PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance
items: Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats
items: A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex
items: Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California
items: The impact of IL-6 and IL-28B gene polymorphisms on treatment outcome of chronic hepatitis C infection among intravenous drug users in Croatia
items: Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity
items: Antimicrobial activity of Tachyplesin 1 against Burkholderia pseudomallei: an in vitro and in silico approach
items: https://peerj.com/articles/2613
items: Nonlinear temperature effects on multifractal complexity of metabolic rate of mice
items: Taxonomy of Platypterygius campylodon and the diversity of the last ichthyosaurs

A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance
type: item
type: AcademicArticle
description: On the Gulf of St. Lawrence coast of Nova Scotia (Canada), recruitment of the barnacle Semibalanus balanoides occurs in May and June. Every year in June between 2005 and 2016, we recorded recruit density for this barnacle at the same wave-exposed rocky intertidal location on this coast. During these 12 years, mean recruit density was lowest in 2015 (198 recruits dm−2) and highest in 2007 (969 recruits dm−2). The highest recruit density observed in a single quadrat was 1,457 recruits dm−2 (in 2011) and the lowest was 34 recruits dm−2 (in 2015). Most barnacle recruits appear during May, which suggests that most pelagic larvae (which develop over 5–6 weeks before benthic settlement) are in the water column in April. An AICc-based model selection approach identified sea surface temperature (SST) in April and the abundance of phytoplankton (food for barnacle larvae, measured as chlorophyll-a concentration –Chl-a–) in April as good explanatory variables. Together, April SST and April Chl-a explained 51% of the observed interannual variation in recruit density, with an overall positive influence. April SST was positively related to March–April air temperature (AT). April Chl-a was negatively related to the April ratio between the number of days with onshore winds (which blow from phytoplankton-limited offshore waters) and the number of days with alongshore winds (phytoplankton is more abundant on coastal waters). Therefore, this study suggests that climatic processes affecting April SST and April Chl-a indirectly influence intertidal barnacle recruitment by influencing larval performance.
format: application/pdf
format: text/html
creator: Ricardo A. Scrosati
creator: Julius A. Ellrich
subject: Aquaculture, Fisheries and Fish Science
subject: Climate Change Biology
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.2623
publisher: PeerJ Inc.
rights: © 2016 Scrosati & Ellrich
abstract: On the Gulf of St. Lawrence coast of Nova Scotia (Canada), recruitment of the barnacle Semibalanus balanoides occurs in May and June. Every year in June between 2005 and 2016, we recorded recruit density for this barnacle at the same wave-exposed rocky intertidal location on this coast. During these 12 years, mean recruit density was lowest in 2015 (198 recruits dm−2) and highest in 2007 (969 recruits dm−2). The highest recruit density observed in a single quadrat was 1,457 recruits dm−2 (in 2011) and the lowest was 34 recruits dm−2 (in 2015). Most barnacle recruits appear during May, which suggests that most pelagic larvae (which develop over 5–6 weeks before benthic settlement) are in the water column in April. An AICc-based model selection approach identified sea surface temperature (SST) in April and the abundance of phytoplankton (food for barnacle larvae, measured as chlorophyll-a concentration –Chl-a–) in April as good explanatory variables. Together, April SST and April Chl-a explained 51% of the observed interannual variation in recruit density, with an overall positive influence. April SST was positively related to March–April air temperature (AT). April Chl-a was negatively related to the April ratio between the number of days with onshore winds (which blow from phytoplankton-limited offshore waters) and the number of days with alongshore winds (phytoplankton is more abundant on coastal waters). Therefore, this study suggests that climatic processes affecting April SST and April Chl-a indirectly influence intertidal barnacle recruitment by influencing larval performance.
bibliographic citation: Scrosati et al. (2016) A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance. PeerJ 4:e2623 https://doi.org/10.7717/peerj.2623
date submitted: 2016-08-17
date accepted: 2016-09-27
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scrosati
  given name: Ricardo A.
