PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Automatic single- and multi-label enzymatic function prediction by machine learning
items: Daily rhythms of behavioral and hormonal patterns in male dromedary camels housed in boxes
items: The adaptive value of habitat preferences from a multi-scale spatial perspective: insights from marsh-nesting avian species
items: The Sensed Presence Questionnaire (SenPQ): initial psychometric validation of a measure of the “Sensed Presence” experience
items: SLIMM: species level identification of microorganisms from metagenomes
items: Status of marine turtle rehabilitation in Queensland
items: Disturbed flow in an aquatic environment may create a sensory refuge for aggregated prey
items: Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
items: Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient
items: Molecular barcoding confirms the presence of exotic Asian seaweeds (Pachymeniopsis gargiuli and Grateloupia turuturu) in the Cantabrian Sea, Bay of Biscay

Automatic single- and multi-label enzymatic function prediction by machine learning
type: item
type: AcademicArticle
description: The number of protein structures in the PDB database has been increasing more than 15-fold since 1999. The creation of computational models predicting enzymatic function is of major importance since such models provide the means to better understand the behavior of newly discovered enzymes when catalyzing chemical reactions. Until now, single-label classification has been widely performed for predicting enzymatic function limiting the application to enzymes performing unique reactions and introducing errors when multi-functional enzymes are examined. Indeed, some enzymes may be performing different reactions and can hence be directly associated with multiple enzymatic functions. In the present work, we propose a multi-label enzymatic function classification scheme that combines structural and amino acid sequence information. We investigate two fusion approaches (in the feature level and decision level) and assess the methodology for general enzymatic function prediction indicated by the first digit of the enzyme commission (EC) code (six main classes) on 40,034 enzymes from the PDB database. The proposed single-label and multi-label models predict correctly the actual functional activities in 97.8% and 95.5% (based on Hamming-loss) of the cases, respectively. Also the multi-label model predicts all possible enzymatic reactions in 85.4% of the multi-labeled enzymes when the number of reactions is unknown. Code and datasets are available at https://figshare.com/s/a63e0bafa9b71fc7cbd7.
format: application/pdf
format: text/html
creator: Shervine Amidi
creator: Afshine Amidi
creator: Dimitrios Vlachakis
creator: Nikos Paragios
creator: Evangelia I. Zacharaki
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.3095
publisher: PeerJ Inc.
rights: © 2017 Amidi et al.
abstract: The number of protein structures in the PDB database has been increasing more than 15-fold since 1999. The creation of computational models predicting enzymatic function is of major importance since such models provide the means to better understand the behavior of newly discovered enzymes when catalyzing chemical reactions. Until now, single-label classification has been widely performed for predicting enzymatic function limiting the application to enzymes performing unique reactions and introducing errors when multi-functional enzymes are examined. Indeed, some enzymes may be performing different reactions and can hence be directly associated with multiple enzymatic functions. In the present work, we propose a multi-label enzymatic function classification scheme that combines structural and amino acid sequence information. We investigate two fusion approaches (in the feature level and decision level) and assess the methodology for general enzymatic function prediction indicated by the first digit of the enzyme commission (EC) code (six main classes) on 40,034 enzymes from the PDB database. The proposed single-label and multi-label models predict correctly the actual functional activities in 97.8% and 95.5% (based on Hamming-loss) of the cases, respectively. Also the multi-label model predicts all possible enzymatic reactions in 85.4% of the multi-labeled enzymes when the number of reactions is unknown. Code and datasets are available at https://figshare.com/s/a63e0bafa9b71fc7cbd7.
bibliographic citation: Amidi et al. (2017) Automatic single- and multi-label enzymatic function prediction by machine learning. PeerJ 5:e3095 https://doi.org/10.7717/peerj.3095
date submitted: 2016-11-30
date accepted: 2017-02-15
issued: 2017-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amidi
  given name: Shervine
author list: Agent
  family name: Amidi
  given name: Afshine
author list: Agent
  family name: Vlachakis
  given name: Dimitrios
author list: Agent
  family name: Paragios
  given name: Nikos
author list: Agent
  family name: Zacharaki
  given name: Evangelia I.
doi: 10.7717/peerj.3095
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-29
copyright: © 2017 Amidi et al.
attribution name: Amidi et al.

