PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cloning, expression and characterization of an ethanol tolerant GH3 β-glucosidase from Myceliophthora thermophila
items: The co-evolution of multiply-informed dispersal: information transfer across landscapes from neighbors and immigrants
items: Pattern classification of brain activation during emotional processing in subclinical depression: psychosis proneness as potential confounding factor
items: Does haemosporidian infection affect hematological and biochemical profiles of the endangered Black-fronted piping-guan (Aburria jacutinga)?
items: Development of guidelines for tertiary education institutions to assist them in supporting students with a mental illness: a Delphi consensus study with Australian professionals and consumers
items: Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data
items: Foundation species loss affects vegetation structure more than ecosystem function in a northeastern USA forest
items: A novel control of human keratin expression: cannabinoid receptor 1-mediated signaling down-regulates the expression of keratins K6 and K16 in human keratinocytes in vitro and in situ
items: Personality change after Internet-delivered cognitive behavior therapy for depression
items: Phenotypic characterization of patients with deletions in the 3’-flanking SHOX region
items: Validation of the Emotiv EPOC® EEG gaming system for measuring research quality auditory ERPs
items: Development and evolution of the unique cetacean dentition
items: A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae
items: Iodine nutrition and toxicity in Atlantic cod (Gadus morhua) larvae
items: Evaluation of animal control measures on pet demographics in Santa Clara County, California, 1993–2006
items: Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus
items: Pain assessment in children undergoing venipuncture: the Wong–Baker faces scale versus skin conductance fluctuations
items: Why sauropods had long necks; and why giraffes have short necks
items: Coronatine inhibits stomatal closure and delays hypersensitive response cell death induced by nonhost bacterial pathogens
items: A perfusion study of the handling of urea and urea analogues by the gills of the dogfish shark (Squalus acanthias)
items: Analysis of innate and acquired resistance to anti-CD20 antibodies in malignant and nonmalignant B cells
items: A practical implementation of de-Pake-ing via weighted Fourier transformation
items: Anti-apoptotic signaling as a cytoprotective mechanism in mammalian hibernation
items: Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice
items: Novel enzyme-polymer conjugates for biotechnological applications
items: Organ homologies in orchid flowers re-interpreted using the Musk Orchid as a model
items: Repeated hands-and-knees positioning during labour: a randomized pilot study
items: Poorer verbal working memory for a second language selectively impacts academic achievement in university medical students
items: Glucose-6-phosphate dehydrogenase regulation in the hepatopancreas of the anoxia-tolerant marine mollusc, Littorina littorea
items: Perceptual elements in Penn & Teller’s “Cups and Balls” magic trick
items: Timing of molt of barn swallows is delayed in a rare Clock genotype
items: Na+/Ca2+ selectivity in the bacterial voltage-gated sodium channel NavAb
items: Fluorescent protein tagging confirms the presence of ribosomal proteins at Drosophila polytene chromosomes
items: Simultaneous recordings of ocular microtremor and microsaccades with a piezoelectric sensor and a video-oculography system
items: Dissecting the mechanisms of squirrel monkey (Saimiri boliviensis) social learning
items: Novel control of lactate dehydrogenase from the freeze tolerant wood frog: role of posttranslational modifications
items: Assessing insect responses to climate change: What are we testing for? Where should we be heading?
items: Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
items: The effects of fixation target size and luminance on microsaccades and square-wave jerks
items: Mutations changing tropomodulin affinity for tropomyosin alter neurite formation and extension
items: Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing
items: Soil carbon determination by thermogravimetrics
items: Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences
items: The roles of STP and LTP in synaptic encoding
items: Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
items: How long is a piece of loop?

Cloning, expression and characterization of an ethanol tolerant GH3 β-glucosidase from Myceliophthora thermophila
type: item
type: AcademicArticle
description: The β-glucosidase gene bgl3a from Myceliophthora thermophila, member of the fungal glycosyl hydrolase (GH) family 3, was cloned and expressed in Pichia pastoris. The mature β-glucosidase gene, which results after the excision of one intron and the secreting signal peptide, was placed under the control of the strong alcohol oxidase promoter (AOX1) in the plasmid pPICZαC. The recombinant enzyme (90 kDa) was purified and characterized in order to evaluate its biotechnological potential. Recombinant P. pastoris efficiently secreted β-glucosidase into the medium and produced high level of enzymatic activity (41 U/ml) after 192 h of growth, under methanol induction. MtBgl3a was able to hydrolyze low molecular weight substrates and polysaccharides containing β-glucosidic residues. The Km was found to be 0.39 mM on p-β-NPG and 2.64 mM on cellobiose. Optimal pH and temperature for the p-β-NPG hydrolysis were 5.0 and 70 °C. The β-glucosidase exhibits a half life of 143 min at 60 °C. Kinetic parameters of inhibition were determined for D-glucose, D-xylose and D-gluconic acid, indicating tolerance of the enzyme for these sugars and oxidized products. The recombinant enzyme was stimulated by short chain alcohols and has been shown to efficiently synthesize methyl-D-glucoside in the presence of methanol due to its transglycosylation activity. The stability of MtBgl3a in ethanol was prominent, and it retained most of its original activity after we exposed it to 50% ethanol for 6 h. The high catalytic performance, good thermal stability and tolerance to elevated concentrations of ethanol, D-xylose and D-glucose qualify this enzyme for use in the hydrolysis of lignocellulosic biomass for biofuel production, as part of an efficient complete multi-enzyme cocktail.
format: application/pdf
format: text/html
creator: Anthi Karnaouri
creator: Evangelos Topakas
creator: Thomas Paschos
creator: Ioanna Taouki
creator: Paul Christakopoulos
subject: Agricultural Science
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.46
publisher: PeerJ Inc.
rights: © 2013 Karnaouri et al.
abstract: The β-glucosidase gene bgl3a from Myceliophthora thermophila, member of the fungal glycosyl hydrolase (GH) family 3, was cloned and expressed in Pichia pastoris. The mature β-glucosidase gene, which results after the excision of one intron and the secreting signal peptide, was placed under the control of the strong alcohol oxidase promoter (AOX1) in the plasmid pPICZαC. The recombinant enzyme (90 kDa) was purified and characterized in order to evaluate its biotechnological potential. Recombinant P. pastoris efficiently secreted β-glucosidase into the medium and produced high level of enzymatic activity (41 U/ml) after 192 h of growth, under methanol induction. MtBgl3a was able to hydrolyze low molecular weight substrates and polysaccharides containing β-glucosidic residues. The Km was found to be 0.39 mM on p-β-NPG and 2.64 mM on cellobiose. Optimal pH and temperature for the p-β-NPG hydrolysis were 5.0 and 70 °C. The β-glucosidase exhibits a half life of 143 min at 60 °C. Kinetic parameters of inhibition were determined for D-glucose, D-xylose and D-gluconic acid, indicating tolerance of the enzyme for these sugars and oxidized products. The recombinant enzyme was stimulated by short chain alcohols and has been shown to efficiently synthesize methyl-D-glucoside in the presence of methanol due to its transglycosylation activity. The stability of MtBgl3a in ethanol was prominent, and it retained most of its original activity after we exposed it to 50% ethanol for 6 h. The high catalytic performance, good thermal stability and tolerance to elevated concentrations of ethanol, D-xylose and D-glucose qualify this enzyme for use in the hydrolysis of lignocellulosic biomass for biofuel production, as part of an efficient complete multi-enzyme cocktail.
bibliographic citation: Karnaouri et al. (2013) Cloning, expression and characterization of an ethanol tolerant GH3 β-glucosidase from Myceliophthora thermophila. PeerJ 1:e46 https://doi.org/10.7717/peerj.46
date submitted: 2012-12-04
date accepted: 2013-02-11
issued: 2013-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Karnaouri
  given name: Anthi
author list: Agent
  family name: Topakas
  given name: Evangelos
author list: Agent
  family name: Paschos
  given name: Thomas
author list: Agent
  family name: Taouki
  given name: Ioanna
author list: Agent
  family name: Christakopoulos
  given name: Paul
doi: 10.7717/peerj.46
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-26
copyright: © 2013 Karnaouri et al.
attribution name: Karnaouri et al.

The co-evolution of multiply-informed dispersal: information transfer across landscapes from neighbors and immigrants
type: item
type: AcademicArticle
description: Dispersal plays a key role in natural systems by shaping spatial population and evolutionary dynamics. Dispersal has been largely treated as a population process with little attention to individual decisions and the influence of information use on the fitness benefits of dispersal despite clear empirical evidence that dispersal behavior varies among individuals. While information on local density is common, more controversial is the notion that indirect information use can easily evolve. We used an individual-based model to ask under what conditions indirect information use in dispersal will evolve. We modeled indirect information provided by immigrant arrival into a population which should be linked to overall metapopulation density. We also modeled direct information use of density which directly impacts fitness. We show that immigrant-dependent dispersal evolves and does so even when density dependent information is available. Use of two sources of information also provides benefits at the metapopulation level by reducing extinction risk and prolonging the persistence of populations. Our results suggest that use of indirect information in dispersal can evolve under conservative conditions and thus could be widespread.
format: application/pdf
format: text/html
creator: Alexis S. Chaine
creator: Stéphane Legendre
creator: Jean Clobert
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.44
publisher: PeerJ Inc.
rights: © 2013 Chaine et al.
abstract: Dispersal plays a key role in natural systems by shaping spatial population and evolutionary dynamics. Dispersal has been largely treated as a population process with little attention to individual decisions and the influence of information use on the fitness benefits of dispersal despite clear empirical evidence that dispersal behavior varies among individuals. While information on local density is common, more controversial is the notion that indirect information use can easily evolve. We used an individual-based model to ask under what conditions indirect information use in dispersal will evolve. We modeled indirect information provided by immigrant arrival into a population which should be linked to overall metapopulation density. We also modeled direct information use of density which directly impacts fitness. We show that immigrant-dependent dispersal evolves and does so even when density dependent information is available. Use of two sources of information also provides benefits at the metapopulation level by reducing extinction risk and prolonging the persistence of populations. Our results suggest that use of indirect information in dispersal can evolve under conservative conditions and thus could be widespread.
bibliographic citation: Chaine et al. (2013) The co-evolution of multiply-informed dispersal: information transfer across landscapes from neighbors and immigrants. PeerJ 1:e44 https://doi.org/10.7717/peerj.44
date submitted: 2012-12-19
date accepted: 2013-02-08
issued: 2013-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Chaine
  given name: Alexis S.
author list: Agent
  family name: Legendre
  given name: Stéphane
author list: Agent
  family name: Clobert
  given name: Jean
doi: 10.7717/peerj.44
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-26
copyright: © 2013 Chaine et al.
attribution name: Chaine et al.

Pattern classification of brain activation during emotional processing in subclinical depression: psychosis proneness as potential confounding factor
type: item
type: AcademicArticle
description: We used Support Vector Machine (SVM) to perform multivariate pattern classification based on brain activation during emotional processing in healthy participants with subclinical depressive symptoms. Six-hundred undergraduate students completed the Beck Depression Inventory II (BDI-II). Two groups were subsequently formed: (i) subclinical (mild) mood disturbance (n = 17) and (ii) no mood disturbance (n = 17). Participants also completed a self-report questionnaire on subclinical psychotic symptoms, the Community Assessment of Psychic Experiences Questionnaire (CAPE) positive subscale. The functional magnetic resonance imaging (fMRI) paradigm entailed passive viewing of negative emotional and neutral scenes. The pattern of brain activity during emotional processing allowed correct group classification with an overall accuracy of 77% (p = 0.002), within a network of regions including the amygdala, insula, anterior cingulate cortex and medial prefrontal cortex. However, further analysis suggested that the classification accuracy could also be explained by subclinical psychotic symptom scores (correlation with SVM weights r = 0.459, p = 0.006). Psychosis proneness may thus be a confounding factor for neuroimaging studies in subclinical depression.
format: application/pdf
format: text/html
creator: Gemma Modinos
creator: Andrea Mechelli
creator: William Pettersson-Yeo
creator: Paul Allen
creator: Philip McGuire
creator: Andre Aleman
subject: Neuroscience
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.42
publisher: PeerJ Inc.
rights: © 2013 Modinos et al.
abstract: We used Support Vector Machine (SVM) to perform multivariate pattern classification based on brain activation during emotional processing in healthy participants with subclinical depressive symptoms. Six-hundred undergraduate students completed the Beck Depression Inventory II (BDI-II). Two groups were subsequently formed: (i) subclinical (mild) mood disturbance (n = 17) and (ii) no mood disturbance (n = 17). Participants also completed a self-report questionnaire on subclinical psychotic symptoms, the Community Assessment of Psychic Experiences Questionnaire (CAPE) positive subscale. The functional magnetic resonance imaging (fMRI) paradigm entailed passive viewing of negative emotional and neutral scenes. The pattern of brain activity during emotional processing allowed correct group classification with an overall accuracy of 77% (p = 0.002), within a network of regions including the amygdala, insula, anterior cingulate cortex and medial prefrontal cortex. However, further analysis suggested that the classification accuracy could also be explained by subclinical psychotic symptom scores (correlation with SVM weights r = 0.459, p = 0.006). Psychosis proneness may thus be a confounding factor for neuroimaging studies in subclinical depression.
bibliographic citation: Modinos et al. (2013) Pattern classification of brain activation during emotional processing in subclinical depression: psychosis proneness as potential confounding factor. PeerJ 1:e42 https://doi.org/10.7717/peerj.42
date submitted: 2012-12-04
date accepted: 2013-01-28
issued: 2013-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Modinos
  given name: Gemma
author list: Agent
  family name: Mechelli
  given name: Andrea
author list: Agent
  family name: Pettersson-Yeo
  given name: William
author list: Agent
  family name: Allen
  given name: Paul
author list: Agent
  family name: McGuire
  given name: Philip
author list: Agent
  family name: Aleman
  given name: Andre
doi: 10.7717/peerj.42
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-26
copyright: © 2013 Modinos et al.
attribution name: Modinos et al.

Does haemosporidian infection affect hematological and biochemical profiles of the endangered Black-fronted piping-guan (Aburria jacutinga)?
type: item
type: AcademicArticle
description: Infectious diseases can cause deleterious effects on bird species, leading to population decline and extinction. Haemosporidia can be recognized by their negative effects on host fitness, including reproductive success and immune responses. In captivity, outbreaks of haemosporidian infection have been observed in birds in zoos and aviaries. The endemic Brazilian Atlantic rainforest species Aburria jacutinga is one of the most endangered species in the Cracidae family, and wild populations of this species are currently found mainly in conservation areas in only two Brazilian states. In this study, we aimed to evaluate the effects of avian haemosporidia on hematological and biochemical parameters in two captive populations of A. jacutinga. Forty-two animals were assessed, and the haemosporidian prevalence was similar for males and females. The occurrence of haemosporidian infection in captive A. jacutinga observed in this study was similar to results found in other captive and wild birds in Brazil. We found three different lineages of haemosporidia. Two lineages were identified as Plasmodium sp., one of which was previously detected in Europe and Asia, and the other is a new lineage closely related to P. gallinaceum. A new third lineage was identified as Haemoproteus sp. We found no significant differences in hematological and biochemical values between infected and non-infected birds, and the haemosporidian lineage did not seem to have an impact on the clinical and physiological parameters of A. jacutinga. This is the first report on an evaluation of natural haemosporidian infections diagnosed by microscopic and molecular methods in A. jacutinga by hematology, blood biochemistry, and serum protein values. Determining physiological parameters, occurrence and an estimation of the impact of haemosporidia in endangered avian species may contribute to the management of species rehabilitation and conservation.
format: application/pdf
format: text/html
creator: Rafael Otávio Cançado Motta
creator: Marcus Vinícius Romero Marques
creator: Francisco Carlos Ferreira Junior
creator: Danielle de Assis Andery
creator: Rodrigo Santos Horta
creator: Renata Barbosa Peixoto
creator: Gustavo Augusto Lacorte
creator: Patrícia de Abreu Moreira
creator: Fabíola de Oliveira Paes Leme
creator: Marília Martins Melo
creator: Nelson Rodrigo da Silva Martins
creator: Érika Martins Braga
subject: Conservation Biology
subject: Parasitology
subject: Veterinary Medicine
description: doi:10.7717/peerj.45
publisher: PeerJ Inc.
rights: © 2013 Motta et al.
abstract: Infectious diseases can cause deleterious effects on bird species, leading to population decline and extinction. Haemosporidia can be recognized by their negative effects on host fitness, including reproductive success and immune responses. In captivity, outbreaks of haemosporidian infection have been observed in birds in zoos and aviaries. The endemic Brazilian Atlantic rainforest species Aburria jacutinga is one of the most endangered species in the Cracidae family, and wild populations of this species are currently found mainly in conservation areas in only two Brazilian states. In this study, we aimed to evaluate the effects of avian haemosporidia on hematological and biochemical parameters in two captive populations of A. jacutinga. Forty-two animals were assessed, and the haemosporidian prevalence was similar for males and females. The occurrence of haemosporidian infection in captive A. jacutinga observed in this study was similar to results found in other captive and wild birds in Brazil. We found three different lineages of haemosporidia. Two lineages were identified as Plasmodium sp., one of which was previously detected in Europe and Asia, and the other is a new lineage closely related to P. gallinaceum. A new third lineage was identified as Haemoproteus sp. We found no significant differences in hematological and biochemical values between infected and non-infected birds, and the haemosporidian lineage did not seem to have an impact on the clinical and physiological parameters of A. jacutinga. This is the first report on an evaluation of natural haemosporidian infections diagnosed by microscopic and molecular methods in A. jacutinga by hematology, blood biochemistry, and serum protein values. Determining physiological parameters, occurrence and an estimation of the impact of haemosporidia in endangered avian species may contribute to the management of species rehabilitation and conservation.
bibliographic citation: Motta et al. (2013) Does haemosporidian infection affect hematological and biochemical profiles of the endangered Black-fronted piping-guan (Aburria jacutinga)?. PeerJ 1:e45 https://doi.org/10.7717/peerj.45
date submitted: 2012-12-03
date accepted: 2013-02-09
issued: 2013-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Motta
  given name: Rafael Otávio Cançado
author list: Agent
  family name: Romero Marques
  given name: Marcus Vinícius
author list: Agent
  family name: Ferreira Junior
  given name: Francisco Carlos
author list: Agent
  family name: Andery
  given name: Danielle de Assis
author list: Agent
  family name: Horta
  given name: Rodrigo Santos
author list: Agent
  family name: Peixoto
  given name: Renata Barbosa
author list: Agent
  family name: Lacorte
  given name: Gustavo Augusto
author list: Agent
  family name: Moreira
  given name: Patrícia de Abreu
author list: Agent
  family name: Paes Leme
  given name: Fabíola de Oliveira
author list: Agent
  family name: Melo
  given name: Marília Martins
author list: Agent
  family name: Martins
  given name: Nelson Rodrigo da Silva
author list: Agent
  family name: Braga
  given name: Érika Martins
doi: 10.7717/peerj.45
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-26
copyright: © 2013 Motta et al.
attribution name: Motta et al.

Development of guidelines for tertiary education institutions to assist them in supporting students with a mental illness: a Delphi consensus study with Australian professionals and consumers
type: item
type: AcademicArticle
description: Background. The age at which most young people are in tertiary education is also the age of peak onset for mental illness. Because mental health problems can have adverse effects on students’ academic performance and welfare, institutions require guidance how they can best provide support. However, the scientific evidence for how best to do this is relatively limited. Therefore a Delphi expert consensus study was carried out with professional and consumer experts. Methods. A systematic review of websites, books and journal articles was conducted to develop a 172 item survey containing strategies that institutions might use to support students with a mental illness. Two panels of Australian experts (74 professionals and 35 consumers) were recruited and independently rated the items over three rounds, with strategies reaching consensus on importance written into the guidelines. Results. The overall response rate across three rounds was 83% (80% consumers, 85% professionals). 155 strategies were endorsed as essential or important by at least 80% of panel members. The endorsed strategies provided information on policy, measures to promote support services, service provision, accessibility of support services, relationships between services, other types of support and issues associated with reasonable adjustments. They also provided guidance on the procedures the institutions should have for making staff aware of issues associated with mental illness, mental illness training, support for staff and communicating with a student with a mental illness. They also covered student rights and responsibilities, the procedures the institutions should have for making students aware of issues associated with mental illness, dealing with mental health crises, funding and research and evaluation. Conclusions. The guidelines provide guidance for tertiary institutions to assist them in supporting students with a mental illness. It is hoped that they may be used to inform policy and prac…
format: application/pdf
format: text/html
creator: Nicola J. Reavley
creator: Anna M. Ross
creator: Eoin Killackey
creator: Anthony F. Jorm
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.43
publisher: PeerJ Inc.
rights: © 2013 Reavley et al.
abstract: Background. The age at which most young people are in tertiary education is also the age of peak onset for mental illness. Because mental health problems can have adverse effects on students’ academic performance and welfare, institutions require guidance how they can best provide support. However, the scientific evidence for how best to do this is relatively limited. Therefore a Delphi expert consensus study was carried out with professional and consumer experts. Methods. A systematic review of websites, books and journal articles was conducted to develop a 172 item survey containing strategies that institutions might use to support students with a mental illness. Two panels of Australian experts (74 professionals and 35 consumers) were recruited and independently rated the items over three rounds, with strategies reaching consensus on importance written into the guidelines. Results. The overall response rate across three rounds was 83% (80% consumers, 85% professionals). 155 strategies were endorsed as essential or important by at least 80% of panel members. The endorsed strategies provided information on policy, measures to promote support services, service provision, accessibility of support services, relationships between services, other types of support and issues associated with reasonable adjustments. They also provided guidance on the procedures the institutions should have for making staff aware of issues associated with mental illness, mental illness training, support for staff and communicating with a student with a mental illness. They also covered student rights and responsibilities, the procedures the institutions should have for making students aware of issues associated with mental illness, dealing with mental health crises, funding and research and evaluation. Conclusions. The guidelines provide guidance for tertiary institutions to assist them in supporting students with a mental illness. It is hoped that they may be used to inform policy and prac…
bibliographic citation: Reavley et al. (2013) Development of guidelines for tertiary education institutions to assist them in supporting students with a mental illness: a Delphi consensus study with Australian professionals and consumers. PeerJ 1:e43 https://doi.org/10.7717/peerj.43
date submitted: 2012-11-13
date accepted: 2013-01-31
issued: 2013-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Reavley
  given name: Nicola J.
author list: Agent
  family name: Ross
  given name: Anna M.
author list: Agent
  family name: Killackey
  given name: Eoin
author list: Agent
  family name: Jorm
  given name: Anthony F.
doi: 10.7717/peerj.43
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-26
copyright: © 2013 Reavley et al.
attribution name: Reavley et al.

Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data
type: item
type: AcademicArticle
description: Accumulating evidence indicates that the intestinal microbiota regulates our physiology and metabolism. Bacteria marketed as probiotics confer health benefits that may arise from their ability to affect the microbiota. Here high-throughput screening of the intestinal microbiota was carried out and integrated with serum lipidomic profiling data to study the impact of probiotic intervention on the intestinal ecosystem, and to explore the associations between the intestinal bacteria and serum lipids. We performed a comprehensive intestinal microbiota analysis using a phylogenetic microarray before and after Lactobacillus rhamnosus GG intervention. While a specific increase in the L. rhamnosus-related bacteria was observed during the intervention, no other changes in the composition or stability of the microbiota were detected. After the intervention, lactobacilli returned to their initial levels. As previously reported, also the serum lipid profiles remained unaltered during the intervention. Based on a high-resolution microbiota analysis, intake of L. rhamnosus GG did not modify the composition of the intestinal ecosystem in healthy adults, indicating that probiotics confer their health effects by other mechanisms. The most prevailing association between the gut microbiota and lipid profiles was a strong positive correlation between uncultured phylotypes of Ruminococcus gnavus-group and polyunsaturated serum triglycerides of dietary origin. Moreover, a positive correlation was detected between serum cholesterol and Collinsella (Coriobacteriaceae). These associations identified with the spectrometric lipidome profiling were corroborated by enzymatically determined cholesterol and triglyceride levels. Actinomycetaceae correlated negatively with triglycerides of highly unsaturated fatty acids while a set of Proteobacteria showed negative correlation with ether phosphatidylcholines. Our results suggest that several members of the Firmicutes, Actinobacteria and Proteobacte…
format: application/pdf
format: text/html
creator: Leo Lahti
creator: Anne Salonen
creator: Riina A. Kekkonen
creator: Jarkko Salojärvi
creator: Jonna Jalanka-Tuovinen
creator: Airi Palva
creator: Matej Orešič
creator: Willem M. de Vos
subject: Clinical Trials
subject: Food Science and Technology
subject: Microbiology
subject: Nutrition
description: doi:10.7717/peerj.32
publisher: PeerJ Inc.
rights: © 2013 Lahti et al.
abstract: Accumulating evidence indicates that the intestinal microbiota regulates our physiology and metabolism. Bacteria marketed as probiotics confer health benefits that may arise from their ability to affect the microbiota. Here high-throughput screening of the intestinal microbiota was carried out and integrated with serum lipidomic profiling data to study the impact of probiotic intervention on the intestinal ecosystem, and to explore the associations between the intestinal bacteria and serum lipids. We performed a comprehensive intestinal microbiota analysis using a phylogenetic microarray before and after Lactobacillus rhamnosus GG intervention. While a specific increase in the L. rhamnosus-related bacteria was observed during the intervention, no other changes in the composition or stability of the microbiota were detected. After the intervention, lactobacilli returned to their initial levels. As previously reported, also the serum lipid profiles remained unaltered during the intervention. Based on a high-resolution microbiota analysis, intake of L. rhamnosus GG did not modify the composition of the intestinal ecosystem in healthy adults, indicating that probiotics confer their health effects by other mechanisms. The most prevailing association between the gut microbiota and lipid profiles was a strong positive correlation between uncultured phylotypes of Ruminococcus gnavus-group and polyunsaturated serum triglycerides of dietary origin. Moreover, a positive correlation was detected between serum cholesterol and Collinsella (Coriobacteriaceae). These associations identified with the spectrometric lipidome profiling were corroborated by enzymatically determined cholesterol and triglyceride levels. Actinomycetaceae correlated negatively with triglycerides of highly unsaturated fatty acids while a set of Proteobacteria showed negative correlation with ether phosphatidylcholines. Our results suggest that several members of the Firmicutes, Actinobacteria and Proteobacte…
bibliographic citation: Lahti et al. (2013) Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. PeerJ 1:e32 https://doi.org/10.7717/peerj.32
date submitted: 2012-12-10
date accepted: 2013-01-15
issued: 2013-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Lahti
  given name: Leo
author list: Agent
  family name: Salonen
  given name: Anne
author list: Agent
  family name: Kekkonen
  given name: Riina A.
author list: Agent
  family name: Salojärvi
  given name: Jarkko
author list: Agent
  family name: Jalanka-Tuovinen
  given name: Jonna
author list: Agent
  family name: Palva
  given name: Airi
author list: Agent
  family name: Orešič
  given name: Matej
author list: Agent
  family name: de Vos
  given name: Willem M.
doi: 10.7717/peerj.32
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-26
copyright: © 2013 Lahti et al.
attribution name: Lahti et al.

Foundation species loss affects vegetation structure more than ecosystem function in a northeastern USA forest
type: item
type: AcademicArticle
description: Loss of foundation tree species rapidly alters ecological processes in forested ecosystems. Tsuga canadensis, an hypothesized foundation species of eastern North American forests, is declining throughout much of its range due to infestation by the nonnative insect Adelges tsugae and by removal through pre-emptive salvage logging. In replicate 0.81-ha plots, T. canadensis was cut and removed, or killed in place by girdling to simulate adelgid damage. Control plots included undisturbed hemlock and mid-successional hardwood stands that represent expected forest composition in 50–100 years. Vegetation richness, understory vegetation cover, soil carbon flux, and nitrogen cycling were measured for two years prior to, and five years following, application of experimental treatments. Litterfall and coarse woody debris (CWD), including snags, stumps, and fallen logs and branches, have been measured since treatments were applied. Overstory basal area was reduced 60%–70% in girdled and logged plots. Mean cover and richness did not change in hardwood or hemlock control plots but increased rapidly in girdled and logged plots. Following logging, litterfall immediately decreased then slowly increased, whereas in girdled plots, there was a short pulse of hemlock litterfall as trees died. CWD volume remained relatively constant throughout but was 3–4× higher in logged plots. Logging and girdling resulted in small, short-term changes in ecosystem dynamics due to rapid regrowth of vegetation but in general, interannual variability exceeded differences among treatments. Soil carbon flux in girdled plots showed the strongest response: 35% lower than controls after three years and slowly increasing thereafter. Ammonium availability increased immediately after logging and two years after girdling, due to increased light and soil temperatures and nutrient pulses from leaf-fall and reduced uptake following tree death. The results from this study illuminate ecological processes underlying pa…
format: application/pdf
format: text/html
creator: David A. Orwig
creator: Audrey A. Barker Plotkin
creator: Eric A. Davidson
creator: Heidi Lux
creator: Kathleen E. Savage
creator: Aaron M. Ellison
subject: Ecology
subject: Ecosystem Science
description: doi:10.7717/peerj.41
publisher: PeerJ Inc.
rights: © 2013 Orwig et al.
abstract: Loss of foundation tree species rapidly alters ecological processes in forested ecosystems. Tsuga canadensis, an hypothesized foundation species of eastern North American forests, is declining throughout much of its range due to infestation by the nonnative insect Adelges tsugae and by removal through pre-emptive salvage logging. In replicate 0.81-ha plots, T. canadensis was cut and removed, or killed in place by girdling to simulate adelgid damage. Control plots included undisturbed hemlock and mid-successional hardwood stands that represent expected forest composition in 50–100 years. Vegetation richness, understory vegetation cover, soil carbon flux, and nitrogen cycling were measured for two years prior to, and five years following, application of experimental treatments. Litterfall and coarse woody debris (CWD), including snags, stumps, and fallen logs and branches, have been measured since treatments were applied. Overstory basal area was reduced 60%–70% in girdled and logged plots. Mean cover and richness did not change in hardwood or hemlock control plots but increased rapidly in girdled and logged plots. Following logging, litterfall immediately decreased then slowly increased, whereas in girdled plots, there was a short pulse of hemlock litterfall as trees died. CWD volume remained relatively constant throughout but was 3–4× higher in logged plots. Logging and girdling resulted in small, short-term changes in ecosystem dynamics due to rapid regrowth of vegetation but in general, interannual variability exceeded differences among treatments. Soil carbon flux in girdled plots showed the strongest response: 35% lower than controls after three years and slowly increasing thereafter. Ammonium availability increased immediately after logging and two years after girdling, due to increased light and soil temperatures and nutrient pulses from leaf-fall and reduced uptake following tree death. The results from this study illuminate ecological processes underlying pa…
bibliographic citation: Orwig et al. (2013) Foundation species loss affects vegetation structure more than ecosystem function in a northeastern USA forest. PeerJ 1:e41 https://doi.org/10.7717/peerj.41
date submitted: 2012-11-13
date accepted: 2013-01-28
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Orwig
  given name: David A.
author list: Agent
  family name: Barker Plotkin
  given name: Audrey A.
author list: Agent
  family name: Davidson
  given name: Eric A.
author list: Agent
  family name: Lux
  given name: Heidi
author list: Agent
  family name: Savage
  given name: Kathleen E.
author list: Agent
  family name: Ellison
  given name: Aaron M.
doi: 10.7717/peerj.41
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Orwig et al.
attribution name: Orwig et al.

A novel control of human keratin expression: cannabinoid receptor 1-mediated signaling down-regulates the expression of keratins K6 and K16 in human keratinocytes in vitro and in situ
type: item
type: AcademicArticle
description: Cannabinoid receptors (CB) are expressed throughout human skin epithelium. CB1 activation inhibits human hair growth and decreases proliferation of epidermal keratinocytes. Since psoriasis is a chronic hyperproliferative, inflammatory skin disease, it is conceivable that the therapeutic modulation of CB signaling, which can inhibit both proliferation and inflammation, could win a place in future psoriasis management. Given that psoriasis is characterized by up-regulation of keratins K6 and K16, we have investigated whether CB1 stimulation modulates their expression in human epidermis. Treatment of organ-cultured human skin with the CB1-specific agonist, arachidonoyl-chloro-ethanolamide (ACEA), decreased K6 and K16 staining intensity in situ. At the gene and protein levels, ACEA also decreased K6 expression of cultured HaCaT keratinocytes, which show some similarities to psoriatic keratinocytes. These effects were partly antagonized by the CB1-specific antagonist, AM251. While CB1-mediated signaling also significantly inhibited human epidermal keratinocyte proliferation in situ, as shown by K6/Ki-67-double immunofluorescence, the inhibitory effect of ACEA on K6 expression in situ was independent of its anti-proliferative effect. Given recent appreciation of the role of K6 as a functionally important protein that regulates epithelial wound healing in mice, it is conceivable that the novel CB1-mediated regulation of keratin 6/16 revealed here also is relevant to wound healing. Taken together, our results suggest that cannabinoids and their receptors constitute a novel, clinically relevant control element of human K6 and K16 expression.
format: application/pdf
format: text/html
creator: Yuval Ramot
creator: Koji Sugawara
creator: Nóra Zákány
creator: Balázs I. Tóth
creator: Tamás Bíró
creator: Ralf Paus
subject: Histology
subject: Anatomy and Physiology
subject: Dermatology
description: doi:10.7717/peerj.40
publisher: PeerJ Inc.
rights: © 2013 Ramot et al.
abstract: Cannabinoid receptors (CB) are expressed throughout human skin epithelium. CB1 activation inhibits human hair growth and decreases proliferation of epidermal keratinocytes. Since psoriasis is a chronic hyperproliferative, inflammatory skin disease, it is conceivable that the therapeutic modulation of CB signaling, which can inhibit both proliferation and inflammation, could win a place in future psoriasis management. Given that psoriasis is characterized by up-regulation of keratins K6 and K16, we have investigated whether CB1 stimulation modulates their expression in human epidermis. Treatment of organ-cultured human skin with the CB1-specific agonist, arachidonoyl-chloro-ethanolamide (ACEA), decreased K6 and K16 staining intensity in situ. At the gene and protein levels, ACEA also decreased K6 expression of cultured HaCaT keratinocytes, which show some similarities to psoriatic keratinocytes. These effects were partly antagonized by the CB1-specific antagonist, AM251. While CB1-mediated signaling also significantly inhibited human epidermal keratinocyte proliferation in situ, as shown by K6/Ki-67-double immunofluorescence, the inhibitory effect of ACEA on K6 expression in situ was independent of its anti-proliferative effect. Given recent appreciation of the role of K6 as a functionally important protein that regulates epithelial wound healing in mice, it is conceivable that the novel CB1-mediated regulation of keratin 6/16 revealed here also is relevant to wound healing. Taken together, our results suggest that cannabinoids and their receptors constitute a novel, clinically relevant control element of human K6 and K16 expression.
bibliographic citation: Ramot et al. (2013) A novel control of human keratin expression: cannabinoid receptor 1-mediated signaling down-regulates the expression of keratins K6 and K16 in human keratinocytes in vitro and in situ. PeerJ 1:e40 https://doi.org/10.7717/peerj.40
date submitted: 2012-11-30
date accepted: 2013-01-28
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Ramot
  given name: Yuval
author list: Agent
  family name: Sugawara
  given name: Koji
author list: Agent
  family name: Zákány
  given name: Nóra
author list: Agent
  family name: Tóth
  given name: Balázs I.
author list: Agent
  family name: Bíró
  given name: Tamás
author list: Agent
  family name: Paus
  given name: Ralf
doi: 10.7717/peerj.40
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Ramot et al.
attribution name: Ramot et al.

Personality change after Internet-delivered cognitive behavior therapy for depression
type: item
type: AcademicArticle
description: Background. The Temperament and Character Inventory (TCI) by Cloninger is a widely used instrument to measure personality dimensions. Two dimensions of the TCI, Harm avoidance (HA) and Self-Directedness (SD), are known to be influenced by depressed mood. This study investigated changes in HA and SD after 10 weeks of Internet-delivered cognitive behavior therapy (ICBT) in a sample of clinically depressed subjects (N = 108). Differences in personality changes among treatment responders and non-responders were also investigated. Exploratory investigations on changes for other TCI dimensions, were also conducted. Methods. Depressed subjects were randomized either to ICBT or to a moderated online discussion group, which served as an active control group. The interventions lasted for 10 weeks. TCI was measured at baseline and after treatment. Depressive symptoms were assessed using the Beck Depression Inventory-II. Results. There were significant changes on HA and SD after ICBT. However, when comparing post-treatment HA and SD to the control, no differences were found. Among responders, larger changes compared to non-responders were found in HA and in SD, as well as in Cooperativeness. Conclusions. The study showed that HA and SD changed after ICBT. The changes in personality seem related to improvement in depression rather than a direct effect of ICBT.
format: application/pdf
format: text/html
creator: Robert Johansson
creator: Caroline Lyssarides
creator: Gerhard Andersson
creator: Andréas Rousseau
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.39
publisher: PeerJ Inc.
rights: © 2013 Johansson et al.
abstract: Background. The Temperament and Character Inventory (TCI) by Cloninger is a widely used instrument to measure personality dimensions. Two dimensions of the TCI, Harm avoidance (HA) and Self-Directedness (SD), are known to be influenced by depressed mood. This study investigated changes in HA and SD after 10 weeks of Internet-delivered cognitive behavior therapy (ICBT) in a sample of clinically depressed subjects (N = 108). Differences in personality changes among treatment responders and non-responders were also investigated. Exploratory investigations on changes for other TCI dimensions, were also conducted. Methods. Depressed subjects were randomized either to ICBT or to a moderated online discussion group, which served as an active control group. The interventions lasted for 10 weeks. TCI was measured at baseline and after treatment. Depressive symptoms were assessed using the Beck Depression Inventory-II. Results. There were significant changes on HA and SD after ICBT. However, when comparing post-treatment HA and SD to the control, no differences were found. Among responders, larger changes compared to non-responders were found in HA and in SD, as well as in Cooperativeness. Conclusions. The study showed that HA and SD changed after ICBT. The changes in personality seem related to improvement in depression rather than a direct effect of ICBT.
bibliographic citation: Johansson et al. (2013) Personality change after Internet-delivered cognitive behavior therapy for depression. PeerJ 1:e39 https://doi.org/10.7717/peerj.39
date submitted: 2012-11-30
date accepted: 2013-01-26
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Johansson
  given name: Robert
author list: Agent
  family name: Lyssarides
  given name: Caroline
author list: Agent
  family name: Andersson
  given name: Gerhard
author list: Agent
  family name: Rousseau
  given name: Andréas
doi: 10.7717/peerj.39
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Johansson et al.
attribution name: Johansson et al.

Phenotypic characterization of patients with deletions in the 3’-flanking SHOX region
type: item
type: AcademicArticle
description: Context. Leri–Weill dyschondrosteosis is a clinically variable skeletal dysplasia, caused by SHOX deletion or mutations, or a deletion of enhancer sequences in the 3’-flanking region. Recently, a 47.5 kb recurrent PAR1 deletion downstream of SHOX was reported, but its frequency and clinical importance are still unknown. Objective. This study aims to compare the clinical features of different sizes of deletions in the 3’-flanking SHOX region in order to determine the relevance of the regulatory sequences in this region. Design. We collected DNA from 28 families with deletions in the 3’-PAR1 region. Clinical data were available from 23 index patients and 21 relatives. Results. In 9 families (20 individuals) a large deletion ( ∼ 200–900 kb) was found and in 19 families (35 individuals) a small deletion was demonstrated, equal to the recently described 47.5 kb PAR1 deletion. Median height SDS, sitting height/height ratio SDS and the presence of Madelung deformity in patients with the 47.5 kb deletion were not significantly different from patients with larger deletions. The index patients had a median height SDS which was slightly lower than in their affected family members (p = 0.08). No significant differences were observed between male and female patients. Conclusions. The phenotype of patients with deletions in the 3’-PAR1 region is remarkably variable. Height, sitting height/height ratio and the presence of Madelung deformity were not significantly different between patients with the 47.5 kb recurrent PAR1 deletion and those with larger deletions, suggesting that this enhancer plays an important role in SHOX expression.
format: application/pdf
format: text/html
creator: Sarina G. Kant
creator: Sander J. Broekman
creator: Caroline C. de Wit
creator: Marloes Bos
creator: Sitha A. Scheltinga
creator: Egbert Bakker
creator: Wilma Oostdijk
creator: Hetty J. van der Kamp
creator: Erik W. van Zwet
creator: Annemieke H. van der Hout
creator: Jan M. Wit
creator: Monique Losekoot
subject: Genetics
subject: Medical Genetics
subject: Pediatrics
subject: Statistics
description: doi:10.7717/peerj.35
publisher: PeerJ Inc.
rights: © 2013 Kant et al.
abstract: Context. Leri–Weill dyschondrosteosis is a clinically variable skeletal dysplasia, caused by SHOX deletion or mutations, or a deletion of enhancer sequences in the 3’-flanking region. Recently, a 47.5 kb recurrent PAR1 deletion downstream of SHOX was reported, but its frequency and clinical importance are still unknown. Objective. This study aims to compare the clinical features of different sizes of deletions in the 3’-flanking SHOX region in order to determine the relevance of the regulatory sequences in this region. Design. We collected DNA from 28 families with deletions in the 3’-PAR1 region. Clinical data were available from 23 index patients and 21 relatives. Results. In 9 families (20 individuals) a large deletion ( ∼ 200–900 kb) was found and in 19 families (35 individuals) a small deletion was demonstrated, equal to the recently described 47.5 kb PAR1 deletion. Median height SDS, sitting height/height ratio SDS and the presence of Madelung deformity in patients with the 47.5 kb deletion were not significantly different from patients with larger deletions. The index patients had a median height SDS which was slightly lower than in their affected family members (p = 0.08). No significant differences were observed between male and female patients. Conclusions. The phenotype of patients with deletions in the 3’-PAR1 region is remarkably variable. Height, sitting height/height ratio and the presence of Madelung deformity were not significantly different between patients with the 47.5 kb recurrent PAR1 deletion and those with larger deletions, suggesting that this enhancer plays an important role in SHOX expression.
bibliographic citation: Kant et al. (2013) Phenotypic characterization of patients with deletions in the 3’-flanking SHOX region. PeerJ 1:e35 https://doi.org/10.7717/peerj.35
date submitted: 2012-11-21
date accepted: 2013-01-18
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kant
  given name: Sarina G.
author list: Agent
  family name: Broekman
  given name: Sander J.
author list: Agent
  family name: de Wit
  given name: Caroline C.
author list: Agent
  family name: Bos
  given name: Marloes
author list: Agent
  family name: Scheltinga
  given name: Sitha A.
author list: Agent
  family name: Bakker
  given name: Egbert
author list: Agent
  family name: Oostdijk
  given name: Wilma
author list: Agent
  family name: van der Kamp
  given name: Hetty J.
author list: Agent
  family name: van Zwet
  given name: Erik W.
author list: Agent
  family name: van der Hout
  given name: Annemieke H.
author list: Agent
  family name: Wit
  given name: Jan M.
author list: Agent
  family name: Losekoot
  given name: Monique
doi: 10.7717/peerj.35
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Kant et al.
attribution name: Kant et al.

