PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Seed morphometric characteristics of European species of Elatine (Elatinaceae)
items: Selection of housekeeping genes as internal controls for quantitative RT-PCR analysis of the veined rapa whelk (Rapana venosa)
items: Transcriptome analysis reveals the regulation of brassinosteroids on petal growth in Gerbera hybrida
items: Quercetin reduces hydroxyurea induced cytotoxicity in immortalized mouse aortic endothelial cells
items: Pond dyes are Culex mosquito oviposition attractants
items: Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators
items: Assessing the utility of an institutional publications officer: a pilot assessment
items: Difference on cone size preferences between two coniferous species by Great Spotted Woodpecker (Dendrocopos major)
items: Largest baleen whale mass mortality during strong El Niño event is likely related to harmful toxic algal bloom
items: Patterns of bleaching and mortality following widespread warming events in 2014 and 2015 at the Hanauma Bay Nature Preserve, Hawai‘i

Seed morphometric characteristics of European species of Elatine (Elatinaceae)
type: item
type: AcademicArticle
description: Elatine L. contains ca. 25 small, herbaceous, annual species distributed in ephemeral waters in both hemispheres. All species are amphibious and characterized by a high degree of morphological variability. The importance of seed morphology in Elatine taxonomy has been emphasized by many authors. The degree of seed curvature and seed coat reticulation have been traditionally considered very important in recognizing individual species of this genus. Seed morphometric characteristics of 10 Elatine species, including all European native taxa, are provided on the basis of material from two or three populations of each species. A total of 24–50 seeds were studied from each population, altogether 1,260 images were used for the morphometric study. In total, six parameters were measured from SEM pictures: object surface area, profile specific perimeter (object circuit), rectangle of the object (a) length, rectangle of the object (b) width, angle of the seed curvature, and number of pits in the seed coat counted in the middle row. Our study shows that the range of morphological variation of seeds in European species of Elatine is great, both between the species and the populations. Discrimination analysis showed that all six traits significantly differentiate the populations studied (λ = 0.001, p < 0.001), and the greatest contributions were “number of pits”, “rectangle_a”, and “the angle curvature”. Multidimensional scaling based on a correlation matrix of Mahalanobis distance of the six features studied revealed the greatest similarity between the three populations of E. alsinastrum, E. macropoda, and E. hexandra. Regarding interspecific differences, a Kruskal–Wallis tests showed that, in many cases, lack of statistically significant differences between species relative to the studied seed traits. If distinction of species is only based on seeds, especially if only a few seeds are evaluated, the following species pairs can be easily confused: E. alsinastrum and E. orthosper…
format: application/pdf
format: text/html
creator: Agnieszka Popiela
creator: Andrzej Łysko
creator: Bożenna Białecka
creator: Magdalena Marta Bihun
creator: Gábor Sramkó
creator: Waldemar Staroń
creator: Anetta Wieczorek
creator: Attila Molnár V.
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.3399
publisher: PeerJ Inc.
rights: © 2017 Popiela et al.
abstract: Elatine L. contains ca. 25 small, herbaceous, annual species distributed in ephemeral waters in both hemispheres. All species are amphibious and characterized by a high degree of morphological variability. The importance of seed morphology in Elatine taxonomy has been emphasized by many authors. The degree of seed curvature and seed coat reticulation have been traditionally considered very important in recognizing individual species of this genus. Seed morphometric characteristics of 10 Elatine species, including all European native taxa, are provided on the basis of material from two or three populations of each species. A total of 24–50 seeds were studied from each population, altogether 1,260 images were used for the morphometric study. In total, six parameters were measured from SEM pictures: object surface area, profile specific perimeter (object circuit), rectangle of the object (a) length, rectangle of the object (b) width, angle of the seed curvature, and number of pits in the seed coat counted in the middle row. Our study shows that the range of morphological variation of seeds in European species of Elatine is great, both between the species and the populations. Discrimination analysis showed that all six traits significantly differentiate the populations studied (λ = 0.001, p < 0.001), and the greatest contributions were “number of pits”, “rectangle_a”, and “the angle curvature”. Multidimensional scaling based on a correlation matrix of Mahalanobis distance of the six features studied revealed the greatest similarity between the three populations of E. alsinastrum, E. macropoda, and E. hexandra. Regarding interspecific differences, a Kruskal–Wallis tests showed that, in many cases, lack of statistically significant differences between species relative to the studied seed traits. If distinction of species is only based on seeds, especially if only a few seeds are evaluated, the following species pairs can be easily confused: E. alsinastrum and E. orthosper…
bibliographic citation: Popiela et al. (2017) Seed morphometric characteristics of European species of Elatine (Elatinaceae). PeerJ 5:e3399 https://doi.org/10.7717/peerj.3399
date submitted: 2016-10-03
date accepted: 2017-05-10
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Popiela
  given name: Agnieszka
author list: Agent
  family name: Łysko
  given name: Andrzej
author list: Agent
  family name: Białecka
  given name: Bożenna
author list: Agent
  family name: Bihun
  given name: Magdalena Marta
author list: Agent
  family name: Sramkó
  given name: Gábor
author list: Agent
  family name: Staroń
  given name: Waldemar
author list: Agent
  family name: Wieczorek
  given name: Anetta
author list: Agent
  family name: Molnár V.
  given name: Attila
doi: 10.7717/peerj.3399
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Popiela et al.
attribution name: Popiela et al.

