in quality. This leads to predictions with larger standard deviations, however the results remain consistent across any prior belief of extinction. Nonetheless, replacing actual quality scores with random quality scores showed little difference, inferring that the quality scores from experts are superfluous. Therefore, we deem the expensive process of obtaining pooled expert estimates as unnecessary, and even when used we recommend that sighting data should have minimal input from experts in terms of assessing the sighting quality at…
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format: text/html
creator: Tamsin E. Lee
creator: Clive Bowman
creator: David L. Roberts
subject: Conservation Biology
subject: Ecology
subject: Mathematical Biology
description: doi:10.7717/peerj.3663
publisher: PeerJ Inc.
rights: © 2017 Lee et al.
abstract: Extinction models vary in the information they require, the simplest considering the rate of certain sightings only. More complicated methods include uncertain sightings and allow for variation in the reliability of uncertain sightings. Generally extinction models require expert opinion, either as a prior belief that a species is extinct, or to establish the quality of a sighting record, or both. Is this subjectivity necessary? We present two models to explore whether the individual quality of sightings, judged by experts, is strongly informative of the probability of extinction: the ‘quality breakpoint method’ and the ‘quality as variance method’. For the first method we use the Barbary lion as an exemplar. For the second method we use the Barbary lion, Alaotra grebe, Jamaican petrel and Pohnpei starling as exemplars. The ‘quality breakpoint method’ uses certain and uncertain sighting records, and the quality of uncertain records, to establish whether a change point in the rate of sightings can be established using a simultaneous Bayesian optimisation with a non-informative prior. For the Barbary lion, there is a change in subjective quality of sightings around 1930. Unexpectedly sighting quality increases after this date. This suggests that including quality scores from experts can lead to irregular effects and may not offer reliable results. As an alternative, we use quality as a measure of variance around the sightings, not a change in quality. This leads to predictions with larger standard deviations, however the results remain consistent across any prior belief of extinction. Nonetheless, replacing actual quality scores with random quality scores showed little difference, inferring that the quality scores from experts are superfluous. Therefore, we deem the expensive process of obtaining pooled expert estimates as unnecessary, and even when used we recommend that sighting data should have minimal input from experts in terms of assessing the sighting quality at…
bibliographic citation: Lee et al. (2017) Are extinction opinions extinct?. PeerJ 5:e3663 https://doi.org/10.7717/peerj.3663
date submitted: 2017-05-02
date accepted: 2017-07-18
issued: 2017-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Tamsin E.
author list: Agent
  family name: Bowman
  given name: Clive
author list: Agent
  family name: Roberts
  given name: David L.
doi: 10.7717/peerj.3663
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-11
copyright: ©2017 Lee et al.
attribution name: Lee et al.

Quid est Clea helena? Evidence for a previously unrecognized radiation of assassin snails (Gastropoda: Buccinoidea: Nassariidae)
type: item
type: AcademicArticle
description: The genus Clea from SE Asia is from one of only two unrelated families among the megadiverse predatory marine Neogastropoda to have successfully conquered continental waters. While little is known about their anatomy, life history and ecology, interest has grown exponentially in recent years owing to their increasing popularity as aquarium pets. However, the systematic affinities of the genus and the validity of the included species have not been robustly explored. Differences in shell, operculum and radula characters support separation of Clea as presently defined into two distinct genera: Clea, for the type species Clea nigricans and its allies, and Anentome for Clea helena and allies. A five-gene mitochondrial (COI, 16S, 12S) and nuclear (H3, 28S) gene dataset confirms the placement of Anentome as a somewhat isolated offshoot of the family Nassariidae and sister to the estuarine Nassodonta. Anatomical data corroborate this grouping and, in conjunction with their phylogenetic placement, support their recognition as a new subfamily, the Anentominae. The assassin snail Anentome helena, a popular import through the aquarium trade so named for their voracious appetite for other snails, is found to comprise a complex of at least four species. None of these likely represents true Anentome helena described from Java, including a specimen purchased through the aquarium trade under this name in the US and one that was recently found introduced in Singapore, both of which were supported as conspecific with a species from Thailand. The introduction of Anentome “helena” through the aquarium trade constitutes a significant threat to native aquatic snail faunas which are often already highly imperiled. Comprehensive systematic revision of this previously unrecognized species complex is urgently needed to facilitate communication and manage this emerging threat.