Validation of the Emotiv EPOC® EEG gaming system for measuring research quality auditory ERPs
type: item
type: AcademicArticle
description: Background. Auditory event-related potentials (ERPs) have proved useful in investigating the role of auditory processing in cognitive disorders such as developmental dyslexia, specific language impairment (SLI), attention deficit hyperactivity disorder (ADHD), schizophrenia, and autism. However, laboratory recordings of auditory ERPs can be lengthy, uncomfortable, or threatening for some participants – particularly children. Recently, a commercial gaming electroencephalography (EEG) system has been developed that is portable, inexpensive, and easy to set up. In this study we tested if auditory ERPs measured using a gaming EEG system (Emotiv EPOC®, www.emotiv.com) were equivalent to those measured by a widely-used, laboratory-based, research EEG system (Neuroscan). Methods. We simultaneously recorded EEGs with the research and gaming EEG systems, whilst presenting 21 adults with 566 standard (1000 Hz) and 100 deviant (1200 Hz) tones under passive (non-attended) and active (attended) conditions. The onset of each tone was marked in the EEGs using a parallel port pulse (Neuroscan) or a stimulus-generated electrical pulse injected into the O1 and O2 channels (Emotiv EPOC®). These markers were used to calculate research and gaming EEG system late auditory ERPs (P1, N1, P2, N2, and P3 peaks) and the mismatch negativity (MMN) in active and passive listening conditions for each participant. Results. Analyses were restricted to frontal sites as these are most commonly reported in auditory ERP research. Intra-class correlations (ICCs) indicated that the morphology of the research and gaming EEG system late auditory ERP waveforms were similar across all participants, but that the research and gaming EEG system MMN waveforms were only similar for participants with non-noisy MMN waveforms (N = 11 out of 21). Peak amplitude and latency measures revealed no significant differences between the size or the timing of the auditory P1, N1, P2, N2, P3, and MMN peaks. Conclusions. Our fi…
format: application/pdf
format: text/html
creator: Nicholas A. Badcock
creator: Petroula Mousikou
creator: Yatin Mahajan
creator: Peter de Lissa
creator: Johnson Thie
creator: Genevieve McArthur
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.38
publisher: PeerJ Inc.
rights: © 2013 Badcock et al.
abstract: Background. Auditory event-related potentials (ERPs) have proved useful in investigating the role of auditory processing in cognitive disorders such as developmental dyslexia, specific language impairment (SLI), attention deficit hyperactivity disorder (ADHD), schizophrenia, and autism. However, laboratory recordings of auditory ERPs can be lengthy, uncomfortable, or threatening for some participants – particularly children. Recently, a commercial gaming electroencephalography (EEG) system has been developed that is portable, inexpensive, and easy to set up. In this study we tested if auditory ERPs measured using a gaming EEG system (Emotiv EPOC®, www.emotiv.com) were equivalent to those measured by a widely-used, laboratory-based, research EEG system (Neuroscan). Methods. We simultaneously recorded EEGs with the research and gaming EEG systems, whilst presenting 21 adults with 566 standard (1000 Hz) and 100 deviant (1200 Hz) tones under passive (non-attended) and active (attended) conditions. The onset of each tone was marked in the EEGs using a parallel port pulse (Neuroscan) or a stimulus-generated electrical pulse injected into the O1 and O2 channels (Emotiv EPOC®). These markers were used to calculate research and gaming EEG system late auditory ERPs (P1, N1, P2, N2, and P3 peaks) and the mismatch negativity (MMN) in active and passive listening conditions for each participant. Results. Analyses were restricted to frontal sites as these are most commonly reported in auditory ERP research. Intra-class correlations (ICCs) indicated that the morphology of the research and gaming EEG system late auditory ERP waveforms were similar across all participants, but that the research and gaming EEG system MMN waveforms were only similar for participants with non-noisy MMN waveforms (N = 11 out of 21). Peak amplitude and latency measures revealed no significant differences between the size or the timing of the auditory P1, N1, P2, N2, P3, and MMN peaks. Conclusions. Our fi…
bibliographic citation: Badcock et al. (2013) Validation of the Emotiv EPOC® EEG gaming system for measuring research quality auditory ERPs. PeerJ 1:e38 https://doi.org/10.7717/peerj.38
date submitted: 2012-12-01
date accepted: 2013-01-22
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Badcock
  given name: Nicholas A.
author list: Agent
  family name: Mousikou
  given name: Petroula
author list: Agent
  family name: Mahajan
  given name: Yatin
author list: Agent
  family name: de Lissa
  given name: Peter
author list: Agent
  family name: Thie
  given name: Johnson
author list: Agent
  family name: McArthur
  given name: Genevieve
doi: 10.7717/peerj.38
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Badcock et al.
attribution name: Badcock et al.

Development and evolution of the unique cetacean dentition
type: item
type: AcademicArticle
description: The evolutionary success of mammals is rooted in their high metabolic rate. A high metabolic rate is sustainable thanks to efficient food processing and that in turn is facilitated by precise occlusion of the teeth and the acquisition of rhythmic mastication. These major evolutionary innovations characterize most members of the Class Mammalia. Cetaceans are one of the few groups of mammals in which precise occlusion has been secondarily lost. Most toothed whales have an increased number of simple crowned teeth that are similar along the tooth row. Evolution toward these specializations began immediately after the time cetaceans transitioned from terrestrial-to-marine environments. The fossil record documents the critical aspects of occlusal evolution of cetaceans, and allows us to pinpoint the evolutionary timing of the macroevolutionary events leading to their unusual dental morphology among mammals. The developmental controls of tooth differentiation and tooth number have been studied in a few mammalian clades, but nothing is known about how these controls differ between cetaceans and mammals that retain functional occlusion. Here we show that pigs, a cetacean relative with regionalized tooth morphology and complex tooth crowns, retain the typical mammalian gene expression patterns that control early tooth differentiation, expressing Bmp4 in the rostral (mesial, anterior) domain of the jaw, and Fgf8 caudally (distal, posterior). By contrast, dolphins have lost these regional differences in dental morphology and the Bmp4 domain is extended into the caudal region of the developing jaw. We hypothesize that the functional constraints underlying mammalian occlusion have been released in cetaceans, facilitating changes in the genetic control of early dental development. Such major developmental changes drive morphological evolution and are correlated with major shifts in diet and food processing during cetacean evolution.
format: application/pdf
format: text/html
creator: Brooke A. Armfield
creator: Zhengui Zheng
creator: Sunil Bajpai
creator: Christopher J. Vinyard
creator: JGM Thewissen
subject: Developmental Biology
subject: Evolutionary Studies
subject: Paleontology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.24
publisher: PeerJ Inc.
rights: © 2013 Armfield et al.
abstract: The evolutionary success of mammals is rooted in their high metabolic rate. A high metabolic rate is sustainable thanks to efficient food processing and that in turn is facilitated by precise occlusion of the teeth and the acquisition of rhythmic mastication. These major evolutionary innovations characterize most members of the Class Mammalia. Cetaceans are one of the few groups of mammals in which precise occlusion has been secondarily lost. Most toothed whales have an increased number of simple crowned teeth that are similar along the tooth row. Evolution toward these specializations began immediately after the time cetaceans transitioned from terrestrial-to-marine environments. The fossil record documents the critical aspects of occlusal evolution of cetaceans, and allows us to pinpoint the evolutionary timing of the macroevolutionary events leading to their unusual dental morphology among mammals. The developmental controls of tooth differentiation and tooth number have been studied in a few mammalian clades, but nothing is known about how these controls differ between cetaceans and mammals that retain functional occlusion. Here we show that pigs, a cetacean relative with regionalized tooth morphology and complex tooth crowns, retain the typical mammalian gene expression patterns that control early tooth differentiation, expressing Bmp4 in the rostral (mesial, anterior) domain of the jaw, and Fgf8 caudally (distal, posterior). By contrast, dolphins have lost these regional differences in dental morphology and the Bmp4 domain is extended into the caudal region of the developing jaw. We hypothesize that the functional constraints underlying mammalian occlusion have been released in cetaceans, facilitating changes in the genetic control of early dental development. Such major developmental changes drive morphological evolution and are correlated with major shifts in diet and food processing during cetacean evolution.
bibliographic citation: Armfield et al. (2013) Development and evolution of the unique cetacean dentition. PeerJ 1:e24 https://doi.org/10.7717/peerj.24
date submitted: 2012-11-28
date accepted: 2013-01-10
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Armfield
  given name: Brooke A.
author list: Agent
  family name: Zheng
  given name: Zhengui
author list: Agent
  family name: Bajpai
  given name: Sunil
author list: Agent
  family name: Vinyard
  given name: Christopher J.
author list: Agent
  family name: Thewissen
  given name: JGM
doi: 10.7717/peerj.24
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Armfield et al.
attribution name: Armfield et al.

A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae
type: item
type: AcademicArticle
description: We investigated microbial communities active in methane oxidation in lake sediment at different oxygen tensions and their response to the addition of nitrate, via stable isotope probing combined with deep metagenomic sequencing. Communities from a total of four manipulated microcosms were analyzed, supplied with 13C-methane in, respectively, ambient air, ambient air with the addition of nitrate, nitrogen atmosphere and nitrogen atmosphere with the addition of nitrate, and these were compared to the community from an unamended sediment sample. We found that the major group involved in methane oxidation in both aerobic and microaerobic conditions were members of the family Methylococcaceae, dominated by species of the genus Methylobacter, and these were stimulated by nitrate in aerobic but not microaerobic conditions. In aerobic conditions, we also noted a pronounced response to both methane and nitrate by members of the family Methylophilaceae that are non-methane-oxidizing methylotrophs, and predominantly by the members of the genus Methylotenera. The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.
format: application/pdf
format: text/html
creator: David A.C. Beck
creator: Marina G. Kalyuzhnaya
creator: Stephanie Malfatti
creator: Susannah G. Tringe
creator: Tijana Glavina del Rio
creator: Natalia Ivanova
creator: Mary E. Lidstrom
creator: Ludmila Chistoserdova
subject: Ecosystem Science
subject: Environmental Sciences
subject: Freshwater Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.23
publisher: PeerJ Inc.
rights: © 2013 Beck et al.
abstract: We investigated microbial communities active in methane oxidation in lake sediment at different oxygen tensions and their response to the addition of nitrate, via stable isotope probing combined with deep metagenomic sequencing. Communities from a total of four manipulated microcosms were analyzed, supplied with 13C-methane in, respectively, ambient air, ambient air with the addition of nitrate, nitrogen atmosphere and nitrogen atmosphere with the addition of nitrate, and these were compared to the community from an unamended sediment sample. We found that the major group involved in methane oxidation in both aerobic and microaerobic conditions were members of the family Methylococcaceae, dominated by species of the genus Methylobacter, and these were stimulated by nitrate in aerobic but not microaerobic conditions. In aerobic conditions, we also noted a pronounced response to both methane and nitrate by members of the family Methylophilaceae that are non-methane-oxidizing methylotrophs, and predominantly by the members of the genus Methylotenera. The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.
bibliographic citation: Beck et al. (2013) A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 1:e23 https://doi.org/10.7717/peerj.23
date submitted: 2012-12-01
date accepted: 2013-01-09
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Beck
  given name: David A.C.
author list: Agent
  family name: Kalyuzhnaya
  given name: Marina G.
author list: Agent
  family name: Malfatti
  given name: Stephanie
author list: Agent
  family name: Tringe
  given name: Susannah G.
author list: Agent
  family name: Glavina del Rio
  given name: Tijana
author list: Agent
  family name: Ivanova
  given name: Natalia
author list: Agent
  family name: Lidstrom
  given name: Mary E.
author list: Agent
  family name: Chistoserdova
  given name: Ludmila
doi: 10.7717/peerj.23
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Beck et al.
attribution name: Beck et al.

Iodine nutrition and toxicity in Atlantic cod (Gadus morhua) larvae
type: item
type: AcademicArticle
description: Copepods as feed promote better growth and development in marine fish larvae than rotifers. However, unlike rotifers, copepods contain several minerals such as iodine (I), at potentially toxic levels. Iodine is an essential trace element and both under and over supply of I can inhibit the production of the I containing thyroid hormones. It is unknown whether marine fish larvae require copepod levels of I or if mechanisms are present that prevent I toxicity. In this study, larval Atlantic cod (Gadus morhua) were fed rotifers enriched to intermediate (26 mg I kg-1 dry weight; MI group) or copepod (129 mg I kg-1 DW; HI group) I levels and compared to cod larvae fed control rotifers (0.6 mg I kg-1 DW). Larval I concentrations were increased by 3 (MI) and 7 (HI) fold compared to controls during the rotifer feeding period. No differences in growth were observed, but the HI diet increased thyroid follicle colloid to epithelium ratios, and affected the essential element concentrations of larvae compared to the other groups. The thyroid follicle morphology in the HI larvae is typical of colloid goitre, a condition resulting from excessive I intake, even though whole body I levels were below those found previously in copepod fed cod larvae. This is the first observation of dietary induced I toxicity in fish, and suggests I toxicity may be determined to a greater extent by bioavailability and nutrient interactions than by total body I concentrations in fish larvae. Rotifers with 0.6 mg I kg-1 DW appeared sufficient to prevent gross signs of I deficiency in cod larvae reared with continuous water exchange, while modelling of cod larvae versus rotifer I levels suggests that optimum I levels in rotifers for cod larvae is 3.5 mg I kg-1 DW.
format: application/pdf
format: text/html
creator: S Penglase
creator: T Harboe
creator: Ø Sæle
creator: S Helland
creator: A Nordgreen
creator: K Hamre
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Nutrition
description: doi:10.7717/peerj.20
publisher: PeerJ Inc.
rights: © 2013 Penglase et al.
abstract: Copepods as feed promote better growth and development in marine fish larvae than rotifers. However, unlike rotifers, copepods contain several minerals such as iodine (I), at potentially toxic levels. Iodine is an essential trace element and both under and over supply of I can inhibit the production of the I containing thyroid hormones. It is unknown whether marine fish larvae require copepod levels of I or if mechanisms are present that prevent I toxicity. In this study, larval Atlantic cod (Gadus morhua) were fed rotifers enriched to intermediate (26 mg I kg-1 dry weight; MI group) or copepod (129 mg I kg-1 DW; HI group) I levels and compared to cod larvae fed control rotifers (0.6 mg I kg-1 DW). Larval I concentrations were increased by 3 (MI) and 7 (HI) fold compared to controls during the rotifer feeding period. No differences in growth were observed, but the HI diet increased thyroid follicle colloid to epithelium ratios, and affected the essential element concentrations of larvae compared to the other groups. The thyroid follicle morphology in the HI larvae is typical of colloid goitre, a condition resulting from excessive I intake, even though whole body I levels were below those found previously in copepod fed cod larvae. This is the first observation of dietary induced I toxicity in fish, and suggests I toxicity may be determined to a greater extent by bioavailability and nutrient interactions than by total body I concentrations in fish larvae. Rotifers with 0.6 mg I kg-1 DW appeared sufficient to prevent gross signs of I deficiency in cod larvae reared with continuous water exchange, while modelling of cod larvae versus rotifer I levels suggests that optimum I levels in rotifers for cod larvae is 3.5 mg I kg-1 DW.
bibliographic citation: Penglase et al. (2013) Iodine nutrition and toxicity in Atlantic cod (Gadus morhua) larvae. PeerJ 1:e20 https://doi.org/10.7717/peerj.20
date submitted: 2012-11-20
date accepted: 2013-01-08
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Penglase
  given name: S
author list: Agent
  family name: Harboe
  given name: T
author list: Agent
  family name: Sæle
  given name: Ø
author list: Agent
  family name: Helland
  given name: S
author list: Agent
  family name: Nordgreen
  given name: A
author list: Agent
  family name: Hamre
  given name: K
doi: 10.7717/peerj.20
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Penglase et al.
attribution name: Penglase et al.

Evaluation of animal control measures on pet demographics in Santa Clara County, California, 1993–2006
type: item
type: AcademicArticle
description: The measurable benefits of animal control programs are unknown and the aim of this study was to determine the impact of these programs on pet population changes. A prospective cross-sectional study of 1000 households was implemented in 2005 to evaluate characteristics of the owned and unowned population of dogs and cats in Santa Clara County, California. The same population was previously studied 12 years earlier. During this time period, the county instituted in 1994 and then subsequently disestablished a municipal spay/neuter voucher program for cats. Dog intakes declined from 1992–2005, as they similarly did for an adjacent county (San Mateo). However, cat intakes declined significantly more in Santa Clara County than San Mateo, with an average annual decline of approximately 700 cats for the 12 year period. Time series analysis showed a greater than expected decline in the number of cats surrendered to shelters in Santa Clara County during the years the voucher program was in effect (1994–2005). The net savings to the county by reducing the number of cat shelter intakes was estimated at approximately $1.5 million. The measurable benefits of animal control programs are unknown and the aim of this study was to determine the impact of these programs on pet population changes.
format: application/pdf
format: text/html
creator: Philip H. Kass
creator: Karen L. Johnson
creator: Hsin-Yi Weng
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.18
publisher: PeerJ Inc.
rights: © 2013 Kass et al.
abstract: The measurable benefits of animal control programs are unknown and the aim of this study was to determine the impact of these programs on pet population changes. A prospective cross-sectional study of 1000 households was implemented in 2005 to evaluate characteristics of the owned and unowned population of dogs and cats in Santa Clara County, California. The same population was previously studied 12 years earlier. During this time period, the county instituted in 1994 and then subsequently disestablished a municipal spay/neuter voucher program for cats. Dog intakes declined from 1992–2005, as they similarly did for an adjacent county (San Mateo). However, cat intakes declined significantly more in Santa Clara County than San Mateo, with an average annual decline of approximately 700 cats for the 12 year period. Time series analysis showed a greater than expected decline in the number of cats surrendered to shelters in Santa Clara County during the years the voucher program was in effect (1994–2005). The net savings to the county by reducing the number of cat shelter intakes was estimated at approximately $1.5 million. The measurable benefits of animal control programs are unknown and the aim of this study was to determine the impact of these programs on pet population changes.
bibliographic citation: Kass et al. (2013) Evaluation of animal control measures on pet demographics in Santa Clara County, California, 1993–2006. PeerJ 1:e18 https://doi.org/10.7717/peerj.18
date submitted: 2012-11-14
date accepted: 2013-01-04
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kass
  given name: Philip H.
author list: Agent
  family name: Johnson
  given name: Karen L.
author list: Agent
  family name: Weng
  given name: Hsin-Yi
doi: 10.7717/peerj.18
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Kass et al.
attribution name: Kass et al.

Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus
type: item
type: AcademicArticle
description: Secondary metabolite (SM) production in filamentous fungi is mechanistically associated with chromatin remodeling of specific SM clusters. One locus recently shown to be involved in SM suppression in Aspergillus nidulans was CclA, a member of the histone 3 lysine 4 methylating COMPASS complex. Here we examine loss of CclA and a putative H3K4 demethylase, HdmA, in the human pathogen Aspergillus fumigatus. Although deletion of hdmA showed no phenotype under the conditions tested, the cclA deletant was deficient in tri- and di-methylation of H3K4 and yielded a slowly growing strain that was rich in the production of several SMs, including gliotoxin. Similar to deletion of other chromatin modifying enzymes, ΔcclA was sensitive to 6-azauracil indicating a defect in transcriptional elongation. Despite the poor growth, the ΔcclA mutant had wild-type pathogenicity in a murine model and the Toll-deficient Drosophila model of invasive aspergillosis. These data indicate that tri- and di-methylation of H3K4 is involved in the regulation of several secondary metabolites in A. fumigatus, however does not contribute to pathogenicity under the conditions tested.
format: application/pdf
format: text/html
creator: Jonathan M. Palmer
creator: Jin Woo Bok
creator: Seul Lee
creator: Taylor R.T. Dagenais
creator: David R. Andes
creator: Dimitrios P. Kontoyiannis
creator: Nancy P. Keller
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.4
publisher: PeerJ Inc.
rights: © 2013 Palmer et al.
abstract: Secondary metabolite (SM) production in filamentous fungi is mechanistically associated with chromatin remodeling of specific SM clusters. One locus recently shown to be involved in SM suppression in Aspergillus nidulans was CclA, a member of the histone 3 lysine 4 methylating COMPASS complex. Here we examine loss of CclA and a putative H3K4 demethylase, HdmA, in the human pathogen Aspergillus fumigatus. Although deletion of hdmA showed no phenotype under the conditions tested, the cclA deletant was deficient in tri- and di-methylation of H3K4 and yielded a slowly growing strain that was rich in the production of several SMs, including gliotoxin. Similar to deletion of other chromatin modifying enzymes, ΔcclA was sensitive to 6-azauracil indicating a defect in transcriptional elongation. Despite the poor growth, the ΔcclA mutant had wild-type pathogenicity in a murine model and the Toll-deficient Drosophila model of invasive aspergillosis. These data indicate that tri- and di-methylation of H3K4 is involved in the regulation of several secondary metabolites in A. fumigatus, however does not contribute to pathogenicity under the conditions tested.
bibliographic citation: Palmer et al. (2013) Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus. PeerJ 1:e4 https://doi.org/10.7717/peerj.4
date submitted: 2012-11-13
date accepted: 2012-12-04
issued: 2013-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Palmer
  given name: Jonathan M.
author list: Agent
  family name: Bok
  given name: Jin Woo
author list: Agent
  family name: Lee
  given name: Seul
author list: Agent
  family name: Dagenais
  given name: Taylor R.T.
author list: Agent
  family name: Andes
  given name: David R.
author list: Agent
  family name: Kontoyiannis
  given name: Dimitrios P.
author list: Agent
  family name: Keller
  given name: Nancy P.
doi: 10.7717/peerj.4
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-19
copyright: © 2013 Palmer et al.
attribution name: Palmer et al.