Selection of housekeeping genes as internal controls for quantitative RT-PCR analysis of the veined rapa whelk (Rapana venosa)
type: item
type: AcademicArticle
description: Background The veined rapa whelk Rapana venosa is an important commercial shellfish in China and quantitative real-time PCR (qRT-PCR) has become the standard method to study gene expression in R. venosa. For accurate and reliable gene expression results, qRT-PCR assays require housekeeping genes as internal controls, which display highly uniform expression in different tissues or stages of development. However, to date no studies have validated housekeeping genes in R. venosa for use as internal controls for qRT-PCR. Methods In this study, we selected the following 13 candidate genes for suitability as internal controls: elongation factor-1α (EF-1α), α-actin (ACT), cytochrome c oxidase subunit 1 (COX1), nicotinamide adenine dinucleotide dehydrogenase (ubiquinone) 1α subcomplex subunit 7 (NDUFA7), 60S ribosomal protein L5 (RL5), 60S ribosomal protein L28 (RL28), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β-tubulin (TUBB), 40S ribosomal protein S25 (RS25), 40S ribosomal protein S8 (RS8), ubiquitin-conjugating enzyme E2 (UBE2), histone H3 (HH3), and peptidyl-prolyl cis-trans isomerase A (PPIA). We measured the expression levels of these 13 candidate internal controls in eight different tissues and twelve larvae developmental stages by qRT-PCR. Further analysis of the expression stability of the tested genes was performed using GeNorm and RefFinder algorithms. Results Of the 13 candidate genes tested, we found that EF-1α was the most stable internal control gene in almost all adult tissue samples investigated with RL5 and RL28 as secondary choices. For the normalization of a single specific tissue, we suggested that EF-1α and NDUFA7 are the best combination in gonad, as well as COX1 and RL28 for intestine, EF-1α and RL5 for kidney, EF-1α and COX1 for gill, EF-1α and RL28 for Leiblein and mantle, EF-1α, RL5, and NDUFA7 for liver, GAPDH, PPIA, and RL28 for hemocyte. From a developmental perspective, we found that RL28 was the most stable gene in all developmental s…
format: application/pdf
format: text/html
creator: Hao Song
creator: Xin Dang
creator: Yuan-qiu He
creator: Tao Zhang
creator: Hai-yan Wang
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3398
publisher: PeerJ Inc.
rights: © 2017 Song et al.
abstract: Background The veined rapa whelk Rapana venosa is an important commercial shellfish in China and quantitative real-time PCR (qRT-PCR) has become the standard method to study gene expression in R. venosa. For accurate and reliable gene expression results, qRT-PCR assays require housekeeping genes as internal controls, which display highly uniform expression in different tissues or stages of development. However, to date no studies have validated housekeeping genes in R. venosa for use as internal controls for qRT-PCR. Methods In this study, we selected the following 13 candidate genes for suitability as internal controls: elongation factor-1α (EF-1α), α-actin (ACT), cytochrome c oxidase subunit 1 (COX1), nicotinamide adenine dinucleotide dehydrogenase (ubiquinone) 1α subcomplex subunit 7 (NDUFA7), 60S ribosomal protein L5 (RL5), 60S ribosomal protein L28 (RL28), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β-tubulin (TUBB), 40S ribosomal protein S25 (RS25), 40S ribosomal protein S8 (RS8), ubiquitin-conjugating enzyme E2 (UBE2), histone H3 (HH3), and peptidyl-prolyl cis-trans isomerase A (PPIA). We measured the expression levels of these 13 candidate internal controls in eight different tissues and twelve larvae developmental stages by qRT-PCR. Further analysis of the expression stability of the tested genes was performed using GeNorm and RefFinder algorithms. Results Of the 13 candidate genes tested, we found that EF-1α was the most stable internal control gene in almost all adult tissue samples investigated with RL5 and RL28 as secondary choices. For the normalization of a single specific tissue, we suggested that EF-1α and NDUFA7 are the best combination in gonad, as well as COX1 and RL28 for intestine, EF-1α and RL5 for kidney, EF-1α and COX1 for gill, EF-1α and RL28 for Leiblein and mantle, EF-1α, RL5, and NDUFA7 for liver, GAPDH, PPIA, and RL28 for hemocyte. From a developmental perspective, we found that RL28 was the most stable gene in all developmental s…
bibliographic citation: Song et al. (2017) Selection of housekeeping genes as internal controls for quantitative RT-PCR analysis of the veined rapa whelk (Rapana venosa). PeerJ 5:e3398 https://doi.org/10.7717/peerj.3398
date submitted: 2017-03-28
date accepted: 2017-05-09
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Hao
author list: Agent
  family name: Dang
  given name: Xin
author list: Agent
  family name: He
  given name: Yuan-qiu
author list: Agent
  family name: Zhang
  given name: Tao
author list: Agent
  family name: Wang
  given name: Hai-yan
doi: 10.7717/peerj.3398
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Song et al.
attribution name: Song et al.

