PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary
items: Effects of shepherds and dogs on livestock depredation by leopards (Panthera pardus) in north-eastern Iran
items: Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment
items: Effectiveness of removals of the invasive lionfish: how many dives are needed to deplete a reef?
items: Tartrazine induces structural and functional aberrations and genotoxic effects in vivo
items: Retrospective observation of drug susceptibility of Candida strains in the years 1999, 2004, and 2015
items: Inhibition of calcineurin by FK506 stimulates germinal vesicle breakdown of mouse oocytes in hypoxanthine-supplemented medium
items: Eotaria citrica, sp. nov., a new stem otariid from the “Topanga” formation of Southern California
items: Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci
items: Using visuo-kinetic virtual reality to induce illusory spinal movement: the MoOVi Illusion

Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary
type: item
type: AcademicArticle
description: Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation.
format: application/pdf
format: text/html
creator: Beatrix Béres
creator: Dóra Kánainé Sipos
creator: Tamás Müller
creator: Ádám Staszny
creator: Milán Farkas
creator: Katalin Bakos
creator: László Orbán
creator: Béla Urbányi
creator: Balázs Kovács
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
description: doi:10.7717/peerj.2804
publisher: PeerJ Inc.
rights: © 2017 Béres et al.
abstract: Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation.
bibliographic citation: Béres et al. (2017) Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary. PeerJ 5:e2804 https://doi.org/10.7717/peerj.2804
date submitted: 2016-08-26
date accepted: 2016-11-19
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Béres
  given name: Beatrix
author list: Agent
  family name: Kánainé Sipos
  given name: Dóra
author list: Agent
  family name: Müller
  given name: Tamás
author list: Agent
  family name: Staszny
  given name: Ádám
author list: Agent
  family name: Farkas
  given name: Milán
author list: Agent
  family name: Bakos
  given name: Katalin
author list: Agent
  family name: Orbán
  given name: László
author list: Agent
  family name: Urbányi
  given name: Béla
author list: Agent
  family name: Kovács
  given name: Balázs
doi: 10.7717/peerj.2804
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Béres et al.
attribution name: Béres et al.

Effects of shepherds and dogs on livestock depredation by leopards (Panthera pardus) in north-eastern Iran
type: item
type: AcademicArticle
description: Human-carnivore conflicts over livestock depredation are increasingly common, yet little is understood about the role of husbandry in conflict mitigation. As shepherds and guarding dogs are most commonly used to curb carnivore attacks on grazing livestock, evaluation and improvement of these practices becomes an important task. We addressed this issue by studying individual leopard (Panthera pardus) attacks on sheep and goats in 34 villages near Golestan National Park, Iran. We obtained and analyzed data on 39 attacks, which included a total loss of 31 sheep and 36 goats in 17 villages. We applied non-parametric testing, Poisson Generalized Linear Modelling (GLM) and model selection to assess how numbers of sheep and goats killed per attack are associated with the presence and absence of shepherds and dogs during attacks, depredation in previous years, villages, seasons, ethnic groups, numbers of sheep and goats kept in villages, and distances from villages to the nearest protected areas. We found that 95.5% of losses were inflicted in forests when sheep and goats were accompanied by shepherds (92.5% of losses) and dogs (77.6%). Leopards tended to kill more sheep and goats per attack (surplus killing) when dogs were absent in villages distant from protected areas, but still inflicted most losses when dogs were present, mainly in villages near protected areas. No other variables affected numbers of sheep and goats killed per attack. These results indicate that local husbandry practices are ineffectual and the mere presence of shepherds and guarding dogs is not enough to secure protection. Shepherds witnessed leopard attacks, but could not deter them while dogs did not exhibit guarding behavior and were sometimes killed by leopards. In an attempt to make practical, low-cost and socially acceptable improvements in local husbandry, we suggest that dogs are raised to create a strong social bond with livestock, shepherds use only best available dogs, small flocks are aggr…
format: application/pdf
format: text/html
creator: Igor Khorozyan
creator: Mahmood Soofi
creator: Mobin Soufi
creator: Amirhossein Khaleghi Hamidi
creator: Arash Ghoddousi
creator: Matthias Waltert
subject: Biodiversity
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Environmental Impacts
description: doi:10.7717/peerj.3049
publisher: PeerJ Inc.