author list: Agent
  family name: Ellrich
  given name: Julius A.
doi: 10.7717/peerj.2623
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: © 2016 Scrosati and Ellrich
attribution name: Scrosati & Ellrich

Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats
type: item
type: AcademicArticle
description: Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health.
format: application/pdf
format: text/html
creator: Massimo Ponti
creator: Francesca Fratangeli
creator: Nicolò Dondi
creator: Marco Segre Reinach
creator: Clara Serra
creator: Michael J. Sweet
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2614
publisher: PeerJ Inc.
rights: © 2016 Ponti et al.
abstract: Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health.
bibliographic citation: Ponti et al. (2016) Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats. PeerJ 4:e2614 https://doi.org/10.7717/peerj.2614
date submitted: 2016-06-08
date accepted: 2016-09-27
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponti
  given name: Massimo
author list: Agent
  family name: Fratangeli
  given name: Francesca
author list: Agent
  family name: Dondi
  given name: Nicolò
author list: Agent
  family name: Segre Reinach
  given name: Marco
author list: Agent
  family name: Serra
  given name: Clara
author list: Agent
  family name: Sweet
  given name: Michael J.
doi: 10.7717/peerj.2614
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Ponti et al.
attribution name: Ponti et al.

A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex
type: item
type: AcademicArticle
description: The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.
format: application/pdf
format: text/html
creator: Hao Zhang
creator: Balázs Brankovics
creator: Theo A.J. van der Lee
creator: Cees Waalwijk
creator: Anne A.D. van Diepeningen
creator: Jin Xu
creator: Jingsheng Xu
creator: Wanquan Chen
creator: Jie Feng
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2609
publisher: PeerJ Inc.
rights: © 2016 Zhang et al.
abstract: The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.
bibliographic citation: Zhang et al. (2016) A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex. PeerJ 4:e2609 https://doi.org/10.7717/peerj.2609
date submitted: 2016-05-06
date accepted: 2016-09-25
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Brankovics
  given name: Balázs
author list: Agent
  family name: van der Lee
  given name: Theo A.J.
author list: Agent
  family name: Waalwijk
  given name: Cees
author list: Agent
  family name: van Diepeningen
  given name: Anne A.D.
author list: Agent
  family name: Xu
  given name: Jin
author list: Agent
  family name: Xu
  given name: Jingsheng
author list: Agent
  family name: Chen
  given name: Wanquan
author list: Agent
  family name: Feng
  given name: Jie
doi: 10.7717/peerj.2609
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Zhang et al.
attribution name: Zhang et al.

Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California
type: item
type: AcademicArticle
description: The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.
format: application/pdf
format: text/html
creator: Erika Magallón-Gayón
creator: Pindaro Diaz-Jaimes
creator: Manuel Uribe-Alcocer
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Conservation Biology
subject: Genetics
description: doi:10.7717/peerj.2583
publisher: PeerJ Inc.
rights: © 2016 Magallón-Gayón et al.
abstract: The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.
bibliographic citation: Magallón-Gayón et al. (2016) Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California. PeerJ 4:e2583 https://doi.org/10.7717/peerj.2583
date submitted: 2016-04-15
date accepted: 2016-09-17
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Magallón-Gayón
  given name: Erika
author list: Agent
  family name: Diaz-Jaimes
  given name: Pindaro
author list: Agent
  family name: Uribe-Alcocer
  given name: Manuel
doi: 10.7717/peerj.2583
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Magallón-Gayón et al.
attribution name: Magallón-Gayón et al.