Pain assessment in children undergoing venipuncture: the Wong–Baker faces scale versus skin conductance fluctuations
type: item
type: AcademicArticle
description: The aim of this study was to evaluate the efficacy of the subjective Wong–Baker faces pain rating scale (WBFS) and of the objective skin conductance fluctuation (SCF) test in assessing pain in children undergoing venipuncture. One-hundred and fifty children (aged 5–16 years) entered the study. All underwent venipuncture at the antecubital fossa to collect blood specimens for routine testing in the same environmental conditions. After venipuncture, the children indicated their pain intensity using the WBFS, whereas the number of SCFs was recorded before, during and after venipuncture. So, pain level was measured in each child with WBFS and SCF. We found that the level of WBFS-assessed pain was lower in all children, particularly those above 8 years of age, than SCF-assessed pain (p < 0.0001). Moreover, the number of SCFs was significantly higher during venipuncture than before or after venipuncture (p < 0.0001). At multivariate regression analysis, age and previous experience of venipuncture influenced the WBFS (β = −1.81, p < 0.001, and β = −0.86, p < 0.001, respectively) but not SCFs. In conclusion, although both procedures can be useful for research and clinical practice, our findings show that WBFS was affected by age and previous venipuncture, whereas SCF produced uniform data. If verified in other studies, our results should be taken into account when using these tools to evaluate pain in children.
format: application/pdf
format: text/html
creator: Francesco Savino
creator: Liliana Vagliano
creator: Simone Ceratto
creator: Fabio Viviani
creator: Roberto Miniero
creator: Fulvio Ricceri
subject: Anesthesiology and Pain Management
subject: Nursing
subject: Pediatrics
description: doi:10.7717/peerj.37
publisher: PeerJ Inc.
rights: © 2013 Savino et al.
abstract: The aim of this study was to evaluate the efficacy of the subjective Wong–Baker faces pain rating scale (WBFS) and of the objective skin conductance fluctuation (SCF) test in assessing pain in children undergoing venipuncture. One-hundred and fifty children (aged 5–16 years) entered the study. All underwent venipuncture at the antecubital fossa to collect blood specimens for routine testing in the same environmental conditions. After venipuncture, the children indicated their pain intensity using the WBFS, whereas the number of SCFs was recorded before, during and after venipuncture. So, pain level was measured in each child with WBFS and SCF. We found that the level of WBFS-assessed pain was lower in all children, particularly those above 8 years of age, than SCF-assessed pain (p < 0.0001). Moreover, the number of SCFs was significantly higher during venipuncture than before or after venipuncture (p < 0.0001). At multivariate regression analysis, age and previous experience of venipuncture influenced the WBFS (β = −1.81, p < 0.001, and β = −0.86, p < 0.001, respectively) but not SCFs. In conclusion, although both procedures can be useful for research and clinical practice, our findings show that WBFS was affected by age and previous venipuncture, whereas SCF produced uniform data. If verified in other studies, our results should be taken into account when using these tools to evaluate pain in children.
bibliographic citation: Savino et al. (2013) Pain assessment in children undergoing venipuncture: the Wong–Baker faces scale versus skin conductance fluctuations. PeerJ 1:e37 https://doi.org/10.7717/peerj.37
date submitted: 2012-11-30
date accepted: 2013-01-21
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Savino
  given name: Francesco
author list: Agent
  family name: Vagliano
  given name: Liliana
author list: Agent
  family name: Ceratto
  given name: Simone
author list: Agent
  family name: Viviani
  given name: Fabio
author list: Agent
  family name: Miniero
  given name: Roberto
author list: Agent
  family name: Ricceri
  given name: Fulvio
doi: 10.7717/peerj.37
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Savino et al.
attribution name: Savino et al.

Why sauropods had long necks; and why giraffes have short necks
type: item
type: AcademicArticle
description: The necks of the sauropod dinosaurs reached 15 m in length: six times longer than that of the world record giraffe and five times longer than those of all other terrestrial animals. Several anatomical features enabled this extreme elongation, including: absolutely large body size and quadrupedal stance providing a stable platform for a long neck; a small, light head that did not orally process food; cervical vertebrae that were both numerous and individually elongate; an efficient air-sac-based respiratory system; and distinctive cervical architecture. Relevant features of sauropod cervical vertebrae include: pneumatic chambers that enabled the bone to be positioned in a mechanically efficient way within the envelope; and muscular attachments of varying importance to the neural spines, epipophyses and cervical ribs. Other long-necked tetrapods lacked important features of sauropods, preventing the evolution of longer necks: for example, giraffes have relatively small torsos and large, heavy heads, share the usual mammalian constraint of only seven cervical vertebrae, and lack an air-sac system and pneumatic bones. Among non-sauropods, their saurischian relatives the theropod dinosaurs seem to have been best placed to evolve long necks, and indeed their necks probably surpassed those of giraffes. But 150 million years of evolution did not suffice for them to exceed a relatively modest 2.5 m.
format: application/pdf
format: text/html
creator: Michael P. Taylor
creator: Mathew J. Wedel
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.36
publisher: PeerJ Inc.
rights: © 2013 Taylor and Wedel
abstract: The necks of the sauropod dinosaurs reached 15 m in length: six times longer than that of the world record giraffe and five times longer than those of all other terrestrial animals. Several anatomical features enabled this extreme elongation, including: absolutely large body size and quadrupedal stance providing a stable platform for a long neck; a small, light head that did not orally process food; cervical vertebrae that were both numerous and individually elongate; an efficient air-sac-based respiratory system; and distinctive cervical architecture. Relevant features of sauropod cervical vertebrae include: pneumatic chambers that enabled the bone to be positioned in a mechanically efficient way within the envelope; and muscular attachments of varying importance to the neural spines, epipophyses and cervical ribs. Other long-necked tetrapods lacked important features of sauropods, preventing the evolution of longer necks: for example, giraffes have relatively small torsos and large, heavy heads, share the usual mammalian constraint of only seven cervical vertebrae, and lack an air-sac system and pneumatic bones. Among non-sauropods, their saurischian relatives the theropod dinosaurs seem to have been best placed to evolve long necks, and indeed their necks probably surpassed those of giraffes. But 150 million years of evolution did not suffice for them to exceed a relatively modest 2.5 m.
bibliographic citation: Taylor et al. (2013) Why sauropods had long necks; and why giraffes have short necks. PeerJ 1:e36 https://doi.org/10.7717/peerj.36
date submitted: 2012-12-03
date accepted: 2013-01-19
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Taylor
  given name: Michael P.
author list: Agent
  family name: Wedel
  given name: Mathew J.
doi: 10.7717/peerj.36
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Taylor and Wedel
attribution name: Taylor and Wedel

Coronatine inhibits stomatal closure and delays hypersensitive response cell death induced by nonhost bacterial pathogens
type: item
type: AcademicArticle
description: Pseudomonas syringae is the most widespread bacterial pathogen in plants. Several strains of P. syringae produce a phytotoxin, coronatine (COR), which acts as a jasmonic acid mimic and inhibits plant defense responses and contributes to disease symptom development. In this study, we found that COR inhibits early defense responses during nonhost disease resistance. Stomatal closure induced by a nonhost pathogen, P. syringae pv. tabaci, was disrupted by COR in tomato epidermal peels. In addition, nonhost HR cell death triggered by P. syringae pv. tabaci on tomato was remarkably delayed when COR was supplemented along with P. syringae pv. tabaci inoculation. Using isochorismate synthase (ICS)-silenced tomato plants and transcript profiles of genes in SA- and JA-related defense pathways, we show that COR suppresses SA-mediated defense during nonhost resistance.
format: application/pdf
format: text/html
creator: Seonghee Lee
creator: Yasuhiro Ishiga
creator: Kristen Clermont
creator: Kirankumar S. Mysore
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.34
publisher: PeerJ Inc.
rights: © 2013 Lee et al.
abstract: Pseudomonas syringae is the most widespread bacterial pathogen in plants. Several strains of P. syringae produce a phytotoxin, coronatine (COR), which acts as a jasmonic acid mimic and inhibits plant defense responses and contributes to disease symptom development. In this study, we found that COR inhibits early defense responses during nonhost disease resistance. Stomatal closure induced by a nonhost pathogen, P. syringae pv. tabaci, was disrupted by COR in tomato epidermal peels. In addition, nonhost HR cell death triggered by P. syringae pv. tabaci on tomato was remarkably delayed when COR was supplemented along with P. syringae pv. tabaci inoculation. Using isochorismate synthase (ICS)-silenced tomato plants and transcript profiles of genes in SA- and JA-related defense pathways, we show that COR suppresses SA-mediated defense during nonhost resistance.
bibliographic citation: Lee et al. (2013) Coronatine inhibits stomatal closure and delays hypersensitive response cell death induced by nonhost bacterial pathogens. PeerJ 1:e34 https://doi.org/10.7717/peerj.34
date submitted: 2012-11-23
date accepted: 2013-01-16
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Lee
  given name: Seonghee
author list: Agent
  family name: Ishiga
  given name: Yasuhiro
author list: Agent
  family name: Clermont
  given name: Kristen
author list: Agent
  family name: Mysore
  given name: Kirankumar S.
doi: 10.7717/peerj.34
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Lee et al.
attribution name: Lee et al.

A perfusion study of the handling of urea and urea analogues by the gills of the dogfish shark (Squalus acanthias)
type: item
type: AcademicArticle
description: The branchial mechanism of urea retention in elasmobranchs was investigated using an in vitro isolated-perfused head preparation, as well as in vivo samples, in the spiny dogfish shark. Both in vivo and in control saline perfusions containing 350 mmol L−1 urea, calculated intracellular urea concentrations in gill epithelial cells were close to extracellular concentrations. Urea efflux to the external water fell only non-significantly, and calculated gill intracellular urea concentration did not change when perfusate urea concentration was reduced from 350 to 175 mmol L−1 with osmotic compensation by 175 mmol L−1 mannitol. However, when the urea analogues thiourea or acetamide were present in the perfusate at concentrations equimolar (175 mmol L−1) to those of urea (175 mmol L−1), urea efflux rates were increased 4-fold and 6.5-fold respectively, and calculated gill intracellular urea concentrations were depressed by about 55%. Analogue efflux rates were similar to urea efflux rates. Previous studies have argued that either the basolateral or apical membranes provided the limiting permeability barrier, and/or that a back-transporter on the basolateral membranes of gill cells is responsible for urea retention. The present results provide new evidence that the apical membrane is the limiting factor in maintaining gill urea impermeability, and raise the prospect that a urea back-transporter, which can be competitively inhibited by thiourea and acetamide, operates at the apical membrane.
format: application/pdf
format: text/html
creator: Chris M. Wood
creator: Hon Jung Liew
creator: Gudrun De Boeck
creator: Patrick J. Walsh
subject: Aquaculture, Fisheries and Fish Science
subject: Anatomy and Physiology
description: doi:10.7717/peerj.33
publisher: PeerJ Inc.
rights: © 2013 Wood et al.
abstract: The branchial mechanism of urea retention in elasmobranchs was investigated using an in vitro isolated-perfused head preparation, as well as in vivo samples, in the spiny dogfish shark. Both in vivo and in control saline perfusions containing 350 mmol L−1 urea, calculated intracellular urea concentrations in gill epithelial cells were close to extracellular concentrations. Urea efflux to the external water fell only non-significantly, and calculated gill intracellular urea concentration did not change when perfusate urea concentration was reduced from 350 to 175 mmol L−1 with osmotic compensation by 175 mmol L−1 mannitol. However, when the urea analogues thiourea or acetamide were present in the perfusate at concentrations equimolar (175 mmol L−1) to those of urea (175 mmol L−1), urea efflux rates were increased 4-fold and 6.5-fold respectively, and calculated gill intracellular urea concentrations were depressed by about 55%. Analogue efflux rates were similar to urea efflux rates. Previous studies have argued that either the basolateral or apical membranes provided the limiting permeability barrier, and/or that a back-transporter on the basolateral membranes of gill cells is responsible for urea retention. The present results provide new evidence that the apical membrane is the limiting factor in maintaining gill urea impermeability, and raise the prospect that a urea back-transporter, which can be competitively inhibited by thiourea and acetamide, operates at the apical membrane.
bibliographic citation: Wood et al. (2013) A perfusion study of the handling of urea and urea analogues by the gills of the dogfish shark (Squalus acanthias). PeerJ 1:e33 https://doi.org/10.7717/peerj.33
date submitted: 2012-11-13
date accepted: 2013-01-16
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Wood
  given name: Chris M.
author list: Agent
  family name: Liew
  given name: Hon Jung
author list: Agent
  family name: De Boeck
  given name: Gudrun
author list: Agent
  family name: Walsh
  given name: Patrick J.
doi: 10.7717/peerj.33
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Wood et al.
attribution name: Wood et al.

Analysis of innate and acquired resistance to anti-CD20 antibodies in malignant and nonmalignant B cells
type: item
type: AcademicArticle
description: The anti-CD20 monoclonal antibody, rituximab, provides a significant therapeutic benefit for patients with B-cell disorders. However, response to therapy varies and relapses are common, so an understanding of both inherited and acquired rituximab resistance is needed. In order to identify mechanisms of inherited resistance, sensitive versus resistant individuals were selected from a survey of 92 immortalized lymphoblastoid B-cell lines from normal individuals. Levels of CD20 protein and surface expression were lower in the resistant group. In contrast, CD20 mRNA levels were not correlated with susceptibility, suggesting regulation at a post-transcriptional level. To examine acquired resistance, resistant sublines were selected from both lymphoblastoid as well as lymphoma cell lines. Confirming previous findings, there was significant down-regulation of CD20 protein expression in all the resistant sublines. CD20 mRNA splice variants are reported to be associated with development of resistance. Three splice variants were observed in our cell lines, each lacking the binding epitope for rituximab, but none were associated with rituximab resistance. The second generation anti-CD20 mAb, ofatumumab, was more active compared with rituximab in vitro in the survey of all B-cell lines, mirroring results that have been reported previously with malignant B-cells. These studies show that normal B-lymphoblastoid cell lines can be used to model both innate and acquired mechanisms of resistance. They validate the important role of CD20 expression and enable future genetic studies to identify additional mediators of anti-CD20 mAb resistance.
format: application/pdf
format: text/html
creator: George W. Small
creator: Howard L. McLeod
creator: Kristy L. Richards
subject: Cell Biology
subject: Molecular Biology
subject: Hematology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.31
publisher: PeerJ Inc.
rights: © 2013 Small et al.
abstract: The anti-CD20 monoclonal antibody, rituximab, provides a significant therapeutic benefit for patients with B-cell disorders. However, response to therapy varies and relapses are common, so an understanding of both inherited and acquired rituximab resistance is needed. In order to identify mechanisms of inherited resistance, sensitive versus resistant individuals were selected from a survey of 92 immortalized lymphoblastoid B-cell lines from normal individuals. Levels of CD20 protein and surface expression were lower in the resistant group. In contrast, CD20 mRNA levels were not correlated with susceptibility, suggesting regulation at a post-transcriptional level. To examine acquired resistance, resistant sublines were selected from both lymphoblastoid as well as lymphoma cell lines. Confirming previous findings, there was significant down-regulation of CD20 protein expression in all the resistant sublines. CD20 mRNA splice variants are reported to be associated with development of resistance. Three splice variants were observed in our cell lines, each lacking the binding epitope for rituximab, but none were associated with rituximab resistance. The second generation anti-CD20 mAb, ofatumumab, was more active compared with rituximab in vitro in the survey of all B-cell lines, mirroring results that have been reported previously with malignant B-cells. These studies show that normal B-lymphoblastoid cell lines can be used to model both innate and acquired mechanisms of resistance. They validate the important role of CD20 expression and enable future genetic studies to identify additional mediators of anti-CD20 mAb resistance.
bibliographic citation: Small et al. (2013) Analysis of innate and acquired resistance to anti-CD20 antibodies in malignant and nonmalignant B cells. PeerJ 1:e31 https://doi.org/10.7717/peerj.31
date submitted: 2012-11-21
date accepted: 2013-01-15
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Small
  given name: George W.
author list: Agent
  family name: McLeod
  given name: Howard L.
author list: Agent
  family name: Richards
  given name: Kristy L.
doi: 10.7717/peerj.31
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Small et al.
attribution name: Small et al.

A practical implementation of de-Pake-ing via weighted Fourier transformation
type: item
type: AcademicArticle
description: We provide an NMRPipe macro to meet an increasing need in membrane biophysics for facile de-Pake-ing of axially symmetric deuterium, and to an extent phosphorous, static lineshapes. The macro implements the development of McCabe & Wassall (1997), and is run as a simple replacement for the usual Fourier transform step in an NMRPipe processing procedure.
format: application/pdf
format: text/html
creator: Marc-Antoine Sani
creator: Daniel K. Weber
creator: Frank Delaglio
creator: Frances Separovic
creator: John D. Gehman
subject: Biophysics
description: doi:10.7717/peerj.30
publisher: PeerJ Inc.
rights: © 2013 Sani et al.
abstract: We provide an NMRPipe macro to meet an increasing need in membrane biophysics for facile de-Pake-ing of axially symmetric deuterium, and to an extent phosphorous, static lineshapes. The macro implements the development of McCabe & Wassall (1997), and is run as a simple replacement for the usual Fourier transform step in an NMRPipe processing procedure.
bibliographic citation: Sani et al. (2013) A practical implementation of de-Pake-ing via weighted Fourier transformation. PeerJ 1:e30 https://doi.org/10.7717/peerj.30
date submitted: 2012-11-28
date accepted: 2013-01-15
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Sani
  given name: Marc-Antoine
author list: Agent
  family name: Weber
  given name: Daniel K.
author list: Agent
  family name: Delaglio
  given name: Frank
author list: Agent
  family name: Separovic
  given name: Frances
author list: Agent
  family name: Gehman
  given name: John D.
doi: 10.7717/peerj.30
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Sani et al.
attribution name: Sani et al.