Transcriptome analysis reveals the regulation of brassinosteroids on petal growth in Gerbera hybrida
type: item
type: AcademicArticle
description: Gerbera hybrida is a cut-flower crop of global importance, and an understanding of the mechanisms underlying petal development is vital for the continued commercial development of this plant species. Brassinosteroids (BRs), a class of phytohormones, are known to play a major role in cell expansion, but their effect on petal growth in G. hybrida is largely unexplored. In this study, we found that the brassinolide (BL), the most active BR, promotes petal growth by lengthening cells in the middle and basal regions of petals, and that this effect on petal growth was greater than that of gibberellin (GA). The RNA-seq (high-throughput cDNA sequencing) technique was employed to investigate the regulatory mechanisms by which BRs control petal growth. A global transcriptome analysis of the response to BRs in petals was conducted and target genes regulated by BR were identified. These differentially expressed genes (DEGs) include various transcription factors (TFs) that were activated during the early stage (0.5 h) of BL treatment, as well as cell wall proteins whose expression was regulated at a late stage (10 h). BR-responsive DEGs are involved in multiple plant hormone signal pathways, hormone biosynthesis and biotic and abiotic stress responses, showing that the regulation of petal growth by BRs is a complex network of processes. Thus, our study provides new insights at the transcriptional level into the molecular mechanisms of BR regulation of petal growth in G. hybrida.
format: application/pdf
format: text/html
creator: Gan Huang
creator: Meixiang Han
creator: Wei Yao
creator: Yaqin Wang
subject: Bioinformatics
subject: Developmental Biology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.3382
publisher: PeerJ Inc.
rights: © 2017 Huang et al.
abstract: Gerbera hybrida is a cut-flower crop of global importance, and an understanding of the mechanisms underlying petal development is vital for the continued commercial development of this plant species. Brassinosteroids (BRs), a class of phytohormones, are known to play a major role in cell expansion, but their effect on petal growth in G. hybrida is largely unexplored. In this study, we found that the brassinolide (BL), the most active BR, promotes petal growth by lengthening cells in the middle and basal regions of petals, and that this effect on petal growth was greater than that of gibberellin (GA). The RNA-seq (high-throughput cDNA sequencing) technique was employed to investigate the regulatory mechanisms by which BRs control petal growth. A global transcriptome analysis of the response to BRs in petals was conducted and target genes regulated by BR were identified. These differentially expressed genes (DEGs) include various transcription factors (TFs) that were activated during the early stage (0.5 h) of BL treatment, as well as cell wall proteins whose expression was regulated at a late stage (10 h). BR-responsive DEGs are involved in multiple plant hormone signal pathways, hormone biosynthesis and biotic and abiotic stress responses, showing that the regulation of petal growth by BRs is a complex network of processes. Thus, our study provides new insights at the transcriptional level into the molecular mechanisms of BR regulation of petal growth in G. hybrida.
bibliographic citation: Huang et al. (2017) Transcriptome analysis reveals the regulation of brassinosteroids on petal growth in Gerbera hybrida. PeerJ 5:e3382 https://doi.org/10.7717/peerj.3382
date submitted: 2017-02-22
date accepted: 2017-05-05
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Gan
author list: Agent
  family name: Han
  given name: Meixiang
author list: Agent
  family name: Yao
  given name: Wei
author list: Agent
  family name: Wang
  given name: Yaqin
doi: 10.7717/peerj.3382
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Huang et al.
attribution name: Huang et al.

Quercetin reduces hydroxyurea induced cytotoxicity in immortalized mouse aortic endothelial cells
type: item
type: AcademicArticle
description: Background Chronic inflammation is a characteristic of sickle cell disease (SCD), and is invariably associated with vascular endothelial injury. Hydroxyurea (HU), a naturally cytotoxic chemotherapeutic agent, is the only FDA drug approved for SCD, and is therefore naturally cytotoxic. Quercetin (QCT) is a dietary flavonoid found ubiquitously in plants and foods that have anti-oxidative and anti-inflammatory characteristics. Our hypothesis is that dietary QCT will decrease cytotoxic effects of lipopolysaccharide (LPS) and HU induced vascular cell damage. Methods Lipopolysaccharide (LPS) was used to induce inflammation in immortalized mouse aortic endothelial cells (iMAECs), providing an in vitro model of inflamed endothelial cells. The cells were exposed to LPS throughout the entire experiment. Interventions included treating the LPS exposed cells with QCT, HU, or QCT + HU over 50 hours. The 50-hour period included 24 hours of varying treatments, followed by two hours of hypoxic exposure and then 24 hours under normal aerobic exposure. Results LDH level was significantly higher for LPS treated versus untreated cells (P = 0.0004). LPS plus 30 micromole QCT reduced the LDH (p = 0.1, trend), whereas LPS plus 100 micromoles HU, significantly increased LDH (p = 0.0004). However, LPS plus treatment with 30 micromoles QCT/100 micromoles HU, significantly reduced LDH, compared with HU alone (p = 0.0002). Discussion These results suggest that quercetin may be effective against vascular endothelial cell damage for iMAECs in vitro. In particular, it shows promise in preventing HU-induced cytotoxicity, surprisingly found from these results. This latter finding is important, and should be given more consideration, since HU is the only FDA-approved drug for treating sickle cell patients, and its use is rapidly increasing.