rights: © 2017 Khorozyan et al.
abstract: Human-carnivore conflicts over livestock depredation are increasingly common, yet little is understood about the role of husbandry in conflict mitigation. As shepherds and guarding dogs are most commonly used to curb carnivore attacks on grazing livestock, evaluation and improvement of these practices becomes an important task. We addressed this issue by studying individual leopard (Panthera pardus) attacks on sheep and goats in 34 villages near Golestan National Park, Iran. We obtained and analyzed data on 39 attacks, which included a total loss of 31 sheep and 36 goats in 17 villages. We applied non-parametric testing, Poisson Generalized Linear Modelling (GLM) and model selection to assess how numbers of sheep and goats killed per attack are associated with the presence and absence of shepherds and dogs during attacks, depredation in previous years, villages, seasons, ethnic groups, numbers of sheep and goats kept in villages, and distances from villages to the nearest protected areas. We found that 95.5% of losses were inflicted in forests when sheep and goats were accompanied by shepherds (92.5% of losses) and dogs (77.6%). Leopards tended to kill more sheep and goats per attack (surplus killing) when dogs were absent in villages distant from protected areas, but still inflicted most losses when dogs were present, mainly in villages near protected areas. No other variables affected numbers of sheep and goats killed per attack. These results indicate that local husbandry practices are ineffectual and the mere presence of shepherds and guarding dogs is not enough to secure protection. Shepherds witnessed leopard attacks, but could not deter them while dogs did not exhibit guarding behavior and were sometimes killed by leopards. In an attempt to make practical, low-cost and socially acceptable improvements in local husbandry, we suggest that dogs are raised to create a strong social bond with livestock, shepherds use only best available dogs, small flocks are aggr…
bibliographic citation: Khorozyan et al. (2017) Effects of shepherds and dogs on livestock depredation by leopards (Panthera pardus) in north-eastern Iran. PeerJ 5:e3049 https://doi.org/10.7717/peerj.3049
date submitted: 2016-11-14
date accepted: 2017-01-30
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khorozyan
  given name: Igor
author list: Agent
  family name: Soofi
  given name: Mahmood
author list: Agent
  family name: Soufi
  given name: Mobin
author list: Agent
  family name: Hamidi
  given name: Amirhossein Khaleghi
author list: Agent
  family name: Ghoddousi
  given name: Arash
author list: Agent
  family name: Waltert
  given name: Matthias
doi: 10.7717/peerj.3049
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Khorozyan et al.
attribution name: Khorozyan et al.

Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment
type: item
type: AcademicArticle
description: The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen’s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers.
format: application/pdf
format: text/html
creator: Valentina S. Vysotskaia
creator: Gregory J. Hogan
creator: Genevieve M. Gould
creator: Xin Wang
creator: Alex D. Robertson
creator: Kevin R. Haas
creator: Mark R. Theilmann
creator: Lindsay Spurka
creator: Peter V. Grauman
creator: Henry H. Lai
creator: Diana Jeon
creator: Genevieve Haliburton
creator: Matt Leggett
creator: Clement S. Chu
creator: Kevin Iori
creator: Jared R. Maguire
creator: Kaylene Ready
creator: Eric A. Evans
creator: Hyunseok P. Kang
creator: Imran S. Haque
subject: Genomics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.3046
publisher: PeerJ Inc.
rights: © 2017 Vysotskaia et al.
abstract: The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen’s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers.
bibliographic citation: Vysotskaia et al. (2017) Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment. PeerJ 5:e3046 https://doi.org/10.7717/peerj.3046
date submitted: 2016-12-07
date accepted: 2017-01-30
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vysotskaia
  given name: Valentina S.
author list: Agent
  family name: Hogan
  given name: Gregory J.
author list: Agent
  family name: Gould
  given name: Genevieve M.