Anti-apoptotic signaling as a cytoprotective mechanism in mammalian hibernation
type: item
type: AcademicArticle
description: In the context of normal cell turnover, apoptosis is a natural phenomenon involved in making essential life and death decisions. Apoptotic pathways balance signals which promote cell death (pro-apoptotic pathways) or counteract these signals (anti-apoptotic pathways). We proposed that changes in anti-apoptotic proteins would occur during mammalian hibernation to aid cell preservation during prolonged torpor under cellular conditions that are highly injurious to most mammals (e.g. low body temperatures, ischemia). Immunoblotting was used to analyze the expression of proteins associated with pro-survival in six tissues of thirteen-lined ground squirrels, Ictidomys tridecemlineatus. The brain showed a concerted response to torpor with significant increases in the levels of all anti-apoptotic targets analyzed (Bcl-2, Bcl-xL, BI-1, Mcl-1, cIAP1/2, xIAP) as well as enhanced phosphorylation of Bcl-2 at S70 and T56. Heart responded similarly with most anti-apoptotic proteins elevated significantly during torpor except for Bcl-xL and xIAP that decreased and Mcl-1 that was unaltered. In liver, BI-1 increased whereas cIAP1/2 decreased. In kidney, there was an increase in BI-1, cIAP and xIAP but decreases in Bcl-xL and p-Bcl-2(T56) content. In brown adipose tissue, protein levels of BI-1, cIAP1/2, and xIAP decreased significantly during torpor (compared with euthermia) whereas Bcl-2, Bcl-xL, Mcl-1 were unaltered; however, Bcl-2 showed enhanced phosphorylation at Thr56 but not at Ser70. In skeletal muscle, only xIAP levels changed significantly during torpor (an increase). The data show that anti-apoptotic pathways have organ-specific responses in hibernators with a prominent potential role in heart and brain where coordinated enhancement of anti-apoptotic proteins occurred in response to torpor.
format: application/pdf
format: text/html
creator: Andrew N. Rouble
creator: Joshua Hefler
creator: Hapsatou Mamady
creator: Kenneth B. Storey
creator: Shannon N. Tessier
subject: Molecular Biology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.29
publisher: PeerJ Inc.
rights: © 2013 Rouble et al.
abstract: In the context of normal cell turnover, apoptosis is a natural phenomenon involved in making essential life and death decisions. Apoptotic pathways balance signals which promote cell death (pro-apoptotic pathways) or counteract these signals (anti-apoptotic pathways). We proposed that changes in anti-apoptotic proteins would occur during mammalian hibernation to aid cell preservation during prolonged torpor under cellular conditions that are highly injurious to most mammals (e.g. low body temperatures, ischemia). Immunoblotting was used to analyze the expression of proteins associated with pro-survival in six tissues of thirteen-lined ground squirrels, Ictidomys tridecemlineatus. The brain showed a concerted response to torpor with significant increases in the levels of all anti-apoptotic targets analyzed (Bcl-2, Bcl-xL, BI-1, Mcl-1, cIAP1/2, xIAP) as well as enhanced phosphorylation of Bcl-2 at S70 and T56. Heart responded similarly with most anti-apoptotic proteins elevated significantly during torpor except for Bcl-xL and xIAP that decreased and Mcl-1 that was unaltered. In liver, BI-1 increased whereas cIAP1/2 decreased. In kidney, there was an increase in BI-1, cIAP and xIAP but decreases in Bcl-xL and p-Bcl-2(T56) content. In brown adipose tissue, protein levels of BI-1, cIAP1/2, and xIAP decreased significantly during torpor (compared with euthermia) whereas Bcl-2, Bcl-xL, Mcl-1 were unaltered; however, Bcl-2 showed enhanced phosphorylation at Thr56 but not at Ser70. In skeletal muscle, only xIAP levels changed significantly during torpor (an increase). The data show that anti-apoptotic pathways have organ-specific responses in hibernators with a prominent potential role in heart and brain where coordinated enhancement of anti-apoptotic proteins occurred in response to torpor.
bibliographic citation: Rouble et al. (2013) Anti-apoptotic signaling as a cytoprotective mechanism in mammalian hibernation. PeerJ 1:e29 https://doi.org/10.7717/peerj.29
date submitted: 2012-11-25
date accepted: 2013-01-11
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Rouble
  given name: Andrew N.
author list: Agent
  family name: Hefler
  given name: Joshua
author list: Agent
  family name: Mamady
  given name: Hapsatou
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Tessier
  given name: Shannon N.
doi: 10.7717/peerj.29
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Rouble et al.
attribution name: Rouble et al.

Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice
type: item
type: AcademicArticle
description: Glycolate oxidase (GLO) is a key enzyme in photorespiration, catalyzing the oxidation of glycolate to glyoxylate. Arabidopsis GLO is required for nonhost defense responses to Pseudomonas syringae and for tobacco Pto/AvrPto-mediated defense responses. We previously described identification of rice GLO1 that interacts with a glutaredoxin protein, which in turn interacts with TGA transcription factors. TGA transcription factors are well known to participate in NPR1/NH1-mediated defense signaling, which is crucial to systemic acquired resistance in plants. Here we demonstrate that reduction of rice GLO1 expression leads to enhanced resistance to Xanthomonas oryzae pv oryzae (Xoo). Constitutive silencing of GLO1 leads to programmed cell death, resulting in a lesion-mimic phenotype and lethality or reduced plant growth and development, consistent with previous reports. Inducible silencing of GLO1, employing a dexamethasone-GVG (Gal4 DNA binding domain-VP16 activation domain-glucocorticoid receptor fusion) inducible system, alleviates these detrimental effects. Silencing of GLO1 results in enhanced resistance to Xoo, increased expression of defense regulators NH1, NH3, and WRKY45, and activation of PR1 expression.
format: application/pdf
format: text/html
creator: Mawsheng Chern
creator: Wei Bai
creator: Xuewei Chen
creator: Patrick E. Canlas
creator: Pamela C. Ronald
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.28
publisher: PeerJ Inc.
rights: © 2013 Chern et al.
abstract: Glycolate oxidase (GLO) is a key enzyme in photorespiration, catalyzing the oxidation of glycolate to glyoxylate. Arabidopsis GLO is required for nonhost defense responses to Pseudomonas syringae and for tobacco Pto/AvrPto-mediated defense responses. We previously described identification of rice GLO1 that interacts with a glutaredoxin protein, which in turn interacts with TGA transcription factors. TGA transcription factors are well known to participate in NPR1/NH1-mediated defense signaling, which is crucial to systemic acquired resistance in plants. Here we demonstrate that reduction of rice GLO1 expression leads to enhanced resistance to Xanthomonas oryzae pv oryzae (Xoo). Constitutive silencing of GLO1 leads to programmed cell death, resulting in a lesion-mimic phenotype and lethality or reduced plant growth and development, consistent with previous reports. Inducible silencing of GLO1, employing a dexamethasone-GVG (Gal4 DNA binding domain-VP16 activation domain-glucocorticoid receptor fusion) inducible system, alleviates these detrimental effects. Silencing of GLO1 results in enhanced resistance to Xoo, increased expression of defense regulators NH1, NH3, and WRKY45, and activation of PR1 expression.
bibliographic citation: Chern et al. (2013) Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice. PeerJ 1:e28 https://doi.org/10.7717/peerj.28
date submitted: 2012-11-15
date accepted: 2013-01-11
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Chern
  given name: Mawsheng
author list: Agent
  family name: Bai
  given name: Wei
author list: Agent
  family name: Chen
  given name: Xuewei
author list: Agent
  family name: Canlas
  given name: Patrick E.
author list: Agent
  family name: Ronald
  given name: Pamela C.
doi: 10.7717/peerj.28
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Chern et al.
attribution name: Chern et al.

Novel enzyme-polymer conjugates for biotechnological applications
type: item
type: AcademicArticle
description: In the present research, a rapid, simple and efficient chemoselective method for the site-directed incorporation of tailor-made polymers into protein to create biocatalysts with excellent properties for pharmaceutical industrial purpose has been performed. First we focused on the protein engineering of the Geobacillus thermocatenulatus lipase 2 (BTL2) to replace the two cysteines (Cys65, Cys296) in the wild type enzyme (BTL-WT) by two serines. Then, by similar mode, a unique cysteine was introduced in the lid area of the protein. For the site-directed polymer incorporation, a set of different tailor-made thiol-ionic-polymers were synthesized and the protein cysteine was previously activated with 2,2-dithiodipyridine (2-PDS) to allow the disulfide exchange. The protected BTL variants were specifically modified with the different polymers in excellent yields, creating a small library of new biocatalysts. Different and important changes in the catalytic properties, possible caused by structural changes in the lid region, were observed. The different modified biocatalysts were tested in the synthesis of intermediates of antiviral and antitumor drugs, like nucleoside analogues and derivatives of phenylglutaric acid. In the hydrolysis of per-acetylated thymidine, the best biocatalyst was the BTL*-193-DextCOOH , where the activity was increased in 3-fold and the regioselectivity was improved, reaching a yield of 92% of 3’-O-acetyl-thymidine. In the case of the asymmetric hydrolysis of dimethyl phenylglutarate, the best result was found with BTL*-193-DextNH2-6000, where the enzyme activity was increased more than 5-fold and the enantiomeric excess was >99%.
format: application/pdf
format: text/html
creator: Oscar Romero
creator: Cintia W. Rivero
creator: Jose M. Guisan
creator: Jose M. Palomo
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.27
publisher: PeerJ Inc.
rights: © 2013 Romero et al.
abstract: In the present research, a rapid, simple and efficient chemoselective method for the site-directed incorporation of tailor-made polymers into protein to create biocatalysts with excellent properties for pharmaceutical industrial purpose has been performed. First we focused on the protein engineering of the Geobacillus thermocatenulatus lipase 2 (BTL2) to replace the two cysteines (Cys65, Cys296) in the wild type enzyme (BTL-WT) by two serines. Then, by similar mode, a unique cysteine was introduced in the lid area of the protein. For the site-directed polymer incorporation, a set of different tailor-made thiol-ionic-polymers were synthesized and the protein cysteine was previously activated with 2,2-dithiodipyridine (2-PDS) to allow the disulfide exchange. The protected BTL variants were specifically modified with the different polymers in excellent yields, creating a small library of new biocatalysts. Different and important changes in the catalytic properties, possible caused by structural changes in the lid region, were observed. The different modified biocatalysts were tested in the synthesis of intermediates of antiviral and antitumor drugs, like nucleoside analogues and derivatives of phenylglutaric acid. In the hydrolysis of per-acetylated thymidine, the best biocatalyst was the BTL*-193-DextCOOH , where the activity was increased in 3-fold and the regioselectivity was improved, reaching a yield of 92% of 3’-O-acetyl-thymidine. In the case of the asymmetric hydrolysis of dimethyl phenylglutarate, the best result was found with BTL*-193-DextNH2-6000, where the enzyme activity was increased more than 5-fold and the enantiomeric excess was >99%.
bibliographic citation: Romero et al. (2013) Novel enzyme-polymer conjugates for biotechnological applications. PeerJ 1:e27 https://doi.org/10.7717/peerj.27
date submitted: 2012-11-15
date accepted: 2013-01-11
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Romero
  given name: Oscar
author list: Agent
  family name: Rivero
  given name: Cintia W.
author list: Agent
  family name: Guisan
  given name: Jose M.
author list: Agent
  family name: Palomo
  given name: Jose M.
doi: 10.7717/peerj.27
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Romero et al.
attribution name: Romero et al.

Organ homologies in orchid flowers re-interpreted using the Musk Orchid as a model
type: item
type: AcademicArticle
description: Background and Aims. The presence of novel structures in orchid flowers, including auricles, rostellum and bursicles on the gynostemium and a lobed labellum, has prompted long-standing homology disputes, fuelled by conflicting evidence from a wide range of sources. Re-assessment of this debate using an improved model is timely, following recent phylogenetic insights and on the cusp of a revolution in developmental genetics. Methods. We use new data from floral development and anatomy in the small-flowered terrestrial orchid Herminium monorchis as a model to explore organ homologies in orchid flowers within the context of a review of recent literature on developmental genetics. Key Results. The apex of the median carpel of Herminium is trilobed, and the bursicles develop from its lateral lobes, relatively late in flower ontogeny. The bursicles enclose the viscidia, which adhere to the tapetal remnants to form a caudicle linking the viscidium with the pollinium. The auricles are initiated earlier than the bursicles, but they also remain unvascularized. The deeply trilobed labellum possesses three vascular traces, in contrast with the lateral petals, each of which contains a single vascular trace. The two lateral labellum traces diverge from the traces supplying the two adjacent lateral sepals. Data from flower ontogeny and anatomy conflict with respect to organ homologies. Conclusions. Much progress has recently been made in understanding the exceptional differentiation shown by orchids among perianth segments, focusing on multiple copies of the DEF/AP3 subclass of B-class MADS-box genes. In contrast, untangling homologies of profound congenital union of multiple floral organs forming the orchid gynostemium is hampered by their profound congenital union, which we ascribe to overlap in gene expression between organs. Thus, the functional morphology of the orchid flower could ultimately reflect extreme synorganization and associated genetic integration. Analogizing the …
format: application/pdf
format: text/html
creator: Paula J. Rudall
creator: Craig D. Perl
creator: Richard M. Bateman
subject: Biodiversity
subject: Developmental Biology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.26
publisher: PeerJ Inc.
rights: © 2013 Rudall et al.
abstract: Background and Aims. The presence of novel structures in orchid flowers, including auricles, rostellum and bursicles on the gynostemium and a lobed labellum, has prompted long-standing homology disputes, fuelled by conflicting evidence from a wide range of sources. Re-assessment of this debate using an improved model is timely, following recent phylogenetic insights and on the cusp of a revolution in developmental genetics. Methods. We use new data from floral development and anatomy in the small-flowered terrestrial orchid Herminium monorchis as a model to explore organ homologies in orchid flowers within the context of a review of recent literature on developmental genetics. Key Results. The apex of the median carpel of Herminium is trilobed, and the bursicles develop from its lateral lobes, relatively late in flower ontogeny. The bursicles enclose the viscidia, which adhere to the tapetal remnants to form a caudicle linking the viscidium with the pollinium. The auricles are initiated earlier than the bursicles, but they also remain unvascularized. The deeply trilobed labellum possesses three vascular traces, in contrast with the lateral petals, each of which contains a single vascular trace. The two lateral labellum traces diverge from the traces supplying the two adjacent lateral sepals. Data from flower ontogeny and anatomy conflict with respect to organ homologies. Conclusions. Much progress has recently been made in understanding the exceptional differentiation shown by orchids among perianth segments, focusing on multiple copies of the DEF/AP3 subclass of B-class MADS-box genes. In contrast, untangling homologies of profound congenital union of multiple floral organs forming the orchid gynostemium is hampered by their profound congenital union, which we ascribe to overlap in gene expression between organs. Thus, the functional morphology of the orchid flower could ultimately reflect extreme synorganization and associated genetic integration. Analogizing the …
bibliographic citation: Rudall et al. (2013) Organ homologies in orchid flowers re-interpreted using the Musk Orchid as a model. PeerJ 1:e26 https://doi.org/10.7717/peerj.26
date submitted: 2012-11-14
date accepted: 2013-01-11
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Rudall
  given name: Paula J.
author list: Agent
  family name: Perl
  given name: Craig D.
author list: Agent
  family name: Bateman
  given name: Richard M.
doi: 10.7717/peerj.26
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Rudall et al.
attribution name: Rudall et al.

Repeated hands-and-knees positioning during labour: a randomized pilot study
type: item
type: AcademicArticle
description: Background. Caesarean birth rates in North America continue to rise, in the absence of benefit for mothers and babies. One reason may be that hospitalized labouring women spend most of their labours in recumbent or semi-recumbent positions. Although hands-and-knees position has theoretical advantages, efforts to encourage its adoption in practice are severely hampered by the lack of compelling evidence that it is beneficial. Before a definitive, large scale trial, with spontaneous vaginal birth as the primary outcome, could be justified in terms of time, effort, and expense, several feasibility and acceptability questions had to be addressed. We aimed to enrol 60 women in a pilot study to assess feasibility and acceptability of the trial protocol, and to obtain estimates of treatment effects on method of birth and persistent back pain. Methods. We conducted a pilot study at two North American hospitals. In ten months of recruitment, 30 nulliparous women in labour at term were randomly allocated to either usual care (use of any position during labour except hands-and-knees) or to try hands-and-knees for 15 min every hour during labour. Data were collected about compliance, acceptability, persistent back pain, intrapartum interventions, and women’s views of their experiences. Results. Although mean length of time from randomization to delivery was over 12 hours, only 9 of the 16 women allocated to repeated hands-and-knees used it more than twice. Two of the 14 in the usual care group used hands-and-knees once. Twenty-seven women had regional analgesia (15 in the hands-and-knees group and 12 in the usual care group). Eleven in the hands-and-knees group and 14 in the usual care group had spontaneous vaginal births. One woman (in the hands-and-knees group) had a vacuum extraction. Four women in the hands-and-knees group and none in the usual care group gave birth by caesarean section. Hourly back pain ratings were highly variable in both groups, covering the full range o…
format: application/pdf
format: text/html
creator: Ellen D. Hodnett
creator: Robyn Stremler
creator: Stephen H. Halpern
creator: Julie Weston
creator: Rory Windrim
subject: Clinical Trials
subject: Gynecology and Obstetrics
subject: Nursing
description: doi:10.7717/peerj.25
publisher: PeerJ Inc.
rights: © 2013 Hodnett et al.
abstract: Background. Caesarean birth rates in North America continue to rise, in the absence of benefit for mothers and babies. One reason may be that hospitalized labouring women spend most of their labours in recumbent or semi-recumbent positions. Although hands-and-knees position has theoretical advantages, efforts to encourage its adoption in practice are severely hampered by the lack of compelling evidence that it is beneficial. Before a definitive, large scale trial, with spontaneous vaginal birth as the primary outcome, could be justified in terms of time, effort, and expense, several feasibility and acceptability questions had to be addressed. We aimed to enrol 60 women in a pilot study to assess feasibility and acceptability of the trial protocol, and to obtain estimates of treatment effects on method of birth and persistent back pain. Methods. We conducted a pilot study at two North American hospitals. In ten months of recruitment, 30 nulliparous women in labour at term were randomly allocated to either usual care (use of any position during labour except hands-and-knees) or to try hands-and-knees for 15 min every hour during labour. Data were collected about compliance, acceptability, persistent back pain, intrapartum interventions, and women’s views of their experiences. Results. Although mean length of time from randomization to delivery was over 12 hours, only 9 of the 16 women allocated to repeated hands-and-knees used it more than twice. Two of the 14 in the usual care group used hands-and-knees once. Twenty-seven women had regional analgesia (15 in the hands-and-knees group and 12 in the usual care group). Eleven in the hands-and-knees group and 14 in the usual care group had spontaneous vaginal births. One woman (in the hands-and-knees group) had a vacuum extraction. Four women in the hands-and-knees group and none in the usual care group gave birth by caesarean section. Hourly back pain ratings were highly variable in both groups, covering the full range o…
bibliographic citation: Hodnett et al. (2013) Repeated hands-and-knees positioning during labour: a randomized pilot study. PeerJ 1:e25 https://doi.org/10.7717/peerj.25
date submitted: 2012-12-20
date accepted: 2013-01-10
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Hodnett
  given name: Ellen D.
author list: Agent
  family name: Stremler
  given name: Robyn
author list: Agent
  family name: Halpern
  given name: Stephen H.
author list: Agent
  family name: Weston
  given name: Julie
author list: Agent
  family name: Windrim
  given name: Rory
doi: 10.7717/peerj.25
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Hodnett et al.
attribution name: Hodnett et al.

Poorer verbal working memory for a second language selectively impacts academic achievement in university medical students
type: item
type: AcademicArticle
description: Working memory (WM) is often poorer for a second language (L2). In low noise conditions, people listening to a language other than their first language (L1) may have similar auditory perception skills for that L2 as native listeners, but do worse in high noise conditions, and this has been attributed to the poorer WM for L2. Given that WM is critical for academic success in children and young adults, these speech in noise effects have implications for academic performance where the language of instruction is L2 for a student. We used a well-established Speech-in-Noise task as a verbal WM (vWM) test, and developed a model correlating vWM and measures of English proficiency and/or usage to scholastic outcomes in a multi-faceted assessment medical education program. Significant differences in Speech-Noise Ratio (SNR50 ) values were observed between medical undergraduates who had learned English before or after five years of age, with the latter group doing worse in the ability to extract whole connected speech in the presence of background multi-talker babble (Student-t tests, p < 0.001). Significant negative correlations were observed between the SNR50 and seven of the nine variables of English usage, learning styles, stress, and musical abilities in a questionnaire administered to the students previously. The remaining two variables, Perceived Stress Scale (PSS) and the Age of Acquisition of English (AoAoE) were significantly positively correlated with the SNR50 , showing that those with a poorer capacity to discriminate simple English sentences from noise had learnt English later in life and had higher levels of stress – all characteristics of the international students. Local students exhibited significantly lower SNR50 scores and were significantly younger when they first learnt English. No significant correlation was detected between the SNR50 and the students’ Visual/Verbal Learning Style (r = −0.023). Standard multiple regression was carried out to assess the r…
format: application/pdf
format: text/html
creator: Collette Mann
creator: Benedict J. Canny
creator: David H. Reser
creator: Ramesh Rajan
subject: Science and Medical Education
description: doi:10.7717/peerj.22
publisher: PeerJ Inc.
rights: © 2013 Mann et al.
abstract: Working memory (WM) is often poorer for a second language (L2). In low noise conditions, people listening to a language other than their first language (L1) may have similar auditory perception skills for that L2 as native listeners, but do worse in high noise conditions, and this has been attributed to the poorer WM for L2. Given that WM is critical for academic success in children and young adults, these speech in noise effects have implications for academic performance where the language of instruction is L2 for a student. We used a well-established Speech-in-Noise task as a verbal WM (vWM) test, and developed a model correlating vWM and measures of English proficiency and/or usage to scholastic outcomes in a multi-faceted assessment medical education program. Significant differences in Speech-Noise Ratio (SNR50 ) values were observed between medical undergraduates who had learned English before or after five years of age, with the latter group doing worse in the ability to extract whole connected speech in the presence of background multi-talker babble (Student-t tests, p < 0.001). Significant negative correlations were observed between the SNR50 and seven of the nine variables of English usage, learning styles, stress, and musical abilities in a questionnaire administered to the students previously. The remaining two variables, Perceived Stress Scale (PSS) and the Age of Acquisition of English (AoAoE) were significantly positively correlated with the SNR50 , showing that those with a poorer capacity to discriminate simple English sentences from noise had learnt English later in life and had higher levels of stress – all characteristics of the international students. Local students exhibited significantly lower SNR50 scores and were significantly younger when they first learnt English. No significant correlation was detected between the SNR50 and the students’ Visual/Verbal Learning Style (r = −0.023). Standard multiple regression was carried out to assess the r…
bibliographic citation: Mann et al. (2013) Poorer verbal working memory for a second language selectively impacts academic achievement in university medical students. PeerJ 1:e22 https://doi.org/10.7717/peerj.22
date submitted: 2012-11-28
date accepted: 2013-01-08
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Mann
  given name: Collette
author list: Agent
  family name: Canny
  given name: Benedict J.
author list: Agent
  family name: Reser
  given name: David H.
author list: Agent
  family name: Rajan
  given name: Ramesh
doi: 10.7717/peerj.22
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Mann et al.
attribution name: Mann et al.