The impact of IL-6 and IL-28B gene polymorphisms on treatment outcome of chronic hepatitis C infection among intravenous drug users in Croatia
type: item
type: AcademicArticle
description: Background Several genes and their single nucleotide polymorphisms (SNPs) are associated with either spontaneous resolution of hepatitis C infection or better treatment-induced viral clearance. We tested a cohort of intravenous drug users (IVDU) diagnosed with chronic hepatitis C virus (HCV) for treatment response and its association with the SNPs in the interleukin-6 (rs1800795-IL6) and the interleukin-28B (rs12979860-IL28B) genes. Methods The study included 110 Croatian IVDU positive for anti-HCV antibody. Genotyping was performed by polymerase chain reaction (PCR) based approach. Patients were treated by standard pegylated-interferon/ribavirin and followed throughout a period of four years, during which sustained virological response (SVR) was determined. All data were analysed with statistical package SPSS 19.0 (IBM Corp, Armonk, NY, USA) and PLINK v1.07 software. Results Patients showed a significantly better response to treatment according to the number of copies of the C allele carried at rs1800795-IL6 (P = 0.034). All but one of the patients with CC genotype achieved SVR (93%), whereas the response rate of patients with GG genotype was 64%. The association of rs1800795-IL6 with SVR status remained significant after further adjustment for patients’ age, fibrosis staging, and viral genotype (OR 2.15, 95% CI 1.16–4.68, P = 0.019). Distributions of allele frequencies at the locus rs12979860-IL28B among the study cohort and the underlying general population were suggestive of a protective effect of CC genotype in acquiring chronic hepatitis C in the Croatian IVDU population. Discussion The rs1800795-IL6 polymorphism is associated with positive response to treatment in IVDU patients positive for HCV infection. A protective role of rs12979860-IL28B CC genotype in acquiring chronic hepatitis C is suggested for Croatian IVDU population.
format: application/pdf
format: text/html
creator: Zoran Bogdanović
creator: Ivana Marinović-Terzić
creator: Sendi Kuret
creator: Ana Jerončić
creator: Nikola Bradarić
creator: Gea Forempoher
creator: Ozren Polašek
creator: Šimun Anđelinović
creator: Janoš Terzić
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Infectious Diseases
subject: Medical Genetics
description: doi:10.7717/peerj.2576
publisher: PeerJ Inc.
rights: © 2016 Bogdanović et al.
abstract: Background Several genes and their single nucleotide polymorphisms (SNPs) are associated with either spontaneous resolution of hepatitis C infection or better treatment-induced viral clearance. We tested a cohort of intravenous drug users (IVDU) diagnosed with chronic hepatitis C virus (HCV) for treatment response and its association with the SNPs in the interleukin-6 (rs1800795-IL6) and the interleukin-28B (rs12979860-IL28B) genes. Methods The study included 110 Croatian IVDU positive for anti-HCV antibody. Genotyping was performed by polymerase chain reaction (PCR) based approach. Patients were treated by standard pegylated-interferon/ribavirin and followed throughout a period of four years, during which sustained virological response (SVR) was determined. All data were analysed with statistical package SPSS 19.0 (IBM Corp, Armonk, NY, USA) and PLINK v1.07 software. Results Patients showed a significantly better response to treatment according to the number of copies of the C allele carried at rs1800795-IL6 (P = 0.034). All but one of the patients with CC genotype achieved SVR (93%), whereas the response rate of patients with GG genotype was 64%. The association of rs1800795-IL6 with SVR status remained significant after further adjustment for patients’ age, fibrosis staging, and viral genotype (OR 2.15, 95% CI 1.16–4.68, P = 0.019). Distributions of allele frequencies at the locus rs12979860-IL28B among the study cohort and the underlying general population were suggestive of a protective effect of CC genotype in acquiring chronic hepatitis C in the Croatian IVDU population. Discussion The rs1800795-IL6 polymorphism is associated with positive response to treatment in IVDU patients positive for HCV infection. A protective role of rs12979860-IL28B CC genotype in acquiring chronic hepatitis C is suggested for Croatian IVDU population.