format: application/pdf
format: text/html
creator: Zachary M. Kiser
creator: Monica D.M. McGee
creator: Racquel J. Wright
creator: Alexander Quarshie
creator: Gale W. Newman
creator: Karen R. Randall
creator: Jonathan K. Stiles
creator: Adel Driss
creator: Jacqueline M. Hibbert
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3376
publisher: PeerJ Inc.
rights: © 2017 Kiser et al.
abstract: Background Chronic inflammation is a characteristic of sickle cell disease (SCD), and is invariably associated with vascular endothelial injury. Hydroxyurea (HU), a naturally cytotoxic chemotherapeutic agent, is the only FDA drug approved for SCD, and is therefore naturally cytotoxic. Quercetin (QCT) is a dietary flavonoid found ubiquitously in plants and foods that have anti-oxidative and anti-inflammatory characteristics. Our hypothesis is that dietary QCT will decrease cytotoxic effects of lipopolysaccharide (LPS) and HU induced vascular cell damage. Methods Lipopolysaccharide (LPS) was used to induce inflammation in immortalized mouse aortic endothelial cells (iMAECs), providing an in vitro model of inflamed endothelial cells. The cells were exposed to LPS throughout the entire experiment. Interventions included treating the LPS exposed cells with QCT, HU, or QCT + HU over 50 hours. The 50-hour period included 24 hours of varying treatments, followed by two hours of hypoxic exposure and then 24 hours under normal aerobic exposure. Results LDH level was significantly higher for LPS treated versus untreated cells (P = 0.0004). LPS plus 30 micromole QCT reduced the LDH (p = 0.1, trend), whereas LPS plus 100 micromoles HU, significantly increased LDH (p = 0.0004). However, LPS plus treatment with 30 micromoles QCT/100 micromoles HU, significantly reduced LDH, compared with HU alone (p = 0.0002). Discussion These results suggest that quercetin may be effective against vascular endothelial cell damage for iMAECs in vitro. In particular, it shows promise in preventing HU-induced cytotoxicity, surprisingly found from these results. This latter finding is important, and should be given more consideration, since HU is the only FDA-approved drug for treating sickle cell patients, and its use is rapidly increasing.
bibliographic citation: Kiser et al. (2017) Quercetin reduces hydroxyurea induced cytotoxicity in immortalized mouse aortic endothelial cells. PeerJ 5:e3376 https://doi.org/10.7717/peerj.3376
date submitted: 2017-03-22
date accepted: 2017-05-04
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kiser
  given name: Zachary M.
author list: Agent
  family name: McGee
  given name: Monica D.M.
author list: Agent
  family name: Wright
  given name: Racquel J.
author list: Agent
  family name: Quarshie
  given name: Alexander
author list: Agent
  family name: Newman
  given name: Gale W.
author list: Agent
  family name: Randall
  given name: Karen R.
author list: Agent
  family name: Stiles
  given name: Jonathan K.
author list: Agent
  family name: Driss
  given name: Adel
author list: Agent
  family name: Hibbert
  given name: Jacqueline M.
doi: 10.7717/peerj.3376
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Kiser et al.
attribution name: Kiser et al.

Pond dyes are Culex mosquito oviposition attractants
type: item
type: AcademicArticle
description: Background British mosquito population distribution, abundance, species composition and potential for mosquito disease transmission are intimately linked to the physical environment. The presence of ponds and water storage can significantly increase the density of particular mosquito species in the garden. Culex pipiens is the mosquito most commonly found in UK gardens and a potential vector of West Nile Virus WNV, although the current risk of transmission is low. However any factors that significantly change the distribution and population of C. pipiens are likely to impact subsequent risk of disease transmission. Pond dyes are used to control algal growth and improve aesthetics of still water reflecting surrounding planting. However, it is well documented that females of some species of mosquito prefer to lay eggs in dark water and/or containers of different colours and we predict that dyed ponds will be attractive to Culex mosquitoes. Methods Black pond dye was used in oviposition choice tests using wild-caught gravid C. pipiens. Larvae from wild-caught C. pipiens were also reared in the pond dye to determine whether it had any impact on survival. An emergence trap caught any adults that emerged from the water. Water butts (80 L) were positioned around university glasshouses and woodland and treated with black pond dye or left undyed. Weekly sampling over a six month period through summer and autumn was performed to quantified numbers of larvae and pupae in each treatment and habitat. Results Gravid female Culex mosquitoes preferred to lay eggs in dyed water. This was highly significant in tests conducted under laboratory conditions and in a semi-field choice test. Despite this, survivorship in black dyed water was significantly reduced compared to undyed water. Seasonal analysis of wild larval and pupal numbers in two habitats with and without dye showed no impact of dye but a significant impact of season and habitat. Mosquitoes were more successful, with signif…
format: application/pdf
format: text/html
creator: Natali Ortiz Perea
creator: Amanda Callaghan
subject: Biosphere Interactions
subject: Ecology
subject: Entomology
subject: Environmental Impacts
subject: Freshwater Biology
description: doi:10.7717/peerj.3361
publisher: PeerJ Inc.