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Robertson
  given name: Alex D.
author list: Agent
  family name: Haas
  given name: Kevin R.
author list: Agent
  family name: Theilmann
  given name: Mark R.
author list: Agent
  family name: Spurka
  given name: Lindsay
author list: Agent
  family name: Grauman
  given name: Peter V.
author list: Agent
  family name: Lai
  given name: Henry H.
author list: Agent
  family name: Jeon
  given name: Diana
author list: Agent
  family name: Haliburton
  given name: Genevieve
author list: Agent
  family name: Leggett
  given name: Matt
author list: Agent
  family name: Chu
  given name: Clement S.
author list: Agent
  family name: Iori
  given name: Kevin
author list: Agent
  family name: Maguire
  given name: Jared R.
author list: Agent
  family name: Ready
  given name: Kaylene
author list: Agent
  family name: Evans
  given name: Eric A.
author list: Agent
  family name: Kang
  given name: Hyunseok P.
author list: Agent
  family name: Haque
  given name: Imran S.
doi: 10.7717/peerj.3046
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Vysotskaia et al.
attribution name: Vysotskaia et al.

Effectiveness of removals of the invasive lionfish: how many dives are needed to deplete a reef?
type: item
type: AcademicArticle
description: Introduced Indo-Pacific red lionfish (Pterois volitans/miles) have spread throughout the greater Caribbean and are associated with a number of negative impacts on reef ecosystems. Human interventions, in the form of culling activities, are becoming common to reduce their numbers and mitigate the negative effects associated with the invasion. However, marine managers must often decide how to best allocate limited resources. Previous work has identified the population size thresholds needed to limit the negative impacts of lionfish. Here we develop a framework that allows managers to predict the removal effort required to achieve specific targets (represented as the percent of lionfish remaining on the reef). We found an important trade-off between time spent removing and achieving an increasingly smaller lionfish density. The model used in our suggested framework requires relatively little data to parameterize, allowing its use with already existing data, permitting managers to tailor their culling strategy to maximize efficiency and rate of success.
format: application/pdf
format: text/html
creator: Paolo Usseglio
creator: Jason D. Selwyn
creator: Alan M. Downey-Wall
creator: J. Derek Hogan
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3043
publisher: PeerJ Inc.
rights: © 2017 Usseglio et al.
abstract: Introduced Indo-Pacific red lionfish (Pterois volitans/miles) have spread throughout the greater Caribbean and are associated with a number of negative impacts on reef ecosystems. Human interventions, in the form of culling activities, are becoming common to reduce their numbers and mitigate the negative effects associated with the invasion. However, marine managers must often decide how to best allocate limited resources. Previous work has identified the population size thresholds needed to limit the negative impacts of lionfish. Here we develop a framework that allows managers to predict the removal effort required to achieve specific targets (represented as the percent of lionfish remaining on the reef). We found an important trade-off between time spent removing and achieving an increasingly smaller lionfish density. The model used in our suggested framework requires relatively little data to parameterize, allowing its use with already existing data, permitting managers to tailor their culling strategy to maximize efficiency and rate of success.
bibliographic citation: Usseglio et al. (2017) Effectiveness of removals of the invasive lionfish: how many dives are needed to deplete a reef?. PeerJ 5:e3043 https://doi.org/10.7717/peerj.3043
date submitted: 2016-04-26
date accepted: 2017-01-28
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Usseglio
  given name: Paolo
author list: Agent
  family name: Selwyn
  given name: Jason D.
author list: Agent
  family name: Downey-Wall
  given name: Alan M.
author list: Agent
  family name: Hogan
  given name: J. Derek
doi: 10.7717/peerj.3043
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Usseglio et al.
attribution name: Usseglio et al.

Tartrazine induces structural and functional aberrations and genotoxic effects in vivo
type: item
type: AcademicArticle
description: Tartrazine is a synthetic organic azo dye widely used in food and pharmaceutical products. The current study aimed to evaluate the possible adverse effect of this coloring food additive on renal and hepatic structures and functions. Also, the genotoxic potential of tartrazine on white blood cells was investigated using comet assay. Twenty adult male Wistar rats were grouped into two groups of 10 each, control- and tartrazine-treated groups. The control group was administered orally with water alone. The experimental group was administered orally with tartrazine (7.5 mg/kg, b.wt.). Our results showed a marked increase in the levels of ALT, AST, ALP, urea, uric acid, creatinine, MDA and NO, and a decreased level of total antioxidants in the serum of rats dosed with tartrazine compared to controls. On the other hand, administration of tartrazine was associated with severe histopathological and cellular alterations of rat liver and kidney tissues and induced DNA damage in leucocytes as detected by comet assay. Taken together, the results showed that tartrazine intake may lead to adverse health effects.