bibliographic citation: Bogdanović et al. (2016) The impact of IL-6 and IL-28B gene polymorphisms on treatment outcome of chronic hepatitis C infection among intravenous drug users in Croatia. PeerJ 4:e2576 https://doi.org/10.7717/peerj.2576
date submitted: 2016-05-09
date accepted: 2016-09-15
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bogdanović
  given name: Zoran
author list: Agent
  family name: Marinović-Terzić
  given name: Ivana
author list: Agent
  family name: Kuret
  given name: Sendi
author list: Agent
  family name: Jerončić
  given name: Ana
author list: Agent
  family name: Bradarić
  given name: Nikola
author list: Agent
  family name: Forempoher
  given name: Gea
author list: Agent
  family name: Polašek
  given name: Ozren
author list: Agent
  family name: Anđelinović
  given name: Šimun
author list: Agent
  family name: Terzić
  given name: Janoš
doi: 10.7717/peerj.2576
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: © 2016 Bogdanović et al.
attribution name: Bogdanović et al.

Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity
type: item
type: AcademicArticle
description: The majority of bacterial foliar plant pathogens must invade the apoplast of host plants through points of ingress, such as stomata or wounds, to replicate to high population density and cause disease. How pathogens navigate plant surfaces to locate invasion sites remains poorly understood. Many bacteria use chemical-directed regulation of flagellar rotation, a process known as chemotaxis, to move towards favorable environmental conditions. Chemotactic sensing of the plant surface is a potential mechanism through which foliar plant pathogens home in on wounds or stomata, but chemotactic systems in foliar plant pathogens are not well characterized. Comparative genomics of the plant pathogen Pseudomonas syringae pathovar tomato (Pto) implicated annotated chemotaxis genes in the recent adaptations of one Pto lineage. We therefore characterized the chemosensory system of Pto. The Pto genome contains two primary chemotaxis gene clusters, che1 and che2. The che2 cluster is flanked by flagellar biosynthesis genes and similar to the canonical chemotaxis gene clusters of other bacteria based on sequence and synteny. Disruption of the primary phosphorelay kinase gene of the che2 cluster, cheA2, eliminated all swimming and surface motility at 21 °C but not 28 °C for Pto. The che1 cluster is located next to Type IV pili biosynthesis genes but disruption of cheA1 has no observable effect on twitching motility for Pto. Disruption of cheA2 also alters in planta fitness of the pathogen with strains lacking functional cheA2 being less fit in host plants but more fit in a non-host interaction.
format: application/pdf
format: text/html
creator: Christopher R. Clarke
creator: Byron W. Hayes
creator: Brendan J. Runde
creator: Eric Markel
creator: Bryan M. Swingle
creator: Boris A. Vinatzer
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2570
publisher: PeerJ Inc.
rights: © 2016 Clarke et al.
abstract: The majority of bacterial foliar plant pathogens must invade the apoplast of host plants through points of ingress, such as stomata or wounds, to replicate to high population density and cause disease. How pathogens navigate plant surfaces to locate invasion sites remains poorly understood. Many bacteria use chemical-directed regulation of flagellar rotation, a process known as chemotaxis, to move towards favorable environmental conditions. Chemotactic sensing of the plant surface is a potential mechanism through which foliar plant pathogens home in on wounds or stomata, but chemotactic systems in foliar plant pathogens are not well characterized. Comparative genomics of the plant pathogen Pseudomonas syringae pathovar tomato (Pto) implicated annotated chemotaxis genes in the recent adaptations of one Pto lineage. We therefore characterized the chemosensory system of Pto. The Pto genome contains two primary chemotaxis gene clusters, che1 and che2. The che2 cluster is flanked by flagellar biosynthesis genes and similar to the canonical chemotaxis gene clusters of other bacteria based on sequence and synteny. Disruption of the primary phosphorelay kinase gene of the che2 cluster, cheA2, eliminated all swimming and surface motility at 21 °C but not 28 °C for Pto. The che1 cluster is located next to Type IV pili biosynthesis genes but disruption of cheA1 has no observable effect on twitching motility for Pto. Disruption of cheA2 also alters in planta fitness of the pathogen with strains lacking functional cheA2 being less fit in host plants but more fit in a non-host interaction.