rights: © 2017 Ortiz Perea and Callaghan
abstract: Background British mosquito population distribution, abundance, species composition and potential for mosquito disease transmission are intimately linked to the physical environment. The presence of ponds and water storage can significantly increase the density of particular mosquito species in the garden. Culex pipiens is the mosquito most commonly found in UK gardens and a potential vector of West Nile Virus WNV, although the current risk of transmission is low. However any factors that significantly change the distribution and population of C. pipiens are likely to impact subsequent risk of disease transmission. Pond dyes are used to control algal growth and improve aesthetics of still water reflecting surrounding planting. However, it is well documented that females of some species of mosquito prefer to lay eggs in dark water and/or containers of different colours and we predict that dyed ponds will be attractive to Culex mosquitoes. Methods Black pond dye was used in oviposition choice tests using wild-caught gravid C. pipiens. Larvae from wild-caught C. pipiens were also reared in the pond dye to determine whether it had any impact on survival. An emergence trap caught any adults that emerged from the water. Water butts (80 L) were positioned around university glasshouses and woodland and treated with black pond dye or left undyed. Weekly sampling over a six month period through summer and autumn was performed to quantified numbers of larvae and pupae in each treatment and habitat. Results Gravid female Culex mosquitoes preferred to lay eggs in dyed water. This was highly significant in tests conducted under laboratory conditions and in a semi-field choice test. Despite this, survivorship in black dyed water was significantly reduced compared to undyed water. Seasonal analysis of wild larval and pupal numbers in two habitats with and without dye showed no impact of dye but a significant impact of season and habitat. Mosquitoes were more successful, with signif…
bibliographic citation: Ortiz Perea et al. (2017) Pond dyes are Culex mosquito oviposition attractants. PeerJ 5:e3361 https://doi.org/10.7717/peerj.3361
date submitted: 2017-02-15
date accepted: 2017-04-27
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ortiz Perea
  given name: Natali
author list: Agent
  family name: Callaghan
  given name: Amanda
doi: 10.7717/peerj.3361
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Ortiz Perea and Callaghan
attribution name: Ortiz Perea and Callaghan

Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators
type: item
type: AcademicArticle
description: Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the mechanism and controls of overall structure, stability, and function of the microbiome. We sought to test how coral microbiome dynamics were affected by interactions between two bacteria: Vibrio coralliilyticus, a known temperature-dependent pathogen of some corals, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged reef-building coral with V. coralliilyticus in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene profiling time-series. Vibrio coralliilyticus inoculation increased the mean relative abundance of Vibrios by greater than 35% from the 4 to 8 hour time point, but not in the 24 & 32 hour time points. However, strong secondary effects of the Vibrio challenge were also observed for the rest of the microbiome such as increased richness (observed species), and reduced stability (increased beta-diversity). Moreover, after the transient increase in Vibrios, two lineages of bacteria (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that V. coralliilyticus challenge opens niche space for these known opportunists. Rhodobacterales increased from 6.99% (±0.05 SEM) to a maximum mean relative abundance of 48.75% (±0.14 SEM) in the final time point and Cytophagales from <0.001% to 3.656%. Halobacteriovorax predators are commonly present at low-abundance on coral surfaces. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming foreign or “a…
format: application/pdf
format: text/html
creator: Rory M. Welsh
creator: Stephanie M. Rosales
creator: Jesse R. Zaneveld
creator: Jérôme P. Payet
creator: Ryan McMinds
creator: Steven L. Hubbs
creator: Rebecca L. Vega Thurber
subject: Bioinformatics
subject: Ecology
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.3315
publisher: PeerJ Inc.
rights: © 2017 Welsh et al.
abstract: Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the mechanism and controls of overall structure, stability, and function of the microbiome. We sought to test how coral microbiome dynamics were affected by interactions between two bacteria: Vibrio coralliilyticus, a known temperature-dependent pathogen of some corals, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged reef-building coral with V. coralliilyticus in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene profiling time-series. Vibrio coralliilyticus inoculation increased the mean relative abundance of Vibrios by greater than 35% from the 4 to 8 hour time point, but not in the 24 & 32 hour time points. However, strong secondary effects of the Vibrio challenge were also observed for the rest of the microbiome such as increased richness (observed species), and reduced stability (increased beta-diversity). Moreover, after the transient increase in Vibrios, two lineages of bacteria (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that V. coralliilyticus challenge opens niche space for these known opportunists. Rhodobacterales increased from 6.99% (±0.05 SEM) to a maximum mean relative abundance of 48.75% (±0.14 SEM) in the final time point and Cytophagales from <0.001% to 3.656%. Halobacteriovorax predators are commonly present at low-abundance on coral surfaces. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming foreign or “a…
bibliographic citation: Welsh et al. (2017) Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators. PeerJ 5:e3315 https://doi.org/10.7717/peerj.3315
date submitted: 2015-11-25
date accepted: 2017-04-14
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Welsh
  given name: Rory M.
author list: Agent
  family name: Rosales
  given name: Stephanie M.
author list: Agent
  family name: Zaneveld
  given name: Jesse R.
author list: Agent
  family name: Payet
  given name: Jérôme P.
author list: Agent
  family name: McMinds
  given name: Ryan
author list: Agent
  family name: Hubbs
  given name: Steven L.
author list: Agent
  family name: Vega Thurber
  given name: Rebecca L.
doi: 10.7717/peerj.3315
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Welsh et al.
attribution name: Welsh et al.