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creator: Ellen E. Strong
creator: Lee Ann Galindo
creator: Yuri I. Kantor
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Taxonomy
subject: Natural Resource Management
description: doi:10.7717/peerj.3638
publisher: PeerJ Inc.
rights: © 2017 Strong et al.
abstract: The genus Clea from SE Asia is from one of only two unrelated families among the megadiverse predatory marine Neogastropoda to have successfully conquered continental waters. While little is known about their anatomy, life history and ecology, interest has grown exponentially in recent years owing to their increasing popularity as aquarium pets. However, the systematic affinities of the genus and the validity of the included species have not been robustly explored. Differences in shell, operculum and radula characters support separation of Clea as presently defined into two distinct genera: Clea, for the type species Clea nigricans and its allies, and Anentome for Clea helena and allies. A five-gene mitochondrial (COI, 16S, 12S) and nuclear (H3, 28S) gene dataset confirms the placement of Anentome as a somewhat isolated offshoot of the family Nassariidae and sister to the estuarine Nassodonta. Anatomical data corroborate this grouping and, in conjunction with their phylogenetic placement, support their recognition as a new subfamily, the Anentominae. The assassin snail Anentome helena, a popular import through the aquarium trade so named for their voracious appetite for other snails, is found to comprise a complex of at least four species. None of these likely represents true Anentome helena described from Java, including a specimen purchased through the aquarium trade under this name in the US and one that was recently found introduced in Singapore, both of which were supported as conspecific with a species from Thailand. The introduction of Anentome “helena” through the aquarium trade constitutes a significant threat to native aquatic snail faunas which are often already highly imperiled. Comprehensive systematic revision of this previously unrecognized species complex is urgently needed to facilitate communication and manage this emerging threat.
bibliographic citation: Strong et al. (2017) Quid est Clea helena? Evidence for a previously unrecognized radiation of assassin snails (Gastropoda: Buccinoidea: Nassariidae). PeerJ 5:e3638 https://doi.org/10.7717/peerj.3638
date submitted: 2017-05-06
date accepted: 2017-07-12
issued: 2017-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strong
  given name: Ellen E.
author list: Agent
  family name: Galindo
  given name: Lee Ann
author list: Agent
  family name: Kantor
  given name: Yuri I.
doi: 10.7717/peerj.3638
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-11
copyright: © 2017 Strong et al.
attribution name: Strong et al.

Atrial fibrillation and psychological factors: a systematic review
type: item
type: AcademicArticle
description: Background Psychological factors have been suggested to have an influence in Atrial Fibrillation (AF) onset, progression, severity and outcomes, but their role is unclear and mainly focused on anxiety and depression. Methods A systematic electronic search had been conducted to identify studies exploring different psychological factors in AF. The search retrieved 832 articles that were reviewed according to inclusion criteria: observational study with a control/comparison group; use of standardized and validated instruments for psychological assessment. Results were summarized qualitatively and quantitatively by effect size measure (Cohen’s d and its 95% confidence interval). Cochrane Collaboration guidelines and the PRISMA Statement were adopted. Results Eight studies were included in the systematic review. Depression was the most studied construct/ but only one study showed a clear link with AF. The remaining studies showed small and non-significant (95% CI [−0.25–1.00]) differences between AF and controls, no differences in frequency of depression history (95% CI [−0.14–0.22]) or in case frequency (95% CI [−0.50–0.04]). Miscellaneous results were found as far as anxiety: AF patients showed higher levels when compared to healthy subjects (95% CI [2.05–2.95]), but findings were inconsistent when compared to other heart diseases. Considering personality and life-events preceding AF, we respectively found a large (95% CI [1.87–2.49]) and a moderate to large effect (95% CI [0.48–0.98]). Discussion The small number of studies does not allow to draw clear-cut conclusions on the involvement of psychological factors in AF. Promising lines of research are related to personality and adverse life-events, and to the increase of longitudinal design studies. Some methodological problems could be overcome by including clinical psychologists in the implementation of research protocols.