Daily rhythms of behavioral and hormonal patterns in male dromedary camels housed in boxes
type: item
type: AcademicArticle
description: Background Daily rhythmicity has been observed for a number of hormonal and behavioral variables in mammals. It can be entrained by several external factors, such as light-dark cycle and scheduled feeding. In dromedary camels, daily rhythmicity has been documented only for melatonin secretion and body temperature. In this study, the daily rhythmicity of behavioral repertoire, cortisol and testosterone levels was investigated in captive male camels. Methods Six clinically healthy male dromedary camels (Camelus dromedarius) were used. The animals were housed in single boxes for 24 h daily and fed twice a day. Over a period of 48 h, behavioral observations were made and blood samples taken every two hours. The data were analyzed using diurnality index, conisor analysis and PROC mixed procedure. Results The diurnality index for rumination and lying down was close to 0 (respectively, 0.09 and 0.19), while the indices for stereotypy, standing, feeding and walking were close to 1 (respectively, 0.74, 0.84, 0.92 and 0.85). Cosinor analysis revealed daily rhythmicity for all behaviors and for cortisol levels (acrophase at 12:57) but not for testosterone. Rumination and lying down (inactive behaviors) reached a peak during the scotophase, whereas feeding, walking and stereotypy (active behaviors) reached a peak during the photophase around midday. Cortisol level and expression of stereotypies peaked before and after food distribution and were negatively correlated (r = − 0.287, P = 0.005). Testosterone levels and expression of sexual behaviors were stimulated by the visual and olfactory contacts with the females and were positively correlated (r = 0.164, P = 0.040). Testosterone was also negatively correlated with cortisol (r = − 0.297; P = 0.003). Discussion These preliminary results provided new knowledge about the daily rhythm of behaviors in camels housed in boxes, suggesting that camels exhibit diurnal behavior pattern in the maintenance conditions outlined in the study.…
format: application/pdf
format: text/html
creator: Lydiane Aubè
creator: Meriem Fatnassi
creator: Davide Monaco
creator: Touhami Khorchani
creator: Giovanni Michele Lacalandra
creator: Mohamed Hammadi
creator: Barbara Padalino
subject: Animal Behavior
subject: Veterinary Medicine
description: doi:10.7717/peerj.3074
publisher: PeerJ Inc.
rights: © 2017 Aubè et al.
abstract: Background Daily rhythmicity has been observed for a number of hormonal and behavioral variables in mammals. It can be entrained by several external factors, such as light-dark cycle and scheduled feeding. In dromedary camels, daily rhythmicity has been documented only for melatonin secretion and body temperature. In this study, the daily rhythmicity of behavioral repertoire, cortisol and testosterone levels was investigated in captive male camels. Methods Six clinically healthy male dromedary camels (Camelus dromedarius) were used. The animals were housed in single boxes for 24 h daily and fed twice a day. Over a period of 48 h, behavioral observations were made and blood samples taken every two hours. The data were analyzed using diurnality index, conisor analysis and PROC mixed procedure. Results The diurnality index for rumination and lying down was close to 0 (respectively, 0.09 and 0.19), while the indices for stereotypy, standing, feeding and walking were close to 1 (respectively, 0.74, 0.84, 0.92 and 0.85). Cosinor analysis revealed daily rhythmicity for all behaviors and for cortisol levels (acrophase at 12:57) but not for testosterone. Rumination and lying down (inactive behaviors) reached a peak during the scotophase, whereas feeding, walking and stereotypy (active behaviors) reached a peak during the photophase around midday. Cortisol level and expression of stereotypies peaked before and after food distribution and were negatively correlated (r = − 0.287, P = 0.005). Testosterone levels and expression of sexual behaviors were stimulated by the visual and olfactory contacts with the females and were positively correlated (r = 0.164, P = 0.040). Testosterone was also negatively correlated with cortisol (r = − 0.297; P = 0.003). Discussion These preliminary results provided new knowledge about the daily rhythm of behaviors in camels housed in boxes, suggesting that camels exhibit diurnal behavior pattern in the maintenance conditions outlined in the study.…
bibliographic citation: Aubè et al. (2017) Daily rhythms of behavioral and hormonal patterns in male dromedary camels housed in boxes. PeerJ 5:e3074 https://doi.org/10.7717/peerj.3074
date submitted: 2016-11-04
date accepted: 2017-02-07
issued: 2017-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aubè
  given name: Lydiane
author list: Agent
  family name: Fatnassi
  given name: Meriem
author list: Agent
  family name: Monaco
  given name: Davide
author list: Agent
  family name: Khorchani
  given name: Touhami
author list: Agent
  family name: Lacalandra
  given name: Giovanni Michele
author list: Agent
  family name: Hammadi
  given name: Mohamed
author list: Agent
  family name: Padalino
  given name: Barbara
doi: 10.7717/peerj.3074
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-29
copyright: ©2017 Aubè et al.
attribution name: Aubè et al.