bibliographic citation: Clarke et al. (2016) Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity. PeerJ 4:e2570 https://doi.org/10.7717/peerj.2570
date submitted: 2016-08-05
date accepted: 2016-09-15
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clarke
  given name: Christopher R.
author list: Agent
  family name: Hayes
  given name: Byron W.
author list: Agent
  family name: Runde
  given name: Brendan J.
author list: Agent
  family name: Markel
  given name: Eric
author list: Agent
  family name: Swingle
  given name: Bryan M.
author list: Agent
  family name: Vinatzer
  given name: Boris A.
doi: 10.7717/peerj.2570
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Clarke et al.
attribution name: Clarke et al.

Antimicrobial activity of Tachyplesin 1 against Burkholderia pseudomallei: an in vitro and in silico approach
type: item
type: AcademicArticle
description: Burkholderia pseudomallei, the causative agent of melioidosis, is intrinsically resistant to many conventional antibiotics. Therefore, alternative antimicrobial agents such as antimicrobial peptides (AMPs) are extensively studied to combat this issue. Our study aims to identify and understand the mode of action of the potential AMP(s) that are effective against B. pseudomallei in both planktonic and biofilm state as well as to predict the possible binding targets on using in vitro and in silico approaches. In the in vitro study, 11 AMPs were tested against 100 B. pseudomallei isolates for planktonic cell susceptibility, where LL-37, and PG1, demonstrated 100.0% susceptibility and TP1 demonstrated 83% susceptibility. Since the B. pseudomallei activity was reported on LL-37 and PG1, TP1 was selected for further investigation. TP1 inhibited B. pseudomallei cells at 61.69 μM, and membrane blebbing was observed using scanning electron microscopy. Moreover, TP1 inhibited B. pseudomallei cell growth, reaching bactericidal endpoint within 2 h post exposure as compared to ceftazidime (CAZ) (8 h). Furthermore, TP1 was shown to suppress the growth of B. pseudomallei cells in biofilm state at concentrations above 221 μM. However, TP1 was cytotoxic to the mammalian cell lines tested. In the in silico study, molecular docking revealed that TP1 demonstrated a strong interaction to the common peptide or inhibitor binding targets for lipopolysaccharide of Escherichia coli, as well as autolysin, pneumolysin, and pneumococcal surface protein A (PspA) of Streptococcus pneumoniae. Homology modelled B. pseudomallei PspA protein (YDP) also showed a favourable binding with a strong electrostatic contribution and nine hydrogen bonds. In conclusion, TP1 demonstrated a good potential as an anti-B. pseudomallei agent.
format: application/pdf
format: text/html
creator: Lyn-Fay Lee
creator: Vanitha Mariappan
creator: Kumutha Malar Vellasamy
creator: Vannajan Sanghiran Lee
creator: Jamuna Vadivelu
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.2468
publisher: PeerJ Inc.
rights: © 2016 Lee et al.
abstract: Burkholderia pseudomallei, the causative agent of melioidosis, is intrinsically resistant to many conventional antibiotics. Therefore, alternative antimicrobial agents such as antimicrobial peptides (AMPs) are extensively studied to combat this issue. Our study aims to identify and understand the mode of action of the potential AMP(s) that are effective against B. pseudomallei in both planktonic and biofilm state as well as to predict the possible binding targets on using in vitro and in silico approaches. In the in vitro study, 11 AMPs were tested against 100 B. pseudomallei isolates for planktonic cell susceptibility, where LL-37, and PG1, demonstrated 100.0% susceptibility and TP1 demonstrated 83% susceptibility. Since the B. pseudomallei activity was reported on LL-37 and PG1, TP1 was selected for further investigation. TP1 inhibited B. pseudomallei cells at 61.69 μM, and membrane blebbing was observed using scanning electron microscopy. Moreover, TP1 inhibited B. pseudomallei cell growth, reaching bactericidal endpoint within 2 h post exposure as compared to ceftazidime (CAZ) (8 h). Furthermore, TP1 was shown to suppress the growth of B. pseudomallei cells in biofilm state at concentrations above 221 μM. However, TP1 was cytotoxic to the mammalian cell lines tested. In the in silico study, molecular docking revealed that TP1 demonstrated a strong interaction to the common peptide or inhibitor binding targets for lipopolysaccharide of Escherichia coli, as well as autolysin, pneumolysin, and pneumococcal surface protein A (PspA) of Streptococcus pneumoniae. Homology modelled B. pseudomallei PspA protein (YDP) also showed a favourable binding with a strong electrostatic contribution and nine hydrogen bonds. In conclusion, TP1 demonstrated a good potential as an anti-B. pseudomallei agent.