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creator: Federica Galli
creator: Lidia Borghi
creator: Stefano Carugo
creator: Marco Cavicchioli
creator: Elena Maria Faioni
creator: Maria Silvia Negroni
creator: Elena Vegni
subject: Cardiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.3537
publisher: PeerJ Inc.
rights: © 2017 Galli et al.
abstract: Background Psychological factors have been suggested to have an influence in Atrial Fibrillation (AF) onset, progression, severity and outcomes, but their role is unclear and mainly focused on anxiety and depression. Methods A systematic electronic search had been conducted to identify studies exploring different psychological factors in AF. The search retrieved 832 articles that were reviewed according to inclusion criteria: observational study with a control/comparison group; use of standardized and validated instruments for psychological assessment. Results were summarized qualitatively and quantitatively by effect size measure (Cohen’s d and its 95% confidence interval). Cochrane Collaboration guidelines and the PRISMA Statement were adopted. Results Eight studies were included in the systematic review. Depression was the most studied construct/ but only one study showed a clear link with AF. The remaining studies showed small and non-significant (95% CI [−0.25–1.00]) differences between AF and controls, no differences in frequency of depression history (95% CI [−0.14–0.22]) or in case frequency (95% CI [−0.50–0.04]). Miscellaneous results were found as far as anxiety: AF patients showed higher levels when compared to healthy subjects (95% CI [2.05–2.95]), but findings were inconsistent when compared to other heart diseases. Considering personality and life-events preceding AF, we respectively found a large (95% CI [1.87–2.49]) and a moderate to large effect (95% CI [0.48–0.98]). Discussion The small number of studies does not allow to draw clear-cut conclusions on the involvement of psychological factors in AF. Promising lines of research are related to personality and adverse life-events, and to the increase of longitudinal design studies. Some methodological problems could be overcome by including clinical psychologists in the implementation of research protocols.
bibliographic citation: Galli et al. (2017) Atrial fibrillation and psychological factors: a systematic review. PeerJ 5:e3537 https://doi.org/10.7717/peerj.3537
date submitted: 2017-03-07
date accepted: 2017-06-12
issued: 2017-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galli
  given name: Federica
author list: Agent
  family name: Borghi
  given name: Lidia
author list: Agent
  family name: Carugo
  given name: Stefano
author list: Agent
  family name: Cavicchioli
  given name: Marco
author list: Agent
  family name: Faioni
  given name: Elena Maria
author list: Agent
  family name: Negroni
  given name: Maria Silvia
author list: Agent
  family name: Vegni
  given name: Elena
doi: 10.7717/peerj.3537
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-11
copyright: ©2017 Galli et al.
attribution name: Galli et al.

Ecological interactions and the Netflix problem
type: item
type: AcademicArticle
description: Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along with a supervised machine learning technique. Recommenders are algorithms developed for companies like Netflix to predict whether a customer will like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for the K nearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species’ phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species’ interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species’ interactions. Further work should focus on developing custom similarity measures specialized for ecology to improve the KNN algorithms and using richer data to capture indirect relationships between species.
format: application/pdf
format: text/html
creator: Philippe Desjardins-Proulx
creator: Idaline Laigle
creator: Timothée Poisot
creator: Dominique Gravel
subject: Bioinformatics
subject: Ecology
description: doi:10.7717/peerj.3644
publisher: PeerJ Inc.
rights: © 2017 Desjardins-Proulx et al.
abstract: Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along with a supervised machine learning technique. Recommenders are algorithms developed for companies like Netflix to predict whether a customer will like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for the K nearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species’ phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species’ interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species’ interactions. Further work should focus on developing custom similarity measures specialized for ecology to improve the KNN algorithms and using richer data to capture indirect relationships between species.
bibliographic citation: Desjardins-Proulx et al. (2017) Ecological interactions and the Netflix problem. PeerJ 5:e3644 https://doi.org/10.7717/peerj.3644
date submitted: 2017-04-25
date accepted: 2017-07-12
issued: 2017-08-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Desjardins-Proulx
  given name: Philippe
author list: Agent
  family name: Laigle
  given name: Idaline
author list: Agent
  family name: Poisot
  given name: Timothée
author list: Agent
  family name: Gravel
  given name: Dominique
doi: 10.7717/peerj.3644
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-10
copyright: ©2017 Desjardins-Proulx et al.
attribution name: Desjardins-Proulx et al.

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