The adaptive value of habitat preferences from a multi-scale spatial perspective: insights from marsh-nesting avian species
type: item
type: AcademicArticle
description: Background Habitat selection and its adaptive outcomes are crucial features for animal life-history strategies. Nevertheless, congruence between habitat preferences and breeding success has been rarely demonstrated, which may result from the single-scale evaluation of animal choices. As habitat selection is a complex multi-scale process in many groups of animal species, investigating adaptiveness of habitat selection in a multi-scale framework is crucial. In this study, we explore whether habitat preferences acting at different spatial scales enhance the fitness of bird species, and check the appropriateness of single vs. multi-scale models. We expected that variables found to be more important for habitat selection at individual scale(s), would coherently play a major role in affecting nest survival at the same scale(s). Methods We considered habitat preferences of two Rallidae species, little crake (Zapornia parva) and water rail (Rallus aquaticus), at three spatial scales (landscape, territory, and nest-site) and related them to nest survival. Single-scale versus multi-scale models (GLS and glmmPQL) were compared to check which model better described adaptiveness of habitat preferences. Consistency between the effect of variables on habitat selection and on nest survival was checked to investigate their adaptive value. Results In both species, multi-scale models for nest survival were more supported than single-scale ones. In little crake, the multi-scale model indicated vegetation density and water depth at the territory scale, as well as vegetation height at nest-site scale, as the most important variables. The first two variables were among the most important for nest survival and habitat selection, and the coherent effects suggested the adaptive value of habitat preferences. In water rail, the multi-scale model of nest survival showed vegetation density at territory scale and extent of emergent vegetation within landscape scale as the most important ones, alt…
format: application/pdf
format: text/html
creator: Jan Jedlikowski
creator: Mattia Brambilla
subject: Animal Behavior
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3164
publisher: PeerJ Inc.
rights: © 2017 Jedlikowski and Brambilla
abstract: Background Habitat selection and its adaptive outcomes are crucial features for animal life-history strategies. Nevertheless, congruence between habitat preferences and breeding success has been rarely demonstrated, which may result from the single-scale evaluation of animal choices. As habitat selection is a complex multi-scale process in many groups of animal species, investigating adaptiveness of habitat selection in a multi-scale framework is crucial. In this study, we explore whether habitat preferences acting at different spatial scales enhance the fitness of bird species, and check the appropriateness of single vs. multi-scale models. We expected that variables found to be more important for habitat selection at individual scale(s), would coherently play a major role in affecting nest survival at the same scale(s). Methods We considered habitat preferences of two Rallidae species, little crake (Zapornia parva) and water rail (Rallus aquaticus), at three spatial scales (landscape, territory, and nest-site) and related them to nest survival. Single-scale versus multi-scale models (GLS and glmmPQL) were compared to check which model better described adaptiveness of habitat preferences. Consistency between the effect of variables on habitat selection and on nest survival was checked to investigate their adaptive value. Results In both species, multi-scale models for nest survival were more supported than single-scale ones. In little crake, the multi-scale model indicated vegetation density and water depth at the territory scale, as well as vegetation height at nest-site scale, as the most important variables. The first two variables were among the most important for nest survival and habitat selection, and the coherent effects suggested the adaptive value of habitat preferences. In water rail, the multi-scale model of nest survival showed vegetation density at territory scale and extent of emergent vegetation within landscape scale as the most important ones, alt…
bibliographic citation: Jedlikowski et al. (2017) The adaptive value of habitat preferences from a multi-scale spatial perspective: insights from marsh-nesting avian species. PeerJ 5:e3164 https://doi.org/10.7717/peerj.3164
date submitted: 2016-11-30
date accepted: 2017-03-08
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jedlikowski