format: application/pdf
format: text/html
creator: Latifa Khayyat
creator: Amina Essawy
creator: Jehan Sorour
creator: Ahmed Soffar
subject: Biochemistry
subject: Molecular Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.3041
publisher: PeerJ Inc.
rights: © 2017 Khayyat et al.
abstract: Tartrazine is a synthetic organic azo dye widely used in food and pharmaceutical products. The current study aimed to evaluate the possible adverse effect of this coloring food additive on renal and hepatic structures and functions. Also, the genotoxic potential of tartrazine on white blood cells was investigated using comet assay. Twenty adult male Wistar rats were grouped into two groups of 10 each, control- and tartrazine-treated groups. The control group was administered orally with water alone. The experimental group was administered orally with tartrazine (7.5 mg/kg, b.wt.). Our results showed a marked increase in the levels of ALT, AST, ALP, urea, uric acid, creatinine, MDA and NO, and a decreased level of total antioxidants in the serum of rats dosed with tartrazine compared to controls. On the other hand, administration of tartrazine was associated with severe histopathological and cellular alterations of rat liver and kidney tissues and induced DNA damage in leucocytes as detected by comet assay. Taken together, the results showed that tartrazine intake may lead to adverse health effects.
bibliographic citation: Khayyat et al. (2017) Tartrazine induces structural and functional aberrations and genotoxic effects in vivo. PeerJ 5:e3041 https://doi.org/10.7717/peerj.3041
date submitted: 2016-12-23
date accepted: 2017-01-28
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khayyat
  given name: Latifa
author list: Agent
  family name: Essawy
  given name: Amina
author list: Agent
  family name: Sorour
  given name: Jehan
author list: Agent
  family name: Soffar
  given name: Ahmed
doi: 10.7717/peerj.3041
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Khayyat et al.
attribution name: Khayyat et al.

Retrospective observation of drug susceptibility of Candida strains in the years 1999, 2004, and 2015
type: item
type: AcademicArticle
description: Introduction There is much literature devoted to the problem of drug resistance and decreased susceptibility of fungi to commonly used antifungals. Aim To analyze drug susceptibility of Candida albicans and non-Candida albicans strains isolated from the hands of people without any symptoms of disease over a 16-year period. Materials and Methods The study included a total of 1,274 Candida-type strains isolated from the hands of people without any symptoms of disease, including: in 1999, 432 strains; in 2004, 368; and in 2015, 454 strains. Biological monitoring of hand surface contamination was performed using the Count-TactTM applicator with Count-Tact plates (bioMerieux). Drug susceptibility was evaluated using FUNGITEST®. Results In 1999, the most strains showed resistance to fluconazole (53.2%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (85.8%). Resistance to more than one drug was 35.8% in 1999, 64.7% in 2004, and 92% in 2015. Mean resistance to azole antifungals significantly increased from 98 ± 39.7 strains in 1999 to 118.3 ± 29.6 in 2015 (p < 0.001). In 1999, the most strains showed resistance to fluconazole (50.6%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (44.9%). Resistance to more than one drug was 52.9% in 1999, 64.3% in 2004, and 88.1% in 2015. Mean resistance to azole antifungals significantly increased from a mean of 76 ± 9.7 strains in 1999, to 95.3 ± 24.2 in 2004, and to 97.3 ± 16.6 in 2015 (p < 0.001). Conclusions We showed increased C. albicans and non-Candida albicans strain resistance to commonly used antifungal chemotherapeutics, mainly imidazole. We found a clear rise in susceptibility of C. albicans and non-Candida albicans strains to several studied antifungals.
format: application/pdf
format: text/html
creator: Cecylia Łukaszuk
creator: Elżbieta Krajewska-Kułak
creator: Wojciech Kułak
subject: Microbiology
subject: Mycology
subject: Drugs and Devices
subject: Public Health
description: doi:10.7717/peerj.3038
publisher: PeerJ Inc.