Assessing the utility of an institutional publications officer: a pilot assessment
type: item
type: AcademicArticle
description: Background The scholarly publication landscape is changing rapidly. We investigated whether the introduction of an institutional publications officer might help facilitate better knowledge of publication topics and related resources, and effectively support researchers to publish. Methods In September 2015, a purpose-built survey about researchers’ knowledge and perceptions of publication practices was administered at five Ottawa area research institutions. Subsequently, we publicly announced a newly hired publications officer (KDC) who then began conducting outreach at two of the institutions. Specifically, the publications officer gave presentations, held one-to-one consultations, developed electronic newsletter content, and generated and maintained a webpage of resources. In March 2016, we re-surveyed our participants regarding their knowledge and perceptions of publishing. Mean scores to the perception questions, and the percent of correct responses to the knowledge questions, pre and post survey, were computed for each item. The difference between these means or calculated percentages was then examined across the survey measures. Results 82 participants completed both surveys. Of this group, 29 indicated that they had exposure to the publications officer, while the remaining 53 indicated they did not. Interaction with the publications officer led to improvements in half of the knowledge items (7/14 variables). While improvements in knowledge of publishing were also found among those who reported not to have interacted with the publications officer (9/14), these effects were often smaller in magnitude. Scores for some publication knowledge variables actually decreased between the pre and post survey (3/14). Effects for researchers’ perceptions of publishing increased for 5/6 variables in the group that interacted with the publications officer. Discussion This pilot provides initial indication that, in a short timeframe, introducing an institutional publications …
format: application/pdf
format: text/html
creator: Kelly D. Cobey
creator: James Galipeau
creator: Larissa Shamseer
creator: David Moher
subject: Ethical Issues
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.3294
publisher: PeerJ Inc.
rights: © 2017 Cobey et al.
abstract: Background The scholarly publication landscape is changing rapidly. We investigated whether the introduction of an institutional publications officer might help facilitate better knowledge of publication topics and related resources, and effectively support researchers to publish. Methods In September 2015, a purpose-built survey about researchers’ knowledge and perceptions of publication practices was administered at five Ottawa area research institutions. Subsequently, we publicly announced a newly hired publications officer (KDC) who then began conducting outreach at two of the institutions. Specifically, the publications officer gave presentations, held one-to-one consultations, developed electronic newsletter content, and generated and maintained a webpage of resources. In March 2016, we re-surveyed our participants regarding their knowledge and perceptions of publishing. Mean scores to the perception questions, and the percent of correct responses to the knowledge questions, pre and post survey, were computed for each item. The difference between these means or calculated percentages was then examined across the survey measures. Results 82 participants completed both surveys. Of this group, 29 indicated that they had exposure to the publications officer, while the remaining 53 indicated they did not. Interaction with the publications officer led to improvements in half of the knowledge items (7/14 variables). While improvements in knowledge of publishing were also found among those who reported not to have interacted with the publications officer (9/14), these effects were often smaller in magnitude. Scores for some publication knowledge variables actually decreased between the pre and post survey (3/14). Effects for researchers’ perceptions of publishing increased for 5/6 variables in the group that interacted with the publications officer. Discussion This pilot provides initial indication that, in a short timeframe, introducing an institutional publications …
bibliographic citation: Cobey et al. (2017) Assessing the utility of an institutional publications officer: a pilot assessment. PeerJ 5:e3294 https://doi.org/10.7717/peerj.3294
date submitted: 2017-02-08
date accepted: 2017-04-10
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cobey
  given name: Kelly D.
author list: Agent
  family name: Galipeau
  given name: James
author list: Agent
  family name: Shamseer
  given name: Larissa
author list: Agent
  family name: Moher
  given name: David
doi: 10.7717/peerj.3294
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Cobey et al.
attribution name: Cobey et al.

Difference on cone size preferences between two coniferous species by Great Spotted Woodpecker (Dendrocopos major)
type: item
type: AcademicArticle
description: The number of species that specialize in pre-dispersal seed predation is relatively small. Examples of specialized pre-dispersal seed predators adapted to feeding on closed cones include vertebrate species like Crossbills, Squirrels, Nutcrackers and Woodpeckers. Seed predation selects against certain phenotypic features of cones and favors another phenotypic features. In this study, we document preferences of the Great Spotted Woodpecker (Dendrocopos major) for specific traits in the cones of Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We found that the Great Spotted Woodpecker prefers to feed on medium sized Norway spruce cones. The results suggest a disruptive selection that favors the extreme cone lengths in Norway spruce. In Scots pine, the woodpeckers avoided cones with large apophyses. Further, the selectivity for the specific characteristics of the cones is probably related to the configuration of the anvil, a place at which woodpeckers extract seeds from the cones. We think that the Great Spotted Woodpecker preferences in relation to the morphological characteristics of cones are a key to the design of the anvil in order to maximize the use of it as a tool for processing cones of both the Norway spruce and the Scots pine.
format: application/pdf
format: text/html
creator: Łukasz Dylewski
creator: Reuven Yosef
creator: Łukasz Myczko
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.3288
publisher: PeerJ Inc.