  given name: Jan
author list: Agent
  family name: Brambilla
  given name: Mattia
doi: 10.7717/peerj.3164
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Jedlikowski and Brambilla
attribution name: Jedlikowski and Brambilla

The Sensed Presence Questionnaire (SenPQ): initial psychometric validation of a measure of the “Sensed Presence” experience
type: item
type: AcademicArticle
description: Background The experience of ‘sensed presence’—a feeling or sense that another entity, individual or being is present despite no clear sensory or perceptual evidence—is known to occur in the general population, appears more frequently in religious or spiritual contexts, and seems to be prominent in certain psychiatric or neurological conditions and may reflect specific functions of social cognition or body-image representation systems in the brain. Previous research has relied on ad-hoc measures of the experience and no specific psychometric scale to measure the experience exists to date. Methods Based on phenomenological description in the literature, we created the 16-item Sensed Presence Questionnaire (SenPQ). We recruited participants from (i) a general population sample, and; (ii) a sample including specific selection for religious affiliation, to complete the SenPQ and additional measures of well-being, schizotypy, social anxiety, social imagery, and spiritual experience. We completed an analysis to test internal reliability, the ability of the SenPQ to distinguish between religious and non-religious participants, and whether the SenPQ was specifically related to positive schizotypical experiences and social imagery. A factor analysis was also conducted to examine underlying latent variables. Results The SenPQ was found to be reliable and valid, with religious participants significantly endorsing more items than non-religious participants, and the scale showing a selective relationship with construct relevant measures. Principal components analysis indicates two potential underlying factors interpreted as reflecting ‘benign’ and ‘malign’ sensed presence experiences. Discussion The SenPQ appears to be a reliable and valid measure of sensed presence experience although further validation in neurological and psychiatric conditions is warranted.
format: application/pdf
format: text/html
creator: Joseph M. Barnby
creator: Vaughan Bell
subject: Anthropology
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3149
publisher: PeerJ Inc.
rights: © 2017 Barnby and Bell
abstract: Background The experience of ‘sensed presence’—a feeling or sense that another entity, individual or being is present despite no clear sensory or perceptual evidence—is known to occur in the general population, appears more frequently in religious or spiritual contexts, and seems to be prominent in certain psychiatric or neurological conditions and may reflect specific functions of social cognition or body-image representation systems in the brain. Previous research has relied on ad-hoc measures of the experience and no specific psychometric scale to measure the experience exists to date. Methods Based on phenomenological description in the literature, we created the 16-item Sensed Presence Questionnaire (SenPQ). We recruited participants from (i) a general population sample, and; (ii) a sample including specific selection for religious affiliation, to complete the SenPQ and additional measures of well-being, schizotypy, social anxiety, social imagery, and spiritual experience. We completed an analysis to test internal reliability, the ability of the SenPQ to distinguish between religious and non-religious participants, and whether the SenPQ was specifically related to positive schizotypical experiences and social imagery. A factor analysis was also conducted to examine underlying latent variables. Results The SenPQ was found to be reliable and valid, with religious participants significantly endorsing more items than non-religious participants, and the scale showing a selective relationship with construct relevant measures. Principal components analysis indicates two potential underlying factors interpreted as reflecting ‘benign’ and ‘malign’ sensed presence experiences. Discussion The SenPQ appears to be a reliable and valid measure of sensed presence experience although further validation in neurological and psychiatric conditions is warranted.
bibliographic citation: Barnby et al. (2017) The Sensed Presence Questionnaire (SenPQ): initial psychometric validation of a measure of the “Sensed Presence” experience. PeerJ 5:e3149 https://doi.org/10.7717/peerj.3149
date submitted: 2016-12-14
date accepted: 2017-03-05
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barnby
  given name: Joseph M.