bibliographic citation: Lee et al. (2016) Antimicrobial activity of Tachyplesin 1 against Burkholderia pseudomallei: an in vitro and in silico approach. PeerJ 4:e2468 https://doi.org/10.7717/peerj.2468
date submitted: 2015-12-04
date accepted: 2016-08-21
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Lyn-Fay
author list: Agent
  family name: Mariappan
  given name: Vanitha
author list: Agent
  family name: Vellasamy
  given name: Kumutha Malar
author list: Agent
  family name: Lee
  given name: Vannajan Sanghiran
author list: Agent
  family name: Vadivelu
  given name: Jamuna
doi: 10.7717/peerj.2468
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: © 2016 Lee et al.
attribution name: Lee et al.

https://peerj.com/articles/2613
type: item
type: AcademicArticle
title: A pilot study examining the effects of low-volume high-intensity interval training and continuous low to moderate intensity training on quality of life, functional capacity and cardiovascular risk factors in cancer survivors
description: Purpose The aim of this study was to evaluate the effects of low-volume high-intensity interval training and continuous low to moderate intensity training on quality of life, functional capacity and cardiovascular disease risk factors in cancer survivors. Methods Cancer survivors within 24 months post-diagnosis were randomly assigned into the low-volume high-intensity interval training group (n = 8) or the continuous low to moderate intensity training group (n = 8) group for 36 sessions (12 weeks) of supervised exercise. The low-volume high-intensity interval training (LVHIIT) group performed 7 × 30 s intervals (≥85% maximal heart rate) and the continuous low to moderate intensity training (CLMIT) group performed continuous aerobic training for 20 min (≤55% maximal heart rate) on a stationary bike or treadmill. Results Significant improvements (time) were observed for 13 of the 23 dependent variables (ES 0.05–0.61, p ≤ 0.05). An interaction effect was observed for six minute walk test (18.53% [32.43–4.63] ES 0.50, p ≤ 0.01) with the LVHIIT group demonstrating greater improvements. Conclusion These preliminary findings suggest that both interventions can induce improvements in quality of life, functional capacity and selected cardiovascular disease risk factors. The LVHIIT program was well tolerated by the participants and our results suggest that LVHIIT is the preferred modality to improve fitness (6MWT); it remains to be seen which intervention elicits the most clinically relevant outcomes for patients. A larger sample size with a control group is required to confirm the significance of these findings.
format: application/pdf
format: text/html
creator: Kellie Toohey
creator: Kate L. Pumpa
creator: Leonard Arnolda
creator: Julie Cooke
creator: Desmond Yip
creator: Paul S. Craft
creator: Stuart Semple
subject: Oncology
subject: Public Health
subject: Translational Medicine
description: doi:10.7717/peerj.2613
publisher: PeerJ Inc.
rights: © 2016 Toohey et al.