Glucose-6-phosphate dehydrogenase regulation in the hepatopancreas of the anoxia-tolerant marine mollusc, Littorina littorea
type: item
type: AcademicArticle
description: Glucose-6-phosphate dehydrogenase (G6PDH) gates flux through the pentose phosphate pathway and is key to cellular antioxidant defense due to its role in producing NADPH. Good antioxidant defenses are crucial for anoxia-tolerant organisms that experience wide variations in oxygen availability. The marine mollusc, Littorina littorea, is an intertidal snail that experiences daily bouts of anoxia/hypoxia with the tide cycle and shows multiple metabolic and enzymatic adaptations that support anaerobiosis. This study investigated the kinetic, physical and regulatory properties of G6PDH from hepatopancreas of L. littorea to determine if the enzyme is differentially regulated in response to anoxia, thereby providing altered pentose phosphate pathway functionality under oxygen stress conditions. Several kinetic properties of G6PDH differed significantly between aerobic and 24 h anoxic conditions; compared with the aerobic state, anoxic G6PDH (assayed at pH 8) showed a 38% decrease in Km G6P and enhanced inhibition by urea, whereas in pH 6 assays Km NADP and maximal activity changed significantly between the two states. The mechanism underlying anoxia-responsive changes in enzyme properties proved to be a change in the phosphorylation state of G6PDH. This was documented with immunoblotting using an anti-phosphoserine antibody, in vitro incubations that stimulated endogenous protein kinases versus protein phosphatases and significantly changed Km G6P, and phosphorylation of the enzyme with 32P-ATP. All these data indicated that the aerobic and anoxic forms of G6PDH were the high and low phosphate forms, respectively, and that phosphorylation state was modulated in response to selected endogenous protein kinases (PKA or PKG) and protein phosphatases (PP1 or PP2C). Anoxia-induced changes in the phosphorylation state of G6PDH may facilitate sustained or increased production of NADPH to enhance antioxidant defense during long term anaerobiosis and/or during the transition back to …
format: application/pdf
format: text/html
creator: Judeh L. Lama
creator: Ryan A.V. Bell
creator: Kenneth B. Storey
subject: Biochemistry
subject: Marine Biology
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.21
publisher: PeerJ Inc.
rights: © 2013 Lama et al.
abstract: Glucose-6-phosphate dehydrogenase (G6PDH) gates flux through the pentose phosphate pathway and is key to cellular antioxidant defense due to its role in producing NADPH. Good antioxidant defenses are crucial for anoxia-tolerant organisms that experience wide variations in oxygen availability. The marine mollusc, Littorina littorea, is an intertidal snail that experiences daily bouts of anoxia/hypoxia with the tide cycle and shows multiple metabolic and enzymatic adaptations that support anaerobiosis. This study investigated the kinetic, physical and regulatory properties of G6PDH from hepatopancreas of L. littorea to determine if the enzyme is differentially regulated in response to anoxia, thereby providing altered pentose phosphate pathway functionality under oxygen stress conditions. Several kinetic properties of G6PDH differed significantly between aerobic and 24 h anoxic conditions; compared with the aerobic state, anoxic G6PDH (assayed at pH 8) showed a 38% decrease in Km G6P and enhanced inhibition by urea, whereas in pH 6 assays Km NADP and maximal activity changed significantly between the two states. The mechanism underlying anoxia-responsive changes in enzyme properties proved to be a change in the phosphorylation state of G6PDH. This was documented with immunoblotting using an anti-phosphoserine antibody, in vitro incubations that stimulated endogenous protein kinases versus protein phosphatases and significantly changed Km G6P, and phosphorylation of the enzyme with 32P-ATP. All these data indicated that the aerobic and anoxic forms of G6PDH were the high and low phosphate forms, respectively, and that phosphorylation state was modulated in response to selected endogenous protein kinases (PKA or PKG) and protein phosphatases (PP1 or PP2C). Anoxia-induced changes in the phosphorylation state of G6PDH may facilitate sustained or increased production of NADPH to enhance antioxidant defense during long term anaerobiosis and/or during the transition back to …
bibliographic citation: Lama et al. (2013) Glucose-6-phosphate dehydrogenase regulation in the hepatopancreas of the anoxia-tolerant marine mollusc, Littorina littorea. PeerJ 1:e21 https://doi.org/10.7717/peerj.21
date submitted: 2012-11-20
date accepted: 2013-01-08
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Lama
  given name: Judeh L.
author list: Agent
  family name: Bell
  given name: Ryan A.V.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.21
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Lama et al.
attribution name: Lama et al.

Perceptual elements in Penn & Teller’s “Cups and Balls” magic trick
type: item
type: AcademicArticle
description: Magic illusions provide the perceptual and cognitive scientist with a toolbox of experimental manipulations and testable hypotheses about the building blocks of conscious experience. Here we studied several sleight-of-hand manipulations in the performance of the classic “Cups and Balls” magic trick (where balls appear and disappear inside upside-down opaque cups). We examined a version inspired by the entertainment duo Penn & Teller, conducted with three opaque and subsequently with three transparent cups. Magician Teller used his right hand to load (i.e. introduce surreptitiously) a small ball inside each of two upside-down cups, one at a time, while using his left hand to remove a different ball from the upside-down bottom of the cup. The sleight at the third cup involved one of six manipulations: (a) standard maneuver, (b) standard maneuver without a third ball, (c) ball placed on the table, (d) ball lifted, (e) ball dropped to the floor, and (f) ball stuck to the cup. Seven subjects watched the videos of the performances while reporting, via button press, whenever balls were removed from the cups/table (button “1”) or placed inside the cups/on the table (button “2”). Subjects’ perception was more accurate with transparent than with opaque cups. Perceptual performance was worse for the conditions where the ball was placed on the table, or stuck to the cup, than for the standard maneuver. The condition in which the ball was lifted displaced the subjects’ gaze position the most, whereas the condition in which there was no ball caused the smallest gaze displacement. Training improved the subjects’ perceptual performance. Occlusion of the magician’s face did not affect the subjects’ perception, suggesting that gaze misdirection does not play a strong role in the Cups and Balls illusion. Our results have implications for how to optimize the performance of this classic magic trick, and for the types of hand and object motion that maximize magic misdirection.
format: application/pdf
format: text/html
creator: Hector Rieiro
creator: Susana Martinez-Conde
creator: Stephen L. Macknik
subject: Neuroscience
description: doi:10.7717/peerj.19
publisher: PeerJ Inc.
rights: © 2013 Rieiro et al.
abstract: Magic illusions provide the perceptual and cognitive scientist with a toolbox of experimental manipulations and testable hypotheses about the building blocks of conscious experience. Here we studied several sleight-of-hand manipulations in the performance of the classic “Cups and Balls” magic trick (where balls appear and disappear inside upside-down opaque cups). We examined a version inspired by the entertainment duo Penn & Teller, conducted with three opaque and subsequently with three transparent cups. Magician Teller used his right hand to load (i.e. introduce surreptitiously) a small ball inside each of two upside-down cups, one at a time, while using his left hand to remove a different ball from the upside-down bottom of the cup. The sleight at the third cup involved one of six manipulations: (a) standard maneuver, (b) standard maneuver without a third ball, (c) ball placed on the table, (d) ball lifted, (e) ball dropped to the floor, and (f) ball stuck to the cup. Seven subjects watched the videos of the performances while reporting, via button press, whenever balls were removed from the cups/table (button “1”) or placed inside the cups/on the table (button “2”). Subjects’ perception was more accurate with transparent than with opaque cups. Perceptual performance was worse for the conditions where the ball was placed on the table, or stuck to the cup, than for the standard maneuver. The condition in which the ball was lifted displaced the subjects’ gaze position the most, whereas the condition in which there was no ball caused the smallest gaze displacement. Training improved the subjects’ perceptual performance. Occlusion of the magician’s face did not affect the subjects’ perception, suggesting that gaze misdirection does not play a strong role in the Cups and Balls illusion. Our results have implications for how to optimize the performance of this classic magic trick, and for the types of hand and object motion that maximize magic misdirection.
bibliographic citation: Rieiro et al. (2013) Perceptual elements in Penn & Teller’s “Cups and Balls” magic trick. PeerJ 1:e19 https://doi.org/10.7717/peerj.19
date submitted: 2012-12-01
date accepted: 2013-01-05
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Rieiro
  given name: Hector
author list: Agent
  family name: Martinez-Conde
  given name: Susana
author list: Agent
  family name: Macknik
  given name: Stephen L.
doi: 10.7717/peerj.19
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Rieiro et al.
attribution name: Rieiro et al.

Timing of molt of barn swallows is delayed in a rare Clock genotype
type: item
type: AcademicArticle
description: Photoperiodic responses are major factors entraining circannual life-cycles, functioning to adaptively synchronize annual routines to seasonal fluctuations in ecological conditions. Photoperiodism in physiology and behaviour is enforced by genes, including the vertebrate Clock orthologues, which are associated, for example, with phenology of migration in fish and breeding in birds. However, the role of Clock in photoperiodic plumage molt processes is unknown. We analyzed variation in molt schedules in relation to Clock genotype, using the long-distance migratory barn swallow (Hirundo rustica) as a model and by identifying males and females using molecular sexing techniques. Consistently with previous studies, we found one very common (Q7) and two rare (Q6, Q8) variants of a functionally significant Clock polyglutamine repeat. Molt schedules of primary wing feathers of swallows during their wintering period in Nigeria differed among Clock genotypes: rare (1.1%) Q7/Q8 heterozygotes had significantly delayed molt compared to the other genotypes. Molt schedules did not differ between males and females, and no differential association between molt and Clock in relation to sex emerged. The same rare Clock genotype that exhibited delayed breeding in Europe was here found to delay molt in Africa. Though based on a limited number of Q7/Q8 individuals from an otherwise very large sample, these novel results suggest that Clock is involved in the photoperiodic control of both molt and breeding, potentially also via reciprocal carry-over effects. If confirmed in species with higher Clock polymorphism, present results may have far-reaching consequences for the study of photoperiodic control of molt and expression of annual routines.
format: application/pdf
format: text/html
creator: Nicola Saino
creator: Maria Romano
creator: Manuela Caprioli
creator: Mauro Fasola
creator: Roberto Lardelli
creator: Pierfrancesco Micheloni
creator: Chiara Scandolara
creator: Diego Rubolini
creator: Luca Gianfranceschi
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.17
publisher: PeerJ Inc.
rights: © 2013 Saino et al.
abstract: Photoperiodic responses are major factors entraining circannual life-cycles, functioning to adaptively synchronize annual routines to seasonal fluctuations in ecological conditions. Photoperiodism in physiology and behaviour is enforced by genes, including the vertebrate Clock orthologues, which are associated, for example, with phenology of migration in fish and breeding in birds. However, the role of Clock in photoperiodic plumage molt processes is unknown. We analyzed variation in molt schedules in relation to Clock genotype, using the long-distance migratory barn swallow (Hirundo rustica) as a model and by identifying males and females using molecular sexing techniques. Consistently with previous studies, we found one very common (Q7) and two rare (Q6, Q8) variants of a functionally significant Clock polyglutamine repeat. Molt schedules of primary wing feathers of swallows during their wintering period in Nigeria differed among Clock genotypes: rare (1.1%) Q7/Q8 heterozygotes had significantly delayed molt compared to the other genotypes. Molt schedules did not differ between males and females, and no differential association between molt and Clock in relation to sex emerged. The same rare Clock genotype that exhibited delayed breeding in Europe was here found to delay molt in Africa. Though based on a limited number of Q7/Q8 individuals from an otherwise very large sample, these novel results suggest that Clock is involved in the photoperiodic control of both molt and breeding, potentially also via reciprocal carry-over effects. If confirmed in species with higher Clock polymorphism, present results may have far-reaching consequences for the study of photoperiodic control of molt and expression of annual routines.
bibliographic citation: Saino et al. (2013) Timing of molt of barn swallows is delayed in a rare Clock genotype. PeerJ 1:e17 https://doi.org/10.7717/peerj.17
date submitted: 2012-11-20
date accepted: 2013-01-04
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Saino
  given name: Nicola
author list: Agent
  family name: Romano
  given name: Maria
author list: Agent
  family name: Caprioli
  given name: Manuela
author list: Agent
  family name: Fasola
  given name: Mauro
author list: Agent
  family name: Lardelli
  given name: Roberto
author list: Agent
  family name: Micheloni
  given name: Pierfrancesco
author list: Agent
  family name: Scandolara
  given name: Chiara
author list: Agent
  family name: Rubolini
  given name: Diego
author list: Agent
  family name: Gianfranceschi
  given name: Luca
doi: 10.7717/peerj.17
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Saino et al.
attribution name: Saino et al.

Na+/Ca2+ selectivity in the bacterial voltage-gated sodium channel NavAb
type: item
type: AcademicArticle
description: The recent publication of a number of high resolution bacterial voltage-gated sodium channel structures has opened the door for the mechanisms employed by these channels to distinguish between ions to be elucidated. The way these channels select between Na+ and K+ has been investigated in computational studies, but the selectivity for Na+ over Ca2+ has not yet been studied in this way. Here we use molecular dynamics simulations to calculate the energetics of Na+ and Ca2+ transport through the channel. Single ion profiles show that Ca2+ experiences a large barrier midway through the selectivity filter that is not seen by Na+. This barrier is caused by the need for Ca2+ to partly dehydrate to pass through this region and the lack of compensating interactions with the protein. Multi-ion profiles show that ions can pass each other in the channel, which is why the presence of Ca2+ does not block Na+ conduction despite binding more strongly in the pore.
format: application/pdf
format: text/html
creator: Ben Corry
subject: Biophysics
subject: Computational Biology
description: doi:10.7717/peerj.16
publisher: PeerJ Inc.
rights: © 2013 Corry
abstract: The recent publication of a number of high resolution bacterial voltage-gated sodium channel structures has opened the door for the mechanisms employed by these channels to distinguish between ions to be elucidated. The way these channels select between Na+ and K+ has been investigated in computational studies, but the selectivity for Na+ over Ca2+ has not yet been studied in this way. Here we use molecular dynamics simulations to calculate the energetics of Na+ and Ca2+ transport through the channel. Single ion profiles show that Ca2+ experiences a large barrier midway through the selectivity filter that is not seen by Na+. This barrier is caused by the need for Ca2+ to partly dehydrate to pass through this region and the lack of compensating interactions with the protein. Multi-ion profiles show that ions can pass each other in the channel, which is why the presence of Ca2+ does not block Na+ conduction despite binding more strongly in the pore.
bibliographic citation: Corry (2013) Na+/Ca2+ selectivity in the bacterial voltage-gated sodium channel NavAb. PeerJ 1:e16 https://doi.org/10.7717/peerj.16
date submitted: 2012-11-30
date accepted: 2013-01-04
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Corry
  given name: Ben
doi: 10.7717/peerj.16
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Corry
attribution name: Corry

Fluorescent protein tagging confirms the presence of ribosomal proteins at Drosophila polytene chromosomes
type: item
type: AcademicArticle
description: Most ribosomal proteins (RPs) are stoichiometrically incorporated into ribosomal subunits and play essential roles in ribosome biogenesis and function. However, a number of RPs appear to have non-ribosomal functions, which involve direct association with pre-mRNA and transcription factors at transcription sites. The consensus is that the RPs found at these sites are off ribosomal subunits, but observation that different RPs are usually found together suggests that ribosomal or ribosomal-like subunits might be present. Notably, it has previously been reported that antibodies against 20 different RPs stain the same Pol II transcription sites in Drosophila polytene chromosomes. Some concerns, however, were raised about the specificity of the antibodies. To investigate further whether RPs are present at transcription sites in Drosophila, we have generated several transgenic flies expressing RPs (RpS2, RpS5a, RpS9, RpS11, RpS13, RpS18, RpL8, RpL11, RpL32, and RpL36) tagged with either green or red fluorescent protein. Imaging of salivary gland cells showed that these proteins are, as expected, abundant in the cytoplasm as well as in the nucleolus. However, these RPs are also apparent in the nucleus in the region occupied by the chromosomes. Indeed, polytene chromosome immunostaining of a representative subset of tagged RPs confirms the association with transcribed loci. Furthermore, characterization of a strain expressing RpL41 functionally tagged at its native genomic locus with YFP, also showed apparent nuclear accumulation and chromosomal association, suggesting that such a nuclear localization pattern might be a shared feature of RPs and is biologically important. We anticipate that the transgenes described here should provide a useful research tool to visualize ribosomal subunits in Drosophila tissues and to study the non-ribosomal functions of RPs.
format: application/pdf
format: text/html
creator: Kushal Nivriti Rugjee
creator: Subhendu Roy Chaudhury
creator: Khalid Al-Jubran
creator: Preethi Ramanathan
creator: Tina Matina
creator: Jikai Wen
creator: Saverio Brogna
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.15
publisher: PeerJ Inc.
rights: © 2013 Rugjee et al.
abstract: Most ribosomal proteins (RPs) are stoichiometrically incorporated into ribosomal subunits and play essential roles in ribosome biogenesis and function. However, a number of RPs appear to have non-ribosomal functions, which involve direct association with pre-mRNA and transcription factors at transcription sites. The consensus is that the RPs found at these sites are off ribosomal subunits, but observation that different RPs are usually found together suggests that ribosomal or ribosomal-like subunits might be present. Notably, it has previously been reported that antibodies against 20 different RPs stain the same Pol II transcription sites in Drosophila polytene chromosomes. Some concerns, however, were raised about the specificity of the antibodies. To investigate further whether RPs are present at transcription sites in Drosophila, we have generated several transgenic flies expressing RPs (RpS2, RpS5a, RpS9, RpS11, RpS13, RpS18, RpL8, RpL11, RpL32, and RpL36) tagged with either green or red fluorescent protein. Imaging of salivary gland cells showed that these proteins are, as expected, abundant in the cytoplasm as well as in the nucleolus. However, these RPs are also apparent in the nucleus in the region occupied by the chromosomes. Indeed, polytene chromosome immunostaining of a representative subset of tagged RPs confirms the association with transcribed loci. Furthermore, characterization of a strain expressing RpL41 functionally tagged at its native genomic locus with YFP, also showed apparent nuclear accumulation and chromosomal association, suggesting that such a nuclear localization pattern might be a shared feature of RPs and is biologically important. We anticipate that the transgenes described here should provide a useful research tool to visualize ribosomal subunits in Drosophila tissues and to study the non-ribosomal functions of RPs.
bibliographic citation: Rugjee et al. (2013) Fluorescent protein tagging confirms the presence of ribosomal proteins at Drosophila polytene chromosomes. PeerJ 1:e15 https://doi.org/10.7717/peerj.15
date submitted: 2012-12-03
date accepted: 2013-01-03
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Rugjee
  given name: Kushal Nivriti
author list: Agent
  family name: Roy Chaudhury
  given name: Subhendu
author list: Agent
  family name: Al-Jubran
  given name: Khalid
author list: Agent
  family name: Ramanathan
  given name: Preethi
author list: Agent
  family name: Matina
  given name: Tina
author list: Agent
  family name: Wen
  given name: Jikai
author list: Agent
  family name: Brogna
  given name: Saverio
doi: 10.7717/peerj.15
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Rugjee et al.
attribution name: Rugjee et al.