author list: Agent
  family name: Bell
  given name: Vaughan
doi: 10.7717/peerj.3149
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Barnby and Bell
attribution name: Barnby and Bell

SLIMM: species level identification of microorganisms from metagenomes
type: item
type: AcademicArticle
description: Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than when using 16S-rDNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins. The existing microbial community profiling tools commonly deal with this problem by either preparing signature-based unique references or assigning an ambiguous read to its least common ancestor in a taxonomic tree. The former method is limited to making use of the reads which can be mapped to the curated regions, while the latter suffer from the lack of uniquely mapped reads at lower (more specific) taxonomic ranks. Moreover, even if the tools exhibited good performance in calling the organisms present in a sample, there is still room for improvement in determining the correct relative abundance of the organisms. We present a new method Species Level Identification of Microorganisms from Metagenomes (SLIMM) which addresses the above issues by using coverage information of reference genomes to remove unlikely genomes from the analysis and subsequently gain more uniquely mapped reads to assign at lower ranks of a taxonomic tree. SLIMM is based on a few, seemingly easy steps which when combined create a tool that outperforms state-of-the-art tools in run-time and memory usage while being on par or better in computing quantitative and qualitative information at species-level.
format: application/pdf
format: text/html
creator: Temesgen Hailemariam Dadi
creator: Bernhard Y. Renard
creator: Lothar H. Wieler
creator: Torsten Semmler
creator: Knut Reinert
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.3138
publisher: PeerJ Inc.
rights: © 2017 Dadi et al.
abstract: Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than when using 16S-rDNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins. The existing microbial community profiling tools commonly deal with this problem by either preparing signature-based unique references or assigning an ambiguous read to its least common ancestor in a taxonomic tree. The former method is limited to making use of the reads which can be mapped to the curated regions, while the latter suffer from the lack of uniquely mapped reads at lower (more specific) taxonomic ranks. Moreover, even if the tools exhibited good performance in calling the organisms present in a sample, there is still room for improvement in determining the correct relative abundance of the organisms. We present a new method Species Level Identification of Microorganisms from Metagenomes (SLIMM) which addresses the above issues by using coverage information of reference genomes to remove unlikely genomes from the analysis and subsequently gain more uniquely mapped reads to assign at lower ranks of a taxonomic tree. SLIMM is based on a few, seemingly easy steps which when combined create a tool that outperforms state-of-the-art tools in run-time and memory usage while being on par or better in computing quantitative and qualitative information at species-level.
bibliographic citation: Dadi et al. (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ 5:e3138 https://doi.org/10.7717/peerj.3138
date submitted: 2016-10-07
date accepted: 2017-03-02
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dadi
  given name: Temesgen Hailemariam
author list: Agent
  family name: Renard
  given name: Bernhard Y.
author list: Agent
  family name: Wieler
  given name: Lothar H.
author list: Agent
  family name: Semmler
  given name: Torsten
author list: Agent
  family name: Reinert
  given name: Knut
doi: 10.7717/peerj.3138
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Dadi et al.
attribution name: Dadi et al.

Status of marine turtle rehabilitation in Queensland
type: item
type: AcademicArticle
description: Rehabilitation of marine turtles in Queensland has multifaceted objectives. It treats individual animals, serves to educate the public, and contributes to conservation. We examined the outcome from rehabilitation, time in rehabilitation, and subsequent recapture and restranding rates of stranded marine turtles between 1996 and 2013 to determine if the benefits associated with this practice are cost-effective as a conservation tool. Of 13,854 marine turtles reported as stranded during this 18-year period, 5,022 of these turtles were stranded alive with the remainder verified as dead or of unknown condition. A total of 2,970 (59%) of these live strandings were transported to a rehabilitation facility. Overall, 1,173/2,970 (39%) turtles were released over 18 years, 101 of which were recaptured: 77 reported as restrandings (20 dead, 13 alive subsequently died, 11 alive subsequently euthanized, 33 alive) and 24 recaptured during normal marine turtle population monitoring or fishing activities. Of the turtles admitted to rehabilitation exhibiting signs of disease, 88% of them died, either unassisted or by euthanasia and 66% of turtles admitted for unknown causes of stranding died either unassisted or by euthanasia. All turtles recorded as having a buoyancy disorder with no other presenting problem or disorder recorded, were released alive. In Queensland, rehabilitation costs approximately $1,000 per animal per year admitted to a center, $2,583 per animal per year released, and $123,750 per animal per year for marine turtles which are presumably successfully returned to the functional population. This practice may not be economically viable in its present configuration, but may be more cost effective as a mobile response unit. Further there is certainly benefit giving individual turtles a chance at survival and educating the public in the perils facing marine turtles. As well, rehabilitation can provide insight into the diseases and environmental stressors causing strandin…
format: application/pdf
format: text/html
creator: Jaylene Flint
creator: Mark Flint
creator: Colin James Limpus
creator: Paul Mills
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.3132
publisher: PeerJ Inc.