rights: © 2017 Dylewski et al.
abstract: The number of species that specialize in pre-dispersal seed predation is relatively small. Examples of specialized pre-dispersal seed predators adapted to feeding on closed cones include vertebrate species like Crossbills, Squirrels, Nutcrackers and Woodpeckers. Seed predation selects against certain phenotypic features of cones and favors another phenotypic features. In this study, we document preferences of the Great Spotted Woodpecker (Dendrocopos major) for specific traits in the cones of Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We found that the Great Spotted Woodpecker prefers to feed on medium sized Norway spruce cones. The results suggest a disruptive selection that favors the extreme cone lengths in Norway spruce. In Scots pine, the woodpeckers avoided cones with large apophyses. Further, the selectivity for the specific characteristics of the cones is probably related to the configuration of the anvil, a place at which woodpeckers extract seeds from the cones. We think that the Great Spotted Woodpecker preferences in relation to the morphological characteristics of cones are a key to the design of the anvil in order to maximize the use of it as a tool for processing cones of both the Norway spruce and the Scots pine.
bibliographic citation: Dylewski et al. (2017) Difference on cone size preferences between two coniferous species by Great Spotted Woodpecker (Dendrocopos major). PeerJ 5:e3288 https://doi.org/10.7717/peerj.3288
date submitted: 2017-01-18
date accepted: 2017-04-10
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dylewski
  given name: Łukasz
author list: Agent
  family name: Yosef
  given name: Reuven
author list: Agent
  family name: Myczko
  given name: Łukasz
doi: 10.7717/peerj.3288
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: ©2017 Dylewski et al.
attribution name: Dylewski et al.

Largest baleen whale mass mortality during strong El Niño event is likely related to harmful toxic algal bloom
type: item
type: AcademicArticle
description: While large mass mortality events (MMEs) are well known for toothed whales, they have been rare in baleen whales due to their less gregarious behavior. Although in most cases the cause of mortality has not been conclusively identified, some baleen whale mortality events have been linked to bio-oceanographic conditions, such as harmful algal blooms (HABs). In Southern Chile, HABs can be triggered by the ocean–atmosphere phenomenon El Niño. The frequency of the strongest El Niño events is increasing due to climate change. In March 2015, by far the largest reported mass mortality of baleen whales took place in a gulf in Southern Chile. Here, we show that the synchronous death of at least 343, primarily sei whales can be attributed to HABs during a building El Niño. Although considered an oceanic species, the sei whales died while feeding near to shore in previously unknown large aggregations. This provides evidence of new feeding grounds for the species. The combination of older and newer remains of whales in the same area indicate that MMEs have occurred more than once in recent years. Large HABs and reports of marine mammal MMEs along the Northeast Pacific coast may indicate similar processes in both hemispheres. Increasing MMEs through HABs may become a serious concern in the conservation of endangered whale species.
format: application/pdf
format: text/html
creator: Verena Häussermann
creator: Carolina S. Gutstein
creator: Michael Bedington
creator: David Cassis
creator: Carlos Olavarria
creator: Andrew C. Dale
creator: Ana M. Valenzuela-Toro
creator: Maria Jose Perez-Alvarez
creator: Hector H. Sepúlveda
creator: Kaitlin M. McConnell
creator: Fanny E. Horwitz
creator: Günter Försterra
subject: Conservation Biology
subject: Ecosystem Science
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.3123
publisher: PeerJ Inc.
rights: © 2017 Häussermann et al.
abstract: While large mass mortality events (MMEs) are well known for toothed whales, they have been rare in baleen whales due to their less gregarious behavior. Although in most cases the cause of mortality has not been conclusively identified, some baleen whale mortality events have been linked to bio-oceanographic conditions, such as harmful algal blooms (HABs). In Southern Chile, HABs can be triggered by the ocean–atmosphere phenomenon El Niño. The frequency of the strongest El Niño events is increasing due to climate change. In March 2015, by far the largest reported mass mortality of baleen whales took place in a gulf in Southern Chile. Here, we show that the synchronous death of at least 343, primarily sei whales can be attributed to HABs during a building El Niño. Although considered an oceanic species, the sei whales died while feeding near to shore in previously unknown large aggregations. This provides evidence of new feeding grounds for the species. The combination of older and newer remains of whales in the same area indicate that MMEs have occurred more than once in recent years. Large HABs and reports of marine mammal MMEs along the Northeast Pacific coast may indicate similar processes in both hemispheres. Increasing MMEs through HABs may become a serious concern in the conservation of endangered whale species.
bibliographic citation: Häussermann et al. (2017) Largest baleen whale mass mortality during strong El Niño event is likely related to harmful toxic algal bloom. PeerJ 5:e3123 https://doi.org/10.7717/peerj.3123
date submitted: 2016-02-12
date accepted: 2017-02-26
issued: 2017-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Häussermann
  given name: Verena
author list: Agent
  family name: Gutstein
  given name: Carolina S.
author list: Agent
  family name: Bedington
  given name: Michael
author list: Agent
  family name: Cassis
  given name: David
author list: Agent
  family name: Olavarria
  given name: Carlos
author list: Agent
  family name: Dale
  given name: Andrew C.
author list: Agent
  family name: Valenzuela-Toro
  given name: Ana M.
author list: Agent
  family name: Perez-Alvarez
  given name: Maria Jose
author list: Agent
  family name: Sepúlveda
  given name: Hector H.
author list: Agent
  family name: McConnell
  given name: Kaitlin M.
author list: Agent
  family name: Horwitz
  given name: Fanny E.
author list: Agent
  family name: Försterra
  given name: Günter
doi: 10.7717/peerj.3123
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-31
copyright: © 2017 Häussermann et al.
attribution name: Häussermann et al.