rights: © 2017 Łukaszuk et al.
abstract: Introduction There is much literature devoted to the problem of drug resistance and decreased susceptibility of fungi to commonly used antifungals. Aim To analyze drug susceptibility of Candida albicans and non-Candida albicans strains isolated from the hands of people without any symptoms of disease over a 16-year period. Materials and Methods The study included a total of 1,274 Candida-type strains isolated from the hands of people without any symptoms of disease, including: in 1999, 432 strains; in 2004, 368; and in 2015, 454 strains. Biological monitoring of hand surface contamination was performed using the Count-TactTM applicator with Count-Tact plates (bioMerieux). Drug susceptibility was evaluated using FUNGITEST®. Results In 1999, the most strains showed resistance to fluconazole (53.2%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (85.8%). Resistance to more than one drug was 35.8% in 1999, 64.7% in 2004, and 92% in 2015. Mean resistance to azole antifungals significantly increased from 98 ± 39.7 strains in 1999 to 118.3 ± 29.6 in 2015 (p < 0.001). In 1999, the most strains showed resistance to fluconazole (50.6%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (44.9%). Resistance to more than one drug was 52.9% in 1999, 64.3% in 2004, and 88.1% in 2015. Mean resistance to azole antifungals significantly increased from a mean of 76 ± 9.7 strains in 1999, to 95.3 ± 24.2 in 2004, and to 97.3 ± 16.6 in 2015 (p < 0.001). Conclusions We showed increased C. albicans and non-Candida albicans strain resistance to commonly used antifungal chemotherapeutics, mainly imidazole. We found a clear rise in susceptibility of C. albicans and non-Candida albicans strains to several studied antifungals.
bibliographic citation: Łukaszuk et al. (2017) Retrospective observation of drug susceptibility of Candida strains in the years 1999, 2004, and 2015. PeerJ 5:e3038 https://doi.org/10.7717/peerj.3038
date submitted: 2016-06-18
date accepted: 2017-01-27
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Łukaszuk
  given name: Cecylia
author list: Agent
  family name: Krajewska-Kułak
  given name: Elżbieta
author list: Agent
  family name: Kułak
  given name: Wojciech
doi: 10.7717/peerj.3038
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Łukaszuk et al.
attribution name: Łukaszuk et al.

Inhibition of calcineurin by FK506 stimulates germinal vesicle breakdown of mouse oocytes in hypoxanthine-supplemented medium
type: item
type: AcademicArticle
description: Calcineurin (CN) is a serine/threonine phosphatase which plays important roles in meiosis maturation in invertebrate oocytes; however, the role of CN in mouse oocytes is relatively unexplored. In this study, we examined the expression, localization and functional roles of CN in mouse oocytes and granulosa cells. The RT-PCR results showed that the β isoform of calcineurin A subunit (Cn A) expressed significantly higher than α and γ isoforms, and the expression of Cn Aβ mRNA obviously decreased in oocytes in which germinal vesicle breakdown (GVBD) occurred, while only B1 of calcineurin B subunit (Cn B) was detected in oocytes and stably expressed during oocytes maturation. The following fluorescence experiment showed that Cn A was mainly located in the nucleus of germinal vesicle (GV) stage oocytes and gruanlosa cells, and subsequently dispersed into the entire cytoplasm after GVBD. The decline of Cn A in oocytes suggested that it may play an important role in GVBD. To further clarify the role of calcineurin during meiotic maturation, FK506 (a calcineurin inhibitor) was used in the culture medium contained hypoxanthine (HX) which could keep mouse oocytes staying at GV stage. As expected, FK506 could induce a significant elevation of GVBD rate and increase the MPF level of denuded oocytes (DOs). Furthermore, FK506 could also play an induction role of GVBD of oocytes in COCs and follicles, and the process could be counteracted by MAPK kinase inhibitor (U0126). Above all, the results implied that calcineurin might play a crucial role in development of mouse oocytes and MPF and MAPK pathways are involved in this process.