rights: © 2017 Flint et al.
abstract: Rehabilitation of marine turtles in Queensland has multifaceted objectives. It treats individual animals, serves to educate the public, and contributes to conservation. We examined the outcome from rehabilitation, time in rehabilitation, and subsequent recapture and restranding rates of stranded marine turtles between 1996 and 2013 to determine if the benefits associated with this practice are cost-effective as a conservation tool. Of 13,854 marine turtles reported as stranded during this 18-year period, 5,022 of these turtles were stranded alive with the remainder verified as dead or of unknown condition. A total of 2,970 (59%) of these live strandings were transported to a rehabilitation facility. Overall, 1,173/2,970 (39%) turtles were released over 18 years, 101 of which were recaptured: 77 reported as restrandings (20 dead, 13 alive subsequently died, 11 alive subsequently euthanized, 33 alive) and 24 recaptured during normal marine turtle population monitoring or fishing activities. Of the turtles admitted to rehabilitation exhibiting signs of disease, 88% of them died, either unassisted or by euthanasia and 66% of turtles admitted for unknown causes of stranding died either unassisted or by euthanasia. All turtles recorded as having a buoyancy disorder with no other presenting problem or disorder recorded, were released alive. In Queensland, rehabilitation costs approximately $1,000 per animal per year admitted to a center, $2,583 per animal per year released, and $123,750 per animal per year for marine turtles which are presumably successfully returned to the functional population. This practice may not be economically viable in its present configuration, but may be more cost effective as a mobile response unit. Further there is certainly benefit giving individual turtles a chance at survival and educating the public in the perils facing marine turtles. As well, rehabilitation can provide insight into the diseases and environmental stressors causing strandin…
bibliographic citation: Flint et al. (2017) Status of marine turtle rehabilitation in Queensland. PeerJ 5:e3132 https://doi.org/10.7717/peerj.3132
date submitted: 2016-11-06
date accepted: 2017-03-01
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flint
  given name: Jaylene
author list: Agent
  family name: Flint
  given name: Mark
author list: Agent
  family name: Limpus
  given name: Colin James
author list: Agent
  family name: Mills
  given name: Paul
doi: 10.7717/peerj.3132
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Flint et al.
attribution name: Flint et al.

Disturbed flow in an aquatic environment may create a sensory refuge for aggregated prey
type: item
type: AcademicArticle
description: Predators use olfactory cues moved within water and air to locate prey. Because prey aggregations may produce more cue and be easier to detect, predation could limit aggregation size. However, disturbance in the flow may diminish the reliability of odour as a prey cue, impeding predator foraging success and efficiency. We explore how different cue concentrations (as a proxy for prey group size) affect risk to prey by fish predators in disturbed (more turbulent or mixed) and non-disturbed (less mixed) flowing water. We find that increasing odour cue concentration increases predation risk and disturbing the flow reduces predation risk. At high cue concentration fish were able to locate the cue source in both disturbed and non-disturbed flow, but at medium concentrations, predators only located the cue source more often than expected by chance in non-disturbed flow. This suggests that objects disturbing flow provide a sensory refuge allowing prey to form larger groups, but that group sizes may be limited by level of disturbance to the flow.
format: application/pdf
format: text/html
creator: Asa Johannesen
creator: Alison M. Dunn
creator: Lesley J. Morrell
subject: Animal Behavior
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.3121
publisher: PeerJ Inc.
rights: © 2017 Johannesen et al.
abstract: Predators use olfactory cues moved within water and air to locate prey. Because prey aggregations may produce more cue and be easier to detect, predation could limit aggregation size. However, disturbance in the flow may diminish the reliability of odour as a prey cue, impeding predator foraging success and efficiency. We explore how different cue concentrations (as a proxy for prey group size) affect risk to prey by fish predators in disturbed (more turbulent or mixed) and non-disturbed (less mixed) flowing water. We find that increasing odour cue concentration increases predation risk and disturbing the flow reduces predation risk. At high cue concentration fish were able to locate the cue source in both disturbed and non-disturbed flow, but at medium concentrations, predators only located the cue source more often than expected by chance in non-disturbed flow. This suggests that objects disturbing flow provide a sensory refuge allowing prey to form larger groups, but that group sizes may be limited by level of disturbance to the flow.
bibliographic citation: Johannesen et al. (2017) Disturbed flow in an aquatic environment may create a sensory refuge for aggregated prey. PeerJ 5:e3121 https://doi.org/10.7717/peerj.3121
date submitted: 2016-10-26
date accepted: 2017-02-25
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johannesen
  given name: Asa
author list: Agent
  family name: Dunn
  given name: Alison M.
author list: Agent
  family name: Morrell
  given name: Lesley J.
doi: 10.7717/peerj.3121
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Johannesen et al.
attribution name: Johannesen et al.

Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
type: item
type: AcademicArticle
description: Background Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.
format: application/pdf
format: text/html
creator: Liliana Santos
creator: Artur Alves
creator: Rui Alves
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.3120
publisher: PeerJ Inc.
rights: © 2017 Santos et al.
abstract: Background Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.
bibliographic citation: Santos et al. (2017) Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe. PeerJ 5:e3120 https://doi.org/10.7717/peerj.3120
date submitted: 2016-12-23
date accepted: 2017-02-24
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Liliana
author list: Agent
  family name: Alves
  given name: Artur
author list: Agent
  family name: Alves
  given name: Rui
doi: 10.7717/peerj.3120
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Santos et al.
attribution name: Santos et al.

Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient
type: item
type: AcademicArticle
description: In the Western honey bee, Apis mellifera, queens and workers have different longevity although they share the same genome. Queens consume royal jelly (RJ) as the main food throughout their life, including as adults, but workers only eat worker jelly when they are larvae less than 3 days old. In order to explore the effect of RJ and the components affecting longevity of worker honey bees, we first determined the optimal dose for prolonging longevity of workers as 4% RJ in 50% sucrose solution, and developed a method of obtaining long lived workers. We then compared the effects of longevity extension by RJ 4% with bee-collected pollen from rapeseed (Brassica napus). Lastly, we determined that a water soluble RJ protein obtained by precipitation with 60% ammonium sulfate (RJP60) contained the main component for longevity extension after comparing the effects of RJ crude protein extract (RJCP), RJP30 (obtained by precipitation with 30% ammonium sulfate), and RJ ethanol extract (RJEE). Understanding what regulates worker longevity has potential to help increase colony productivity and improve crop pollination efficiency.
format: application/pdf
format: text/html
creator: Wenchao Yang
creator: Yuanyuan Tian
creator: Mingfeng Han
creator: Xiaoqing Miao
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.3118
publisher: PeerJ Inc.
rights: © 2017 Yang et al.
abstract: In the Western honey bee, Apis mellifera, queens and workers have different longevity although they share the same genome. Queens consume royal jelly (RJ) as the main food throughout their life, including as adults, but workers only eat worker jelly when they are larvae less than 3 days old. In order to explore the effect of RJ and the components affecting longevity of worker honey bees, we first determined the optimal dose for prolonging longevity of workers as 4% RJ in 50% sucrose solution, and developed a method of obtaining long lived workers. We then compared the effects of longevity extension by RJ 4% with bee-collected pollen from rapeseed (Brassica napus). Lastly, we determined that a water soluble RJ protein obtained by precipitation with 60% ammonium sulfate (RJP60) contained the main component for longevity extension after comparing the effects of RJ crude protein extract (RJCP), RJP30 (obtained by precipitation with 30% ammonium sulfate), and RJ ethanol extract (RJEE). Understanding what regulates worker longevity has potential to help increase colony productivity and improve crop pollination efficiency.
bibliographic citation: Yang et al. (2017) Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient. PeerJ 5:e3118 https://doi.org/10.7717/peerj.3118
date submitted: 2016-11-18
date accepted: 2017-02-23
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Wenchao
author list: Agent
  family name: Tian
  given name: Yuanyuan
author list: Agent
  family name: Han
  given name: Mingfeng
author list: Agent
  family name: Miao
  given name: Xiaoqing
doi: 10.7717/peerj.3118
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Yang et al.
attribution name: Yang et al.