abstract: Purpose The aim of this study was to evaluate the effects of low-volume high-intensity interval training and continuous low to moderate intensity training on quality of life, functional capacity and cardiovascular disease risk factors in cancer survivors. Methods Cancer survivors within 24 months post-diagnosis were randomly assigned into the low-volume high-intensity interval training group (n = 8) or the continuous low to moderate intensity training group (n = 8) group for 36 sessions (12 weeks) of supervised exercise. The low-volume high-intensity interval training (LVHIIT) group performed 7 × 30 s intervals (≥85% maximal heart rate) and the continuous low to moderate intensity training (CLMIT) group performed continuous aerobic training for 20 min (≤55% maximal heart rate) on a stationary bike or treadmill. Results Significant improvements (time) were observed for 13 of the 23 dependent variables (ES 0.05–0.61, p ≤ 0.05). An interaction effect was observed for six minute walk test (18.53% [32.43–4.63] ES 0.50, p ≤ 0.01) with the LVHIIT group demonstrating greater improvements. Conclusion These preliminary findings suggest that both interventions can induce improvements in quality of life, functional capacity and selected cardiovascular disease risk factors. The LVHIIT program was well tolerated by the participants and our results suggest that LVHIIT is the preferred modality to improve fitness (6MWT); it remains to be seen which intervention elicits the most clinically relevant outcomes for patients. A larger sample size with a control group is required to confirm the significance of these findings.
bibliographic citation: Toohey et al. (2016) A pilot study examining the effects of low-volume high-intensity interval training and continuous low to moderate intensity training on quality of life, functional capacity and cardiovascular risk factors in cancer survivors. PeerJ 4:e2613 https://doi.org/10.7717/peerj.2613
date submitted: 2015-12-01
date accepted: 2016-09-27
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Toohey
  given name: Kellie
author list: Agent
  family name: Pumpa
  given name: Kate L.
author list: Agent
  family name: Arnolda
  given name: Leonard
author list: Agent
  family name: Cooke
  given name: Julie
author list: Agent
  family name: Yip
  given name: Desmond
author list: Agent
  family name: Craft
  given name: Paul S.
author list: Agent
  family name: Semple
  given name: Stuart
doi: 10.7717/peerj.2613
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Toohey et al.
attribution name: Toohey et al.

Nonlinear temperature effects on multifractal complexity of metabolic rate of mice
type: item
type: AcademicArticle
description: Complex physiological dynamics have been argued to be a signature of healthy physiological function. Here we test whether the complexity of metabolic rate fluctuations in small endotherms decreases with lower environmental temperatures. To do so, we examine the multifractal temporal scaling properties of the rate of change in oxygen consumption r(VO2), in the laboratory mouse Mus musculus, assessing their long range correlation properties across seven different environmental temperatures, ranging from 0 °C to 30 °C. To do so, we applied multifractal detrended fluctuation analysis (MF-DFA), finding that r(VO2) fluctuations show two scaling regimes. For small time scales below the crossover time (approximately 102 s), either monofractal or weak multifractal dynamics are observed depending on whether Ta < 15 °C or Ta > 15 °C respectively. For larger time scales, r(VO2) fluctuations are characterized by an asymptotic scaling exponent that indicates multifractal anti-persistent or uncorrelated dynamics. For both scaling regimes, a generalization of the multiplicative cascade model provides very good fits for the Renyi exponents τ(q), showing that the infinite number of exponents h(q) can be described by only two independent parameters, a and b. We also show that the long-range correlation structure of r(VO2) time series differs from randomly shuffled series, and may not be explained as an artifact of stochastic sampling of a linear frequency spectrum. These results show that metabolic rate dynamics in a well studied micro-endotherm are consistent with a highly non-linear feedback control system.
format: application/pdf
format: text/html
creator: Fabio A. Labra
creator: Jose M. Bogdanovich
creator: Francisco Bozinovic
subject: Computational Biology
subject: Ecology
subject: Mathematical Biology
subject: Statistics
description: doi:10.7717/peerj.2607
publisher: PeerJ Inc.
rights: © 2016 Labra et al.