format: application/pdf
format: text/html
creator: Li Wang
creator: Yan-Hong Zhen
creator: Xiao-Ming Liu
creator: Jing Cao
creator: Yan-Ling Wang
creator: Li-Jun Huo
subject: Cell Biology
subject: Developmental Biology
description: doi:10.7717/peerj.3032
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Calcineurin (CN) is a serine/threonine phosphatase which plays important roles in meiosis maturation in invertebrate oocytes; however, the role of CN in mouse oocytes is relatively unexplored. In this study, we examined the expression, localization and functional roles of CN in mouse oocytes and granulosa cells. The RT-PCR results showed that the β isoform of calcineurin A subunit (Cn A) expressed significantly higher than α and γ isoforms, and the expression of Cn Aβ mRNA obviously decreased in oocytes in which germinal vesicle breakdown (GVBD) occurred, while only B1 of calcineurin B subunit (Cn B) was detected in oocytes and stably expressed during oocytes maturation. The following fluorescence experiment showed that Cn A was mainly located in the nucleus of germinal vesicle (GV) stage oocytes and gruanlosa cells, and subsequently dispersed into the entire cytoplasm after GVBD. The decline of Cn A in oocytes suggested that it may play an important role in GVBD. To further clarify the role of calcineurin during meiotic maturation, FK506 (a calcineurin inhibitor) was used in the culture medium contained hypoxanthine (HX) which could keep mouse oocytes staying at GV stage. As expected, FK506 could induce a significant elevation of GVBD rate and increase the MPF level of denuded oocytes (DOs). Furthermore, FK506 could also play an induction role of GVBD of oocytes in COCs and follicles, and the process could be counteracted by MAPK kinase inhibitor (U0126). Above all, the results implied that calcineurin might play a crucial role in development of mouse oocytes and MPF and MAPK pathways are involved in this process.
bibliographic citation: Wang et al. (2017) Inhibition of calcineurin by FK506 stimulates germinal vesicle breakdown of mouse oocytes in hypoxanthine-supplemented medium. PeerJ 5:e3032 https://doi.org/10.7717/peerj.3032
date submitted: 2016-10-17
date accepted: 2017-01-26
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Zhen
  given name: Yan-Hong
author list: Agent
  family name: Liu
  given name: Xiao-Ming
author list: Agent
  family name: Cao
  given name: Jing
author list: Agent
  family name: Wang
  given name: Yan-Ling
author list: Agent
  family name: Huo
  given name: Li-Jun
doi: 10.7717/peerj.3032
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Wang et al.
attribution name: Wang et al.

Eotaria citrica, sp. nov., a new stem otariid from the “Topanga” formation of Southern California
type: item
type: AcademicArticle
description: A new taxon of stem otariid, Eotaria citrica sp. nov., is described from the upper Burdigalian to lower Langhian “Topanga” formation of Orange County, California. The new species is described from mandibular and dental remains that show a unique combination of plesiomorphic and derived characters. Specifically, it is characterized by having trenchant and prominent paraconid cusps in p3–m1, lingual cingula of p2–4 with faint crenulations, premolars and molars with vestigial metaconid, bilobed root of m2 and a genial tuberosity located under p3. Furthermore, additional material of the contemporaneous Eotaria crypta is described, providing new information on the morphology of this taxon. Both species of Eotaria represent the earliest stem otariids, reinforcing the hypothesis that the group originated in the north Eastern Pacific Region. At present, the “Topanga” Fm. pinniped fauna includes Eotaria citrica, Eotaria crypta, the desmatophocid Allodesmus sp., the odobenids Neotherium sp., Pelagiarctos sp. and includes the oldest records of crown pinnipeds in California. Overall this pinniped fauna is similar to the nearly contemporaneous Sharktooth Hill bonebed. However, unambiguous records of Eotaria are still missing from Sharktooth Hill. This absence may be due to taphonomic or paleoenvironmental factors. The new “Topanga” record presented here was integrated into an overview of the late Oligocene through early Pleistocene pinniped faunas of Southern California. The results show an overall increase in body size over time until the Pleistocene. Furthermore, desmatophocids were the largest pinnipeds during the middle Miocene, but were extinct by the beginning of the late Miocene. Odobenids diversified and became the dominant pinnipeds in late Miocene through Pleistocene assemblages, usually approaching or exceeding 3 m in body length, while otariids remained as the smallest taxa. This pattern contrasts with modern assemblages, in which the phocid Mirounga angustirostris i…
format: application/pdf
format: text/html
creator: Jorge Velez-Juarbe
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.3022
publisher: PeerJ Inc.