Molecular barcoding confirms the presence of exotic Asian seaweeds (Pachymeniopsis gargiuli and Grateloupia turuturu) in the Cantabrian Sea, Bay of Biscay
type: item
type: AcademicArticle
description: Background The introduction of exotic species can have serious consequences for marine ecosystems. On the shores of the Cantabrian Sea (North of Spain) there are no routine examinations of seaweeds that combine molecular and morphological methods for early detection of exotic species making it difficult to assess in the early stages their establishment and expansion processes as a result of anthropogenic activities (e.g., shipping and/or aquaculture). Methods In this work we used both morphological identification and molecular barcoding (COI-5P and rbcL genes) of red algae collected in Asturias, Bay of Biscay (Gijón and Candás harbours) and from the University of Oviedo’s herbarium samples. Results The results confirmed the presence of exotic Asian seaweeds Pachymeniopsis gargiuli and Grateloupia turuturu Yamada on Cantabrian Sea shores. Several individuals of these species were fertile and developing cystocarps when collected, underlining the risk of possible expansion or continued establishment. This study constitutes the first report of the Asian P. gargiuli in this area of the Bay of Biscay. Conclusions Here the presence of the exotic species of the Halymeniales P. gargiuli is confirmed. We hypothesize that this species may have been established some time ago as a cryptic introduction with G. turuturu in Galician shores. The detection of these species on the shores of the Cantabrian Sea is relevant since introductions of Pachymeniopsis species could have been overlooked on other European coasts, probably mixed with G. turuturu and P. lanceolata. Our results confirm one new alien seaweed species that has been detected using molecular methods (COI-5P region and rbcL genes barcoding) on North Atlantic shores: the Asian native P. gargiuli. This demonstrates that routine screening for early detection of exotic algae in the Cantabrian Sea can be used for risk assessment. Genetic barcoding should be done using both rbcL gene and COI-5P regions since, although COI-datab…
format: application/pdf
format: text/html
creator: Marcos Montes
creator: Jose M. Rico
creator: Eva García-Vazquez
creator: Yaisel J. Borrell Pichs
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3116
publisher: PeerJ Inc.
rights: © 2017 Montes et al.
abstract: Background The introduction of exotic species can have serious consequences for marine ecosystems. On the shores of the Cantabrian Sea (North of Spain) there are no routine examinations of seaweeds that combine molecular and morphological methods for early detection of exotic species making it difficult to assess in the early stages their establishment and expansion processes as a result of anthropogenic activities (e.g., shipping and/or aquaculture). Methods In this work we used both morphological identification and molecular barcoding (COI-5P and rbcL genes) of red algae collected in Asturias, Bay of Biscay (Gijón and Candás harbours) and from the University of Oviedo’s herbarium samples. Results The results confirmed the presence of exotic Asian seaweeds Pachymeniopsis gargiuli and Grateloupia turuturu Yamada on Cantabrian Sea shores. Several individuals of these species were fertile and developing cystocarps when collected, underlining the risk of possible expansion or continued establishment. This study constitutes the first report of the Asian P. gargiuli in this area of the Bay of Biscay. Conclusions Here the presence of the exotic species of the Halymeniales P. gargiuli is confirmed. We hypothesize that this species may have been established some time ago as a cryptic introduction with G. turuturu in Galician shores. The detection of these species on the shores of the Cantabrian Sea is relevant since introductions of Pachymeniopsis species could have been overlooked on other European coasts, probably mixed with G. turuturu and P. lanceolata. Our results confirm one new alien seaweed species that has been detected using molecular methods (COI-5P region and rbcL genes barcoding) on North Atlantic shores: the Asian native P. gargiuli. This demonstrates that routine screening for early detection of exotic algae in the Cantabrian Sea can be used for risk assessment. Genetic barcoding should be done using both rbcL gene and COI-5P regions since, although COI-datab…
bibliographic citation: Montes et al. (2017) Molecular barcoding confirms the presence of exotic Asian seaweeds (Pachymeniopsis gargiuli and Grateloupia turuturu) in the Cantabrian Sea, Bay of Biscay. PeerJ 5:e3116 https://doi.org/10.7717/peerj.3116
date submitted: 2016-10-03
date accepted: 2017-02-23
issued: 2017-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montes
  given name: Marcos
author list: Agent
  family name: Rico
  given name: Jose M.
author list: Agent
  family name: García-Vazquez
  given name: Eva
author list: Agent
  family name: Borrell Pichs
  given name: Yaisel J.
doi: 10.7717/peerj.3116
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-28
copyright: ©2017 Montes et al.
attribution name: Montes et al.

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