abstract: Complex physiological dynamics have been argued to be a signature of healthy physiological function. Here we test whether the complexity of metabolic rate fluctuations in small endotherms decreases with lower environmental temperatures. To do so, we examine the multifractal temporal scaling properties of the rate of change in oxygen consumption r(VO2), in the laboratory mouse Mus musculus, assessing their long range correlation properties across seven different environmental temperatures, ranging from 0 °C to 30 °C. To do so, we applied multifractal detrended fluctuation analysis (MF-DFA), finding that r(VO2) fluctuations show two scaling regimes. For small time scales below the crossover time (approximately 102 s), either monofractal or weak multifractal dynamics are observed depending on whether Ta < 15 °C or Ta > 15 °C respectively. For larger time scales, r(VO2) fluctuations are characterized by an asymptotic scaling exponent that indicates multifractal anti-persistent or uncorrelated dynamics. For both scaling regimes, a generalization of the multiplicative cascade model provides very good fits for the Renyi exponents τ(q), showing that the infinite number of exponents h(q) can be described by only two independent parameters, a and b. We also show that the long-range correlation structure of r(VO2) time series differs from randomly shuffled series, and may not be explained as an artifact of stochastic sampling of a linear frequency spectrum. These results show that metabolic rate dynamics in a well studied micro-endotherm are consistent with a highly non-linear feedback control system.
bibliographic citation: Labra et al. (2016) Nonlinear temperature effects on multifractal complexity of metabolic rate of mice. PeerJ 4:e2607 https://doi.org/10.7717/peerj.2607
date submitted: 2015-12-10
date accepted: 2016-09-24
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Labra
  given name: Fabio A.
author list: Agent
  family name: Bogdanovich
  given name: Jose M.
author list: Agent
  family name: Bozinovic
  given name: Francisco
doi: 10.7717/peerj.2607
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Labra et al.
attribution name: Labra et al.

Taxonomy of Platypterygius campylodon and the diversity of the last ichthyosaurs
type: item
type: AcademicArticle
description: A complex and confusing taxonomy has concealed the diversity dynamics of Cretaceous ichthyosaurs (Reptilia) for decades. The near totality of Albian-Cenomanian remains from Eurasia has been assigned, by default, to the loosely defined entity Platypterygius campylodon, whose holotype was supposed to be lost. By thoroughly examining the Cenomanian ichthyosaur collections from the UK, I redescribe the syntypic series of Platypterygius campylodon. This material, along with a handful of other coeval remains, is diagnostic and seemingly differs from the vast majority of Cretaceous remains previously assigned to this taxon. A lectotype for Platypterygius campylodon is designated and I reassign this species to Pervushovisaurus campylodon nov. comb. The feeding ecology of this species is assessed and conforms to the scenario of an early Cenomanian diversity drop prior to the latest Cenomanian final extinction.
format: application/pdf
format: text/html
creator: Valentin Fischer
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.2604
publisher: PeerJ Inc.
rights: © 2016 Fischer
abstract: A complex and confusing taxonomy has concealed the diversity dynamics of Cretaceous ichthyosaurs (Reptilia) for decades. The near totality of Albian-Cenomanian remains from Eurasia has been assigned, by default, to the loosely defined entity Platypterygius campylodon, whose holotype was supposed to be lost. By thoroughly examining the Cenomanian ichthyosaur collections from the UK, I redescribe the syntypic series of Platypterygius campylodon. This material, along with a handful of other coeval remains, is diagnostic and seemingly differs from the vast majority of Cretaceous remains previously assigned to this taxon. A lectotype for Platypterygius campylodon is designated and I reassign this species to Pervushovisaurus campylodon nov. comb. The feeding ecology of this species is assessed and conforms to the scenario of an early Cenomanian diversity drop prior to the latest Cenomanian final extinction.
bibliographic citation: Fischer (2016) Taxonomy of Platypterygius campylodon and the diversity of the last ichthyosaurs. PeerJ 4:e2604 https://doi.org/10.7717/peerj.2604
date submitted: 2016-08-12
date accepted: 2016-09-24
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fischer
  given name: Valentin
doi: 10.7717/peerj.2604
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Fischer
attribution name: Fischer

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