rights: © 2017 Velez-Juarbe
abstract: A new taxon of stem otariid, Eotaria citrica sp. nov., is described from the upper Burdigalian to lower Langhian “Topanga” formation of Orange County, California. The new species is described from mandibular and dental remains that show a unique combination of plesiomorphic and derived characters. Specifically, it is characterized by having trenchant and prominent paraconid cusps in p3–m1, lingual cingula of p2–4 with faint crenulations, premolars and molars with vestigial metaconid, bilobed root of m2 and a genial tuberosity located under p3. Furthermore, additional material of the contemporaneous Eotaria crypta is described, providing new information on the morphology of this taxon. Both species of Eotaria represent the earliest stem otariids, reinforcing the hypothesis that the group originated in the north Eastern Pacific Region. At present, the “Topanga” Fm. pinniped fauna includes Eotaria citrica, Eotaria crypta, the desmatophocid Allodesmus sp., the odobenids Neotherium sp., Pelagiarctos sp. and includes the oldest records of crown pinnipeds in California. Overall this pinniped fauna is similar to the nearly contemporaneous Sharktooth Hill bonebed. However, unambiguous records of Eotaria are still missing from Sharktooth Hill. This absence may be due to taphonomic or paleoenvironmental factors. The new “Topanga” record presented here was integrated into an overview of the late Oligocene through early Pleistocene pinniped faunas of Southern California. The results show an overall increase in body size over time until the Pleistocene. Furthermore, desmatophocids were the largest pinnipeds during the middle Miocene, but were extinct by the beginning of the late Miocene. Odobenids diversified and became the dominant pinnipeds in late Miocene through Pleistocene assemblages, usually approaching or exceeding 3 m in body length, while otariids remained as the smallest taxa. This pattern contrasts with modern assemblages, in which the phocid Mirounga angustirostris i…
bibliographic citation: Velez-Juarbe (2017) Eotaria citrica, sp. nov., a new stem otariid from the “Topanga” formation of Southern California. PeerJ 5:e3022 https://doi.org/10.7717/peerj.3022
date submitted: 2016-08-19
date accepted: 2017-01-24
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Velez-Juarbe
  given name: Jorge
doi: 10.7717/peerj.3022
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: © 2017 Velez-Juarbe
attribution name: Velez-Juarbe

Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci
type: item
type: AcademicArticle
description: Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.
format: application/pdf
format: text/html
creator: Caroline E. Dubé
creator: Serge Planes
creator: Yuxiang Zhou
creator: Véronique Berteaux-Lecellier
creator: Emilie Boissin
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.2936
publisher: PeerJ Inc.
rights: © 2017 Dubé et al.
abstract: Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.
bibliographic citation: Dubé et al. (2017) Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci. PeerJ 5:e2936 https://doi.org/10.7717/peerj.2936
date submitted: 2016-08-10
date accepted: 2016-12-22
issued: 2017-02-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dubé
  given name: Caroline E.
author list: Agent
  family name: Planes
  given name: Serge
author list: Agent
  family name: Zhou
  given name: Yuxiang
author list: Agent
  family name: Berteaux-Lecellier
  given name: Véronique
author list: Agent
  family name: Boissin
  given name: Emilie
doi: 10.7717/peerj.2936
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-23
copyright: ©2017 Dubé et al.
attribution name: Dubé et al.