Patterns of bleaching and mortality following widespread warming events in 2014 and 2015 at the Hanauma Bay Nature Preserve, Hawai‘i
type: item
type: AcademicArticle
description: Drastic increases in global carbon emissions in the past century have led to elevated sea surface temperatures that negatively affect coral reef organisms. Worldwide coral bleaching-related mortality is increasing and data has shown even isolated and protected reefs are vulnerable to the effects of global climate change. In 2014 and 2015, coral reefs in the main Hawaiian Islands (MHI) suffered up to 90% bleaching, with higher than 50% subsequent mortality in some areas. The location and severity of bleaching and mortality was strongly influenced by the spatial and temporal patterns of elevated seawater temperatures. The main objective of this research was to understand the spatial extent of bleaching mortality in Hanauma Bay Nature Preserve (HBNP), O‘ahu, Hawai‘i to gain a baseline understanding of the physical processes that influence localized bleaching dynamics. Surveys at HBNP in October 2015 and January 2016 revealed extensive bleaching (47%) and high levels of coral mortality (9.8%). Bleaching was highly variable among the four HBNP sectors and ranged from a low of ∼31% in the central bay at Channel (CH) to a high of 57% in the area most frequented by visitors (Keyhole; KH). The highest levels of bleaching occurred in two sectors with different circulation patterns: KH experienced comparatively low circulation velocity and a low temperature increase while Witches Brew (WB) and Backdoors (BD) experienced higher circulation velocity and higher temperature increase. Cumulative mortality was highest at WB (5.0%) and at BD (2.9%) although WB circulation velocity is significantly higher. HBNP is minimally impacted by local factors that can lead to decline such as high fishing pressure or sedimentation although human use is high. Despite the lack of these influences, high coral mortality occurred. Visitor impacts are strikingly different in the two sectors that experienced the highest mortality evidenced by the differences in coral cover associated with visitor use h…
format: application/pdf
format: text/html
creator: Ku‘ulei S. Rodgers
creator: Keisha D. Bahr
creator: Paul L. Jokiel
creator: Angela Richards Donà
subject: Climate Change Biology
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.3355
publisher: PeerJ Inc.
rights: © 2017 Rodgers et al.
abstract: Drastic increases in global carbon emissions in the past century have led to elevated sea surface temperatures that negatively affect coral reef organisms. Worldwide coral bleaching-related mortality is increasing and data has shown even isolated and protected reefs are vulnerable to the effects of global climate change. In 2014 and 2015, coral reefs in the main Hawaiian Islands (MHI) suffered up to 90% bleaching, with higher than 50% subsequent mortality in some areas. The location and severity of bleaching and mortality was strongly influenced by the spatial and temporal patterns of elevated seawater temperatures. The main objective of this research was to understand the spatial extent of bleaching mortality in Hanauma Bay Nature Preserve (HBNP), O‘ahu, Hawai‘i to gain a baseline understanding of the physical processes that influence localized bleaching dynamics. Surveys at HBNP in October 2015 and January 2016 revealed extensive bleaching (47%) and high levels of coral mortality (9.8%). Bleaching was highly variable among the four HBNP sectors and ranged from a low of ∼31% in the central bay at Channel (CH) to a high of 57% in the area most frequented by visitors (Keyhole; KH). The highest levels of bleaching occurred in two sectors with different circulation patterns: KH experienced comparatively low circulation velocity and a low temperature increase while Witches Brew (WB) and Backdoors (BD) experienced higher circulation velocity and higher temperature increase. Cumulative mortality was highest at WB (5.0%) and at BD (2.9%) although WB circulation velocity is significantly higher. HBNP is minimally impacted by local factors that can lead to decline such as high fishing pressure or sedimentation although human use is high. Despite the lack of these influences, high coral mortality occurred. Visitor impacts are strikingly different in the two sectors that experienced the highest mortality evidenced by the differences in coral cover associated with visitor use h…
bibliographic citation: Rodgers et al. (2017) Patterns of bleaching and mortality following widespread warming events in 2014 and 2015 at the Hanauma Bay Nature Preserve, Hawai‘i. PeerJ 5:e3355 https://doi.org/10.7717/peerj.3355
date submitted: 2017-01-06
date accepted: 2017-04-26
issued: 2017-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodgers
  given name: Ku‘ulei S.
author list: Agent
  family name: Bahr
  given name: Keisha D.
author list: Agent
  family name: Jokiel
  given name: Paul L.
author list: Agent
  family name: Richards Donà
  given name: Angela
doi: 10.7717/peerj.3355
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-30
copyright: ©2017 Rodgers et al.
attribution name: Rodgers et al.

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