Using visuo-kinetic virtual reality to induce illusory spinal movement: the MoOVi Illusion
type: item
type: AcademicArticle
description: Background Illusions that alter perception of the body provide novel opportunities to target brain-based contributions to problems such as persistent pain. One example of this, mirror therapy, uses vision to augment perceived movement of a painful limb to treat pain. Since mirrors can’t be used to induce augmented neck or other spinal movement, we aimed to test whether such an illusion could be achieved using virtual reality, in advance of testing its potential therapeutic benefit. We hypothesised that perceived head rotation would depend on visually suggested movement. Method In a within-subjects repeated measures experiment, 24 healthy volunteers performed neck movements to 50o of rotation, while a virtual reality system delivered corresponding visual feedback that was offset by a factor of 50%–200%—the Motor Offset Visual Illusion (MoOVi)—thus simulating more or less movement than that actually occurring. At 50o of real-world head rotation, participants pointed in the direction that they perceived they were facing. The discrepancy between actual and perceived direction was measured and compared between conditions. The impact of including multisensory (auditory and visual) feedback, the presence of a virtual body reference, and the use of 360o immersive virtual reality with and without three-dimensional properties, was also investigated. Results Perception of head movement was dependent on visual-kinaesthetic feedback (p = 0.001, partial eta squared = 0.17). That is, altered visual feedback caused a kinaesthetic drift in the direction of the visually suggested movement. The magnitude of the drift was not moderated by secondary variables such as the addition of illusory auditory feedback, the presence of a virtual body reference, or three-dimensionality of the scene. Discussion Virtual reality can be used to augment perceived movement and body position, such that one can perform a small movement, yet perceive a large one. The MoOVi technique tested here has clear p…
format: application/pdf
format: text/html
creator: Daniel S. Harvie
creator: Ross T. Smith
creator: Estin V. Hunter
creator: Miles G. Davis
creator: Michele Sterling
creator: G. Lorimer Moseley
subject: Anesthesiology and Pain Management
subject: Drugs and Devices
subject: Human-Computer Interaction
subject: Neuroscience
description: doi:10.7717/peerj.3023
publisher: PeerJ Inc.
rights: © 2017 Harvie et al.
abstract: Background Illusions that alter perception of the body provide novel opportunities to target brain-based contributions to problems such as persistent pain. One example of this, mirror therapy, uses vision to augment perceived movement of a painful limb to treat pain. Since mirrors can’t be used to induce augmented neck or other spinal movement, we aimed to test whether such an illusion could be achieved using virtual reality, in advance of testing its potential therapeutic benefit. We hypothesised that perceived head rotation would depend on visually suggested movement. Method In a within-subjects repeated measures experiment, 24 healthy volunteers performed neck movements to 50o of rotation, while a virtual reality system delivered corresponding visual feedback that was offset by a factor of 50%–200%—the Motor Offset Visual Illusion (MoOVi)—thus simulating more or less movement than that actually occurring. At 50o of real-world head rotation, participants pointed in the direction that they perceived they were facing. The discrepancy between actual and perceived direction was measured and compared between conditions. The impact of including multisensory (auditory and visual) feedback, the presence of a virtual body reference, and the use of 360o immersive virtual reality with and without three-dimensional properties, was also investigated. Results Perception of head movement was dependent on visual-kinaesthetic feedback (p = 0.001, partial eta squared = 0.17). That is, altered visual feedback caused a kinaesthetic drift in the direction of the visually suggested movement. The magnitude of the drift was not moderated by secondary variables such as the addition of illusory auditory feedback, the presence of a virtual body reference, or three-dimensionality of the scene. Discussion Virtual reality can be used to augment perceived movement and body position, such that one can perform a small movement, yet perceive a large one. The MoOVi technique tested here has clear p…
bibliographic citation: Harvie et al. (2017) Using visuo-kinetic virtual reality to induce illusory spinal movement: the MoOVi Illusion. PeerJ 5:e3023 https://doi.org/10.7717/peerj.3023
date submitted: 2016-11-10
date accepted: 2017-01-24
issued: 2017-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harvie
  given name: Daniel S.
author list: Agent
  family name: Smith
  given name: Ross T.
author list: Agent
  family name: Hunter
  given name: Estin V.
author list: Agent
  family name: Davis
  given name: Miles G.
author list: Agent
  family name: Sterling
  given name: Michele
author list: Agent
  family name: Moseley
  given name: G. Lorimer
doi: 10.7717/peerj.3023
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-22
copyright: ©2017 Harvie et al.
attribution name: Harvie et al.

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