Simultaneous recordings of ocular microtremor and microsaccades with a piezoelectric sensor and a video-oculography system
type: item
type: AcademicArticle
description: Our eyes are in continuous motion. Even when we attempt to fix our gaze, we produce so called “fixational eye movements”, which include microsaccades, drift, and ocular microtremor (OMT). Microsaccades, the largest and fastest type of fixational eye movement, shift the retinal image from several dozen to several hundred photoreceptors and have equivalent physical characteristics to saccades, only on a smaller scale (Martinez-Conde, Otero-Millan & Macknik, 2013). OMT occurs simultaneously with drift and is the smallest of the fixational eye movements (∼1 photoreceptor width, >0.5 arcmin), with dominant frequencies ranging from 70 Hz to 103 Hz (Martinez-Conde, Macknik & Hubel, 2004). Due to OMT’s small amplitude and high frequency, the most accurate and stringent way to record it is the piezoelectric transduction method. Thus, OMT studies are far rarer than those focusing on microsaccades or drift. Here we conducted simultaneous recordings of OMT and microsaccades with a piezoelectric device and a commercial infrared video tracking system. We set out to determine whether OMT could help to restore perceptually faded targets during attempted fixation, and we also wondered whether the piezoelectric sensor could affect the characteristics of microsaccades. Our results showed that microsaccades, but not OMT, counteracted perceptual fading. We moreover found that the piezoelectric sensor affected microsaccades in a complex way, and that the oculomotor system adjusted to the stress brought on by the sensor by adjusting the magnitudes of microsaccades.
format: application/pdf
format: text/html
creator: Michael B. McCamy
creator: Niamh Collins
creator: Jorge Otero-Millan
creator: Mohammed Al-Kalbani
creator: Stephen L. Macknik
creator: Davis Coakley
creator: Xoana G. Troncoso
creator: Gerard Boyle
creator: Vinodh Narayanan
creator: Thomas R. Wolf
creator: Susana Martinez-Conde
subject: Neuroscience
description: doi:10.7717/peerj.14
publisher: PeerJ Inc.
rights: © 2013 McCamy et al.
abstract: Our eyes are in continuous motion. Even when we attempt to fix our gaze, we produce so called “fixational eye movements”, which include microsaccades, drift, and ocular microtremor (OMT). Microsaccades, the largest and fastest type of fixational eye movement, shift the retinal image from several dozen to several hundred photoreceptors and have equivalent physical characteristics to saccades, only on a smaller scale (Martinez-Conde, Otero-Millan & Macknik, 2013). OMT occurs simultaneously with drift and is the smallest of the fixational eye movements (∼1 photoreceptor width, >0.5 arcmin), with dominant frequencies ranging from 70 Hz to 103 Hz (Martinez-Conde, Macknik & Hubel, 2004). Due to OMT’s small amplitude and high frequency, the most accurate and stringent way to record it is the piezoelectric transduction method. Thus, OMT studies are far rarer than those focusing on microsaccades or drift. Here we conducted simultaneous recordings of OMT and microsaccades with a piezoelectric device and a commercial infrared video tracking system. We set out to determine whether OMT could help to restore perceptually faded targets during attempted fixation, and we also wondered whether the piezoelectric sensor could affect the characteristics of microsaccades. Our results showed that microsaccades, but not OMT, counteracted perceptual fading. We moreover found that the piezoelectric sensor affected microsaccades in a complex way, and that the oculomotor system adjusted to the stress brought on by the sensor by adjusting the magnitudes of microsaccades.
bibliographic citation: McCamy et al. (2013) Simultaneous recordings of ocular microtremor and microsaccades with a piezoelectric sensor and a video-oculography system. PeerJ 1:e14 https://doi.org/10.7717/peerj.14
date submitted: 2012-11-20
date accepted: 2013-01-03
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: McCamy
  given name: Michael B.
author list: Agent
  family name: Collins
  given name: Niamh
author list: Agent
  family name: Otero-Millan
  given name: Jorge
author list: Agent
  family name: Al-Kalbani
  given name: Mohammed
author list: Agent
  family name: Macknik
  given name: Stephen L.
author list: Agent
  family name: Coakley
  given name: Davis
author list: Agent
  family name: Troncoso
  given name: Xoana G.
author list: Agent
  family name: Boyle
  given name: Gerard
author list: Agent
  family name: Narayanan
  given name: Vinodh
author list: Agent
  family name: Wolf
  given name: Thomas R.
author list: Agent
  family name: Martinez-Conde
  given name: Susana
doi: 10.7717/peerj.14
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 McCamy et al.
attribution name: McCamy et al.

Dissecting the mechanisms of squirrel monkey (Saimiri boliviensis) social learning
type: item
type: AcademicArticle
description: Although the social learning abilities of monkeys have been well documented, this research has only focused on a few species. Furthermore, of those that also incorporated dissections of social learning mechanisms, the majority studied either capuchins (Cebus apella) or marmosets (Callithrix jacchus). To gain a broader understanding of how monkeys gain new skills, we tested squirrel monkeys (Saimiri boliviensis) which have never been studied in tests of social learning mechanisms. To determine whether S. boliviensis can socially learn, we ran “open diffusion” tests with monkeys housed in two social groups (N = 23). Over the course of 10 20-min sessions, the monkeys in each group observed a trained group member retrieving a mealworm from a bidirectional task (the “Slide-box”). Two thirds (67%) of these monkeys both learned how to operate the Slide-box and they also moved the door significantly more times in the direction modeled by the trained demonstrator than the alternative direction. To tease apart the underlying social learning mechanisms we ran a series of three control conditions with 35 squirrel monkeys that had no previous experience with the Slide-box. The first replicated the experimental open diffusion sessions but without the inclusion of a trained model, the second was a no-information control with dyads of monkeys, and the third was a ‘ghost’ display shown to individual monkeys. The first two controls tested for the importance of social support (mere presence effect) and the ghost display showed the affordances of the task to the monkeys. The monkeys showed a certain level of success in the group control (54% of subjects solved the task on one or more occasions) and paired controls (28% were successful) but none were successful in the ghost control. We propose that the squirrel monkeys’ learning, observed in the experimental open diffusion tests, can be best described by a combination of social learning mechanisms in concert; in this case, those mechani…
format: application/pdf
format: text/html
creator: LM Hopper
creator: AN Holmes
creator: LE Williams
creator: SF Brosnan
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.13
publisher: PeerJ Inc.
rights: © 2013 Hopper et al.
abstract: Although the social learning abilities of monkeys have been well documented, this research has only focused on a few species. Furthermore, of those that also incorporated dissections of social learning mechanisms, the majority studied either capuchins (Cebus apella) or marmosets (Callithrix jacchus). To gain a broader understanding of how monkeys gain new skills, we tested squirrel monkeys (Saimiri boliviensis) which have never been studied in tests of social learning mechanisms. To determine whether S. boliviensis can socially learn, we ran “open diffusion” tests with monkeys housed in two social groups (N = 23). Over the course of 10 20-min sessions, the monkeys in each group observed a trained group member retrieving a mealworm from a bidirectional task (the “Slide-box”). Two thirds (67%) of these monkeys both learned how to operate the Slide-box and they also moved the door significantly more times in the direction modeled by the trained demonstrator than the alternative direction. To tease apart the underlying social learning mechanisms we ran a series of three control conditions with 35 squirrel monkeys that had no previous experience with the Slide-box. The first replicated the experimental open diffusion sessions but without the inclusion of a trained model, the second was a no-information control with dyads of monkeys, and the third was a ‘ghost’ display shown to individual monkeys. The first two controls tested for the importance of social support (mere presence effect) and the ghost display showed the affordances of the task to the monkeys. The monkeys showed a certain level of success in the group control (54% of subjects solved the task on one or more occasions) and paired controls (28% were successful) but none were successful in the ghost control. We propose that the squirrel monkeys’ learning, observed in the experimental open diffusion tests, can be best described by a combination of social learning mechanisms in concert; in this case, those mechani…
bibliographic citation: Hopper et al. (2013) Dissecting the mechanisms of squirrel monkey (Saimiri boliviensis) social learning. PeerJ 1:e13 https://doi.org/10.7717/peerj.13
date submitted: 2012-11-13
date accepted: 2013-01-02
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Hopper
  given name: LM
author list: Agent
  family name: Holmes
  given name: AN
author list: Agent
  family name: Williams
  given name: LE
author list: Agent
  family name: Brosnan
  given name: SF
doi: 10.7717/peerj.13
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Hopper et al.
attribution name: Hopper et al.

Novel control of lactate dehydrogenase from the freeze tolerant wood frog: role of posttranslational modifications
type: item
type: AcademicArticle
description: Lactate dehydrogenase (LDH), the terminal enzyme of anaerobic glycolysis, plays a crucial role both in sustaining glycolytic ATP production under oxygen-limiting conditions and in facilitating the catabolism of accumulated lactate when stress conditions are relieved. In this study, the effects on LDH of in vivo freezing and dehydration stresses (both of which impose hypoxia/anoxia stress on tissues) were examined in skeletal muscle of the freeze-tolerant wood frog, Rana sylvatica. LDH from muscle of control, frozen and dehydrated wood frogs was purified to homogeneity in a two-step process. The kinetic properties and stability of purified LDH were analyzed, revealing no significant differences in Vmax, Km and I50 values between control and frozen LDH. However, control and dehydrated LDH differed significantly in Km values for pyruvate, lactate, and NAD, I50 urea, and in temperature, glucose, and urea effects on these parameters. The possibility that posttranslational modification of LDH was responsible for the stable differences in enzyme behavior between control and dehydrated states was assessed using ProQ diamond staining to detect phosphorylation and immunoblotting to detect acetylation, methylation, ubiquitination, SUMOylation and nitrosylation of the enzyme. LDH from muscle of dehydrated wood frogs showed significantly lower levels of acetylation, providing one of the first demonstrations of a potential role for protein acetylation in the stress-responsive control of a metabolic enzyme.
format: application/pdf
format: text/html
creator: Jean Abboud
creator: Kenneth B. Storey
subject: Biochemistry
subject: Cell Biology
description: doi:10.7717/peerj.12
publisher: PeerJ Inc.
rights: © 2013 Abboud and Storey
abstract: Lactate dehydrogenase (LDH), the terminal enzyme of anaerobic glycolysis, plays a crucial role both in sustaining glycolytic ATP production under oxygen-limiting conditions and in facilitating the catabolism of accumulated lactate when stress conditions are relieved. In this study, the effects on LDH of in vivo freezing and dehydration stresses (both of which impose hypoxia/anoxia stress on tissues) were examined in skeletal muscle of the freeze-tolerant wood frog, Rana sylvatica. LDH from muscle of control, frozen and dehydrated wood frogs was purified to homogeneity in a two-step process. The kinetic properties and stability of purified LDH were analyzed, revealing no significant differences in Vmax, Km and I50 values between control and frozen LDH. However, control and dehydrated LDH differed significantly in Km values for pyruvate, lactate, and NAD, I50 urea, and in temperature, glucose, and urea effects on these parameters. The possibility that posttranslational modification of LDH was responsible for the stable differences in enzyme behavior between control and dehydrated states was assessed using ProQ diamond staining to detect phosphorylation and immunoblotting to detect acetylation, methylation, ubiquitination, SUMOylation and nitrosylation of the enzyme. LDH from muscle of dehydrated wood frogs showed significantly lower levels of acetylation, providing one of the first demonstrations of a potential role for protein acetylation in the stress-responsive control of a metabolic enzyme.
bibliographic citation: Abboud et al. (2013) Novel control of lactate dehydrogenase from the freeze tolerant wood frog: role of posttranslational modifications. PeerJ 1:e12 https://doi.org/10.7717/peerj.12
date submitted: 2012-11-26
date accepted: 2013-01-02
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Abboud
  given name: Jean
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.12
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Abboud and Storey
attribution name: Abboud and Storey

Assessing insect responses to climate change: What are we testing for? Where should we be heading?
type: item
type: AcademicArticle
description: To understand how researchers are tackling globally important issues, it is crucial to identify whether current research is comprehensive enough to make substantive predictions about general responses. We examined how research on climate change affecting insects is being assessed, what factors are being tested and the localities of studies, from 1703 papers published between 1985 and August 2012. Most published research (64%) is generated from Europe and North America and being dedicated to core data analysis, with 29% of the studies analysed dedicated to Lepidoptera and 22% Diptera: which are well above their contribution to the currently identified insect species richness (estimated at 13% and 17% respectively). Research publications on Coleoptera fall well short of their proportional contribution (19% of publications but 39% of insect species identified), and to a lesser extent so do Hemiptera, and Hymenoptera. Species specific responses to changes in temperature by assessing distribution/range shifts or changes in abundance were the most commonly used methods of assessing the impact of climate change on insects. Research on insects and climate change to date is dominated by manuscripts assessing butterflies in Europe, insects of economic and/or environmental concern in forestry, agriculture, and model organisms. The research on understanding how insects will respond to a rapidly changing climate is still in its infancy, but the current trends of publications give a good basis for how we are attempting to assess insect responses. In particular, there is a crucial need for broader studies of ecological, behavioural, physiological and life history responses to be addressed across a greater range of geographic locations, particularly Asia, Africa and Australasia, and in areas of high human population growth and habitat modification. It is still too early in our understanding of taxa responses to climate change to know if charismatic taxa, such as butterflies, or dis…
format: application/pdf
format: text/html
creator: Nigel R. Andrew
creator: Sarah J. Hill
creator: Matthew Binns
creator: Md Habibullah Bahar
creator: Emma V. Ridley
creator: Myung-Pyo Jung
creator: Chris Fyfe
creator: Michelle Yates
creator: Mohammad Khusro
subject: Biodiversity
subject: Climate Change Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.11
publisher: PeerJ Inc.
rights: © 2013 Andrew et al.
abstract: To understand how researchers are tackling globally important issues, it is crucial to identify whether current research is comprehensive enough to make substantive predictions about general responses. We examined how research on climate change affecting insects is being assessed, what factors are being tested and the localities of studies, from 1703 papers published between 1985 and August 2012. Most published research (64%) is generated from Europe and North America and being dedicated to core data analysis, with 29% of the studies analysed dedicated to Lepidoptera and 22% Diptera: which are well above their contribution to the currently identified insect species richness (estimated at 13% and 17% respectively). Research publications on Coleoptera fall well short of their proportional contribution (19% of publications but 39% of insect species identified), and to a lesser extent so do Hemiptera, and Hymenoptera. Species specific responses to changes in temperature by assessing distribution/range shifts or changes in abundance were the most commonly used methods of assessing the impact of climate change on insects. Research on insects and climate change to date is dominated by manuscripts assessing butterflies in Europe, insects of economic and/or environmental concern in forestry, agriculture, and model organisms. The research on understanding how insects will respond to a rapidly changing climate is still in its infancy, but the current trends of publications give a good basis for how we are attempting to assess insect responses. In particular, there is a crucial need for broader studies of ecological, behavioural, physiological and life history responses to be addressed across a greater range of geographic locations, particularly Asia, Africa and Australasia, and in areas of high human population growth and habitat modification. It is still too early in our understanding of taxa responses to climate change to know if charismatic taxa, such as butterflies, or dis…
bibliographic citation: Andrew et al. (2013) Assessing insect responses to climate change: What are we testing for? Where should we be heading?. PeerJ 1:e11 https://doi.org/10.7717/peerj.11
date submitted: 2012-11-12
date accepted: 2012-12-31
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Andrew
  given name: Nigel R.
author list: Agent
  family name: Hill
  given name: Sarah J.
author list: Agent
  family name: Binns
  given name: Matthew
author list: Agent
  family name: Bahar
  given name: Md Habibullah
author list: Agent
  family name: Ridley
  given name: Emma V.
author list: Agent
  family name: Jung
  given name: Myung-Pyo
author list: Agent
  family name: Fyfe
  given name: Chris
author list: Agent
  family name: Yates
  given name: Michelle
author list: Agent
  family name: Khusro
  given name: Mohammad
doi: 10.7717/peerj.11
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Andrew et al.
attribution name: Andrew et al.

Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
type: item
type: AcademicArticle
description: The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks.
format: application/pdf
format: text/html
creator: Frank Emmert-Streib
subject: Bioinformatics
subject: Computational Biology
subject: Mathematical Biology
subject: Statistics
description: doi:10.7717/peerj.10
publisher: PeerJ Inc.
rights: © 2013 Emmert-Streib
abstract: The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks.
bibliographic citation: Emmert-Streib (2013) Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors. PeerJ 1:e10 https://doi.org/10.7717/peerj.10
date submitted: 2012-11-13
date accepted: 2012-12-31
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Emmert-Streib
  given name: Frank
doi: 10.7717/peerj.10
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Emmert-Streib
attribution name: Emmert-Streib

The effects of fixation target size and luminance on microsaccades and square-wave jerks
type: item
type: AcademicArticle
description: A large amount of classic and contemporary vision studies require subjects to fixate a target. Target fixation serves as a normalizing factor across studies, promoting the field’s ability to compare and contrast experiments. Yet, fixation target parameters, including luminance, contrast, size, shape and color, vary across studies, potentially affecting the interpretation of results. Previous research on the effects of fixation target size and luminance on the control of fixation position rendered conflicting results, and no study has examined the effects of fixation target characteristics on square-wave jerks, the most common type of saccadic intrusion. Here we set out to determine the effects of fixation target size and luminance on the characteristics of microsaccades and square-wave jerks, over a large range of stimulus parameters. Human subjects fixated a circular target with varying luminance and size while we recorded their eye movements with an infrared video tracker (EyeLink 1000, SR Research). We detected microsaccades and SWJs automatically with objective algorithms developed previously. Microsaccade rates decreased linearly and microsaccade magnitudes increased linearly with target size. The percent of microsaccades forming part of SWJs decreased, and the time from the end of the initial SWJ saccade to the beginning of the second SWJ saccade (SWJ inter-saccadic interval; ISI) increased with target size. The microsaccadic preference for horizontal direction also decreased moderately with target size . Target luminance did not affect significantly microsaccades or SWJs, however. In the absence of a fixation target, microsaccades became scarcer and larger, while SWJ prevalence decreased and SWJ ISIs increased. Thus, the choice of fixation target can affect experimental outcomes, especially in human factors and in visual and oculomotor studies. These results have implications for previous and future research conducted under fixation conditions, and should enc…
format: application/pdf
format: text/html
creator: Michael B. McCamy
creator: Ali Najafian Jazi
creator: Jorge Otero-Millan
creator: Stephen L. Macknik
creator: Susana Martinez-Conde
subject: Neuroscience
description: doi:10.7717/peerj.9
publisher: PeerJ Inc.
rights: © 2013 McCamy et al.
abstract: A large amount of classic and contemporary vision studies require subjects to fixate a target. Target fixation serves as a normalizing factor across studies, promoting the field’s ability to compare and contrast experiments. Yet, fixation target parameters, including luminance, contrast, size, shape and color, vary across studies, potentially affecting the interpretation of results. Previous research on the effects of fixation target size and luminance on the control of fixation position rendered conflicting results, and no study has examined the effects of fixation target characteristics on square-wave jerks, the most common type of saccadic intrusion. Here we set out to determine the effects of fixation target size and luminance on the characteristics of microsaccades and square-wave jerks, over a large range of stimulus parameters. Human subjects fixated a circular target with varying luminance and size while we recorded their eye movements with an infrared video tracker (EyeLink 1000, SR Research). We detected microsaccades and SWJs automatically with objective algorithms developed previously. Microsaccade rates decreased linearly and microsaccade magnitudes increased linearly with target size. The percent of microsaccades forming part of SWJs decreased, and the time from the end of the initial SWJ saccade to the beginning of the second SWJ saccade (SWJ inter-saccadic interval; ISI) increased with target size. The microsaccadic preference for horizontal direction also decreased moderately with target size . Target luminance did not affect significantly microsaccades or SWJs, however. In the absence of a fixation target, microsaccades became scarcer and larger, while SWJ prevalence decreased and SWJ ISIs increased. Thus, the choice of fixation target can affect experimental outcomes, especially in human factors and in visual and oculomotor studies. These results have implications for previous and future research conducted under fixation conditions, and should enc…
bibliographic citation: McCamy et al. (2013) The effects of fixation target size and luminance on microsaccades and square-wave jerks. PeerJ 1:e9 https://doi.org/10.7717/peerj.9
date submitted: 2012-11-27
date accepted: 2012-12-30
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: McCamy
  given name: Michael B.
author list: Agent
  family name: Najafian Jazi
  given name: Ali
author list: Agent
  family name: Otero-Millan
  given name: Jorge
author list: Agent
  family name: Macknik
  given name: Stephen L.
author list: Agent
  family name: Martinez-Conde
  given name: Susana
doi: 10.7717/peerj.9
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 McCamy et al.
attribution name: McCamy et al.

Mutations changing tropomodulin affinity for tropomyosin alter neurite formation and extension
type: item
type: AcademicArticle
description: Assembly of the actin cytoskeleton is an important part of formation of neurites in developing neurons. Tropomodulin, a tropomyosin-dependent capping protein for the pointed end of the actin filament, is one of the key players in this process. Tropomodulin binds tropomyosin in two binding sites. Tmod1 and Tmod2, tropomodulin isoforms found in neurons, were overexpressed in PC12 cells, a model system for neuronal differentiation. Tmod1 did not affect neuronal differentiation; while cells expressing Tmod2 showed a significant reduction in the number and the length of neurites. Both tropomodulins bind short α-, γ- and δ-tropomyosin isoforms. Mutations in one of the tropomyosin-binding sites of Tmod1, which increased its affinity to short γ- and δ-tropomyosin isoforms, caused a decrease in binding short α-tropomyosin isoforms along with a 2-fold decrease in the length of neurites. Our data demonstrate that Tmod1 is involved in neuronal differentiation for proper neurite formation and outgrowth, and that Tmod2 inhibits these processes. The mutations in the tropomyosin-binding site of Tmod1 impair neurite outgrowth, suggesting that the integrity of this binding site is critical for the proper function of Tmod1 during neuronal differentiation.
format: application/pdf
format: text/html
creator: Natalia Moroz
creator: Laurent Guillaud
creator: Brinda Desai
creator: Alla S. Kostyukova
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.7
publisher: PeerJ Inc.
rights: © 2013 Moroz et al.
abstract: Assembly of the actin cytoskeleton is an important part of formation of neurites in developing neurons. Tropomodulin, a tropomyosin-dependent capping protein for the pointed end of the actin filament, is one of the key players in this process. Tropomodulin binds tropomyosin in two binding sites. Tmod1 and Tmod2, tropomodulin isoforms found in neurons, were overexpressed in PC12 cells, a model system for neuronal differentiation. Tmod1 did not affect neuronal differentiation; while cells expressing Tmod2 showed a significant reduction in the number and the length of neurites. Both tropomodulins bind short α-, γ- and δ-tropomyosin isoforms. Mutations in one of the tropomyosin-binding sites of Tmod1, which increased its affinity to short γ- and δ-tropomyosin isoforms, caused a decrease in binding short α-tropomyosin isoforms along with a 2-fold decrease in the length of neurites. Our data demonstrate that Tmod1 is involved in neuronal differentiation for proper neurite formation and outgrowth, and that Tmod2 inhibits these processes. The mutations in the tropomyosin-binding site of Tmod1 impair neurite outgrowth, suggesting that the integrity of this binding site is critical for the proper function of Tmod1 during neuronal differentiation.
bibliographic citation: Moroz et al. (2013) Mutations changing tropomodulin affinity for tropomyosin alter neurite formation and extension. PeerJ 1:e7 https://doi.org/10.7717/peerj.7
date submitted: 2012-11-12
date accepted: 2012-12-15
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Moroz
  given name: Natalia
author list: Agent
  family name: Guillaud
  given name: Laurent
author list: Agent
  family name: Desai
  given name: Brinda
author list: Agent
  family name: Kostyukova
  given name: Alla S.
doi: 10.7717/peerj.7
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Moroz et al.
attribution name: Moroz et al.

Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing
type: item
type: AcademicArticle
description: Background. Inherited BRCA gene mutations convey a high risk for breast and ovarian cancer, but current guidelines limit BRCA mutation testing to women with early-onset cancer and relatives of mutation-positive cases. Benefits and risks of providing this information directly to consumers are unknown. Methods. To assess and quantify emotional and behavioral reactions of consumers to their 23andMe Personal Genome Service® report of three BRCA mutations that are common in Ashkenazi Jews, we invited all 136 BRCA1 and BRCA2 mutation-positive individuals in the 23andMe customer database who had chosen to view their BRCA reports to participate in this IRB-approved study. We also invited 160 mutation-negative customers who were matched for age, sex and ancestry. Semi-structured phone interviews were completed for 32 mutation carriers, 16 women and 16 men, and 31 non-carriers. Questions addressed personal and family history of cancer, decision and timing of viewing the BRCA report, recollection of the result, emotional responses, perception of personal cancer risk, information sharing, and actions taken or planned. Results. Eleven women and 14 men had received the unexpected result that they are carriers of a BRCA1 185delAG or 5382insC, or BRCA2 6174delT mutation. None of them reported extreme anxiety and four experienced moderate anxiety that was transitory. Remarkably, five women and six men described their response as neutral. Most carrier women sought medical advice and four underwent risk-reducing procedures after confirmatory mutation testing. Male carriers realized that their test results implied genetic risk for female relatives, and several of them felt considerably burdened by this fact. Sharing mutation information with family members led to screening of at least 30 relatives and identification of 13 additional carriers. Non-carriers did not report inappropriate actions, such as foregoing cancer screening. All but one of the 32 mutation-positive participants appre…
format: application/pdf
format: text/html
creator: Uta Francke
creator: Cheri Dijamco
creator: Amy K. Kiefer
creator: Nicholas Eriksson
creator: Bianca Moiseff
creator: Joyce Y. Tung
creator: Joanna L. Mountain
subject: Genetics
subject: Genomics
subject: Medical Genetics
subject: Ethical Issues
description: doi:10.7717/peerj.8
publisher: PeerJ Inc.
rights: © 2013 Francke et al.
abstract: Background. Inherited BRCA gene mutations convey a high risk for breast and ovarian cancer, but current guidelines limit BRCA mutation testing to women with early-onset cancer and relatives of mutation-positive cases. Benefits and risks of providing this information directly to consumers are unknown. Methods. To assess and quantify emotional and behavioral reactions of consumers to their 23andMe Personal Genome Service® report of three BRCA mutations that are common in Ashkenazi Jews, we invited all 136 BRCA1 and BRCA2 mutation-positive individuals in the 23andMe customer database who had chosen to view their BRCA reports to participate in this IRB-approved study. We also invited 160 mutation-negative customers who were matched for age, sex and ancestry. Semi-structured phone interviews were completed for 32 mutation carriers, 16 women and 16 men, and 31 non-carriers. Questions addressed personal and family history of cancer, decision and timing of viewing the BRCA report, recollection of the result, emotional responses, perception of personal cancer risk, information sharing, and actions taken or planned. Results. Eleven women and 14 men had received the unexpected result that they are carriers of a BRCA1 185delAG or 5382insC, or BRCA2 6174delT mutation. None of them reported extreme anxiety and four experienced moderate anxiety that was transitory. Remarkably, five women and six men described their response as neutral. Most carrier women sought medical advice and four underwent risk-reducing procedures after confirmatory mutation testing. Male carriers realized that their test results implied genetic risk for female relatives, and several of them felt considerably burdened by this fact. Sharing mutation information with family members led to screening of at least 30 relatives and identification of 13 additional carriers. Non-carriers did not report inappropriate actions, such as foregoing cancer screening. All but one of the 32 mutation-positive participants appre…
bibliographic citation: Francke et al. (2013) Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing. PeerJ 1:e8 https://doi.org/10.7717/peerj.8
date submitted: 2012-11-13
date accepted: 2012-12-23
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Francke
  given name: Uta
author list: Agent
  family name: Dijamco
  given name: Cheri
author list: Agent
  family name: Kiefer
  given name: Amy K.
author list: Agent
  family name: Eriksson
  given name: Nicholas
author list: Agent
  family name: Moiseff
  given name: Bianca
author list: Agent
  family name: Tung
  given name: Joyce Y.
author list: Agent
  family name: Mountain
  given name: Joanna L.
doi: 10.7717/peerj.8
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Francke et al.
attribution name: Francke et al.

Soil carbon determination by thermogravimetrics
type: item
type: AcademicArticle
description: Determination of soil constituents and structure has a vital role in agriculture generally. Methods for the determination of soil carbon have in particular gained greater currency in recent times because of the potential that soils offer in providing offsets for greenhouse gas (CO2-equivalent) emissions. Ideally, soil carbon which can also be quite diverse in its makeup and origin, should be measureable by readily accessible, affordable and reliable means. Loss-on-ignition is still a widely used method being suitably simple and available but may have limitations for soil C monitoring. How can these limitations be better defined and understood where such a method is required to detect relatively small changes during soil-C building? Thermogravimetric (TGA) instrumentation to measure carbonaceous components has become more interesting because of its potential to separate carbon and other components using very precise and variable heating programs. TGA related studies were undertaken to assist our understanding in the quantification of soil carbon when using methods such as loss-on-ignition. Combining instrumentation so that mass changes can be monitored by mass spectrometer ion currents has elucidated otherwise hidden features of thermal methods enabling the interpretation and evaluation of mass-loss patterns. Soil thermogravimetric work has indicated that loss-on-ignition methods are best constrained to temperatures from 200 to 430 °C for reliable determination for soil organic carbon especially where clay content is higher. In the absence of C-specific detection where mass only changes are relied upon, exceeding this temperature incurs increasing contributions from inorganic sources adding to mass losses with diminishing contributions related to organic matter. The smaller amounts of probably more recalcitrant organic matter released at the higher temperatures may represent mineral associated material and/or simply more refractory forms.
format: application/pdf
format: text/html
creator: Robert Pallasser
creator: Budiman Minasny
creator: Alex B. McBratney
subject: Soil Science
description: doi:10.7717/peerj.6
publisher: PeerJ Inc.
rights: © 2013 Pallasser et al.
abstract: Determination of soil constituents and structure has a vital role in agriculture generally. Methods for the determination of soil carbon have in particular gained greater currency in recent times because of the potential that soils offer in providing offsets for greenhouse gas (CO2-equivalent) emissions. Ideally, soil carbon which can also be quite diverse in its makeup and origin, should be measureable by readily accessible, affordable and reliable means. Loss-on-ignition is still a widely used method being suitably simple and available but may have limitations for soil C monitoring. How can these limitations be better defined and understood where such a method is required to detect relatively small changes during soil-C building? Thermogravimetric (TGA) instrumentation to measure carbonaceous components has become more interesting because of its potential to separate carbon and other components using very precise and variable heating programs. TGA related studies were undertaken to assist our understanding in the quantification of soil carbon when using methods such as loss-on-ignition. Combining instrumentation so that mass changes can be monitored by mass spectrometer ion currents has elucidated otherwise hidden features of thermal methods enabling the interpretation and evaluation of mass-loss patterns. Soil thermogravimetric work has indicated that loss-on-ignition methods are best constrained to temperatures from 200 to 430 °C for reliable determination for soil organic carbon especially where clay content is higher. In the absence of C-specific detection where mass only changes are relied upon, exceeding this temperature incurs increasing contributions from inorganic sources adding to mass losses with diminishing contributions related to organic matter. The smaller amounts of probably more recalcitrant organic matter released at the higher temperatures may represent mineral associated material and/or simply more refractory forms.
bibliographic citation: Pallasser et al. (2013) Soil carbon determination by thermogravimetrics. PeerJ 1:e6 https://doi.org/10.7717/peerj.6
date submitted: 2012-11-13
date accepted: 2012-12-08
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Pallasser
  given name: Robert
author list: Agent
  family name: Minasny
  given name: Budiman
author list: Agent
  family name: McBratney
  given name: Alex B.
doi: 10.7717/peerj.6
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Pallasser et al.
attribution name: Pallasser et al.

Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences
type: item
type: AcademicArticle
description: Fragments of prostatic acid phosphatase (PAP248-286) in human semen dramatically increase HIV infection efficiency by increasing virus adhesion to target cells. PAP248-286 only enhances HIV infection in the form of amyloid aggregates termed SEVI (Semen Enhancer of Viral Infection), however monomeric PAP248-286 aggregates very slowly in isolation. It has therefore been suggested that SEVI fiber formation in vivo may be promoted by exogenous factors. We show here that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus) infection. Kinetic analysis of the cross-seeding effect shows an unusual pattern. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP (islet amyloid polypeptide) and Aβ1−40) with curli showed varied results. Curli cross-seeding decreased the lag-time of IAPP amyloid formation but strongly inhibited IAPP elongation. Curli cross-seeding exerted a complicated concentration dependent effect on Aβ1−40 fibrillogenesis kinetics. Combined, these results suggest that the interaction of amyloidogenic proteins with preformed fibers of a different type can take a variety of forms and is not limited to epitaxial nucleation between proteins of similar sequence. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross-seeding may be a more general phenomenon than previously supposed.
format: application/pdf
format: text/html
creator: Kevin Hartman
creator: Jeffrey R. Brender
creator: Kazuaki Monde
creator: Akira Ono
creator: Margery L. Evans
creator: Nataliya Popovych
creator: Matthew R. Chapman
creator: Ayyalusamy Ramamoorthy
subject: Biochemistry
subject: Biophysics
description: doi:10.7717/peerj.5
publisher: PeerJ Inc.
rights: © 2013 Hartman et al.
abstract: Fragments of prostatic acid phosphatase (PAP248-286) in human semen dramatically increase HIV infection efficiency by increasing virus adhesion to target cells. PAP248-286 only enhances HIV infection in the form of amyloid aggregates termed SEVI (Semen Enhancer of Viral Infection), however monomeric PAP248-286 aggregates very slowly in isolation. It has therefore been suggested that SEVI fiber formation in vivo may be promoted by exogenous factors. We show here that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus) infection. Kinetic analysis of the cross-seeding effect shows an unusual pattern. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP (islet amyloid polypeptide) and Aβ1−40) with curli showed varied results. Curli cross-seeding decreased the lag-time of IAPP amyloid formation but strongly inhibited IAPP elongation. Curli cross-seeding exerted a complicated concentration dependent effect on Aβ1−40 fibrillogenesis kinetics. Combined, these results suggest that the interaction of amyloidogenic proteins with preformed fibers of a different type can take a variety of forms and is not limited to epitaxial nucleation between proteins of similar sequence. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross-seeding may be a more general phenomenon than previously supposed.
bibliographic citation: Hartman et al. (2013) Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences. PeerJ 1:e5 https://doi.org/10.7717/peerj.5
date submitted: 2012-11-14
date accepted: 2012-12-05
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Hartman
  given name: Kevin
author list: Agent
  family name: Brender
  given name: Jeffrey R.
author list: Agent
  family name: Monde
  given name: Kazuaki
author list: Agent
  family name: Ono
  given name: Akira
author list: Agent
  family name: Evans
  given name: Margery L.
author list: Agent
  family name: Popovych
  given name: Nataliya
author list: Agent
  family name: Chapman
  given name: Matthew R.
author list: Agent
  family name: Ramamoorthy
  given name: Ayyalusamy
doi: 10.7717/peerj.5
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Hartman et al.
attribution name: Hartman et al.

The roles of STP and LTP in synaptic encoding
type: item
type: AcademicArticle
description: Long-term potentiation (LTP), a cellular model of learning and memory, is generally regarded as a unitary phenomenon that alters the strength of synaptic transmission by increasing the postsynaptic response to the release of a quantum of neurotransmitter. LTP, at CA3-CA1 synapses in the hippocampus, contains a stimulation-labile phase of short-term potentiation (STP, or transient LTP, t-LTP) that decays into stable LTP. By studying the responses of populations of neurons to brief bursts of high-frequency afferent stimulation before and after the induction of LTP, we found that synaptic responses during bursts are potentiated equally during LTP but not during STP. We show that STP modulates the frequency response of synaptic transmission whereas LTP preserves the fidelity. Thus, STP and LTP have different functional consequences for the transfer of synaptic information.
format: application/pdf
format: text/html
creator: Arturas Volianskis
creator: Graham L. Collingridge
creator: Morten S. Jensen
subject: Neuroscience
description: doi:10.7717/peerj.3
publisher: PeerJ Inc.
rights: © 2013 Volianskis et al.
abstract: Long-term potentiation (LTP), a cellular model of learning and memory, is generally regarded as a unitary phenomenon that alters the strength of synaptic transmission by increasing the postsynaptic response to the release of a quantum of neurotransmitter. LTP, at CA3-CA1 synapses in the hippocampus, contains a stimulation-labile phase of short-term potentiation (STP, or transient LTP, t-LTP) that decays into stable LTP. By studying the responses of populations of neurons to brief bursts of high-frequency afferent stimulation before and after the induction of LTP, we found that synaptic responses during bursts are potentiated equally during LTP but not during STP. We show that STP modulates the frequency response of synaptic transmission whereas LTP preserves the fidelity. Thus, STP and LTP have different functional consequences for the transfer of synaptic information.
bibliographic citation: Volianskis et al. (2013) The roles of STP and LTP in synaptic encoding. PeerJ 1:e3 https://doi.org/10.7717/peerj.3
date submitted: 2012-11-13
date accepted: 2012-12-03
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Volianskis
  given name: Arturas
author list: Agent
  family name: Collingridge
  given name: Graham L.
author list: Agent
  family name: Jensen
  given name: Morten S.
doi: 10.7717/peerj.3
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Volianskis et al.
attribution name: Volianskis et al.

Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
type: item
type: AcademicArticle
description: Recent studies revealed that a significant fraction of any given proteome is presented by proteins that do not have unique 3D structures as a whole or in significant parts. These intrinsically disordered proteins possess dramatic structural and functional variability, being especially enriched in signaling and regulatory functions since their lack of fixed structure defines their ability to be involved in interaction with several proteins and allows them to be re-used in multiple pathways. Among recognized disorder-based protein functions are interactions with nucleic acids and multi-target binding; i.e., the functions ascribed to many spliceosomal proteins. Therefore, the spliceosome, a multimegadalton ribonucleoprotein machine catalyzing the excision of introns from eukaryotic pre-mRNAs, represents an attractive target for the focused analysis of the abundance and functionality of intrinsic disorder in its proteinaceous components. In yeast cells, spliceosome consists of five small nuclear RNAs (U1, U2, U4, U5, and U6) and a range of associated proteins. Some of these proteins constitute cores of the corresponding snRNA-protein complexes known as small nuclear ribonucleoproteins (snRNPs). Other spliceosomal proteins have various auxiliary functions. To gain better understanding of the functional roles of intrinsic disorder, we have studied the prevalence of intrinsically disordered proteins in the yeast spliceosome using a wide array of bioinformatics methods. Our study revealed that similar to the proteins associated with human spliceosomes (Korneta & Bujnicki, 2012), proteins found in the yeast spliceosome are enriched in intrinsic disorder.
format: application/pdf
format: text/html
creator: Maria de Lourdes Coelho Ribeiro
creator: Julio Espinosa
creator: Sameen Islam
creator: Osvaldo Martinez
creator: Jayesh Jamnadas Thanki
creator: Stephanie Mazariegos
creator: Tam Nguyen
creator: Maya Larina
creator: Bin Xue
creator: Vladimir N. Uversky
subject: Biochemistry
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.2
publisher: PeerJ Inc.
rights: © 2013 Coelho Ribeiro et al.
abstract: Recent studies revealed that a significant fraction of any given proteome is presented by proteins that do not have unique 3D structures as a whole or in significant parts. These intrinsically disordered proteins possess dramatic structural and functional variability, being especially enriched in signaling and regulatory functions since their lack of fixed structure defines their ability to be involved in interaction with several proteins and allows them to be re-used in multiple pathways. Among recognized disorder-based protein functions are interactions with nucleic acids and multi-target binding; i.e., the functions ascribed to many spliceosomal proteins. Therefore, the spliceosome, a multimegadalton ribonucleoprotein machine catalyzing the excision of introns from eukaryotic pre-mRNAs, represents an attractive target for the focused analysis of the abundance and functionality of intrinsic disorder in its proteinaceous components. In yeast cells, spliceosome consists of five small nuclear RNAs (U1, U2, U4, U5, and U6) and a range of associated proteins. Some of these proteins constitute cores of the corresponding snRNA-protein complexes known as small nuclear ribonucleoproteins (snRNPs). Other spliceosomal proteins have various auxiliary functions. To gain better understanding of the functional roles of intrinsic disorder, we have studied the prevalence of intrinsically disordered proteins in the yeast spliceosome using a wide array of bioinformatics methods. Our study revealed that similar to the proteins associated with human spliceosomes (Korneta & Bujnicki, 2012), proteins found in the yeast spliceosome are enriched in intrinsic disorder.
bibliographic citation: Coelho Ribeiro et al. (2013) Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome. PeerJ 1:e2 https://doi.org/10.7717/peerj.2
date submitted: 2012-11-13
date accepted: 2012-12-01
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Coelho Ribeiro
  given name: Maria de Lourdes
author list: Agent
  family name: Espinosa
  given name: Julio
author list: Agent
  family name: Islam
  given name: Sameen
author list: Agent
  family name: Martinez
  given name: Osvaldo
author list: Agent
  family name: Thanki
  given name: Jayesh Jamnadas
author list: Agent
  family name: Mazariegos
  given name: Stephanie
author list: Agent
  family name: Nguyen
  given name: Tam
author list: Agent
  family name: Larina
  given name: Maya
author list: Agent
  family name: Xue
  given name: Bin
author list: Agent
  family name: Uversky
  given name: Vladimir N.
doi: 10.7717/peerj.2
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Coelho Ribeiro et al.
attribution name: Coelho Ribeiro et al.

How long is a piece of loop?
type: item
type: AcademicArticle
description: Loops are irregular structures which connect two secondary structure elements in proteins. They often play important roles in function, including enzyme reactions and ligand binding. Despite their importance, their structure remains difficult to predict. Most protein loop structure prediction methods sample local loop segments and score them. In particular protein loop classifications and database search methods depend heavily on local properties of loops. Here we examine the distance between a loop’s end points (span). We find that the distribution of loop span appears to be independent of the number of residues in the loop, in other words the separation between the anchors of a loop does not increase with an increase in the number of loop residues. Loop span is also unaffected by the secondary structures at the end points, unless the two anchors are part of an anti-parallel beta sheet. As loop span appears to be independent of global properties of the protein we suggest that its distribution can be described by a random fluctuation model based on the Maxwell–Boltzmann distribution. It is believed that the primary difficulty in protein loop structure prediction comes from the number of residues in the loop. Following the idea that loop span is an independent local property, we investigate its effect on protein loop structure prediction and show how normalised span (loop stretch) is related to the structural complexity of loops. Highly contracted loops are more difficult to predict than stretched loops.
format: application/pdf
format: text/html
creator: Yoonjoo Choi
creator: Sumeet Agarwal
creator: Charlotte M. Deane
subject: Biochemistry
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
description: doi:10.7717/peerj.1
publisher: PeerJ Inc.
rights: © 2013 Choi et al.
abstract: Loops are irregular structures which connect two secondary structure elements in proteins. They often play important roles in function, including enzyme reactions and ligand binding. Despite their importance, their structure remains difficult to predict. Most protein loop structure prediction methods sample local loop segments and score them. In particular protein loop classifications and database search methods depend heavily on local properties of loops. Here we examine the distance between a loop’s end points (span). We find that the distribution of loop span appears to be independent of the number of residues in the loop, in other words the separation between the anchors of a loop does not increase with an increase in the number of loop residues. Loop span is also unaffected by the secondary structures at the end points, unless the two anchors are part of an anti-parallel beta sheet. As loop span appears to be independent of global properties of the protein we suggest that its distribution can be described by a random fluctuation model based on the Maxwell–Boltzmann distribution. It is believed that the primary difficulty in protein loop structure prediction comes from the number of residues in the loop. Following the idea that loop span is an independent local property, we investigate its effect on protein loop structure prediction and show how normalised span (loop stretch) is related to the structural complexity of loops. Highly contracted loops are more difficult to predict than stretched loops.
bibliographic citation: Choi et al. (2013) How long is a piece of loop?. PeerJ 1:e1 https://doi.org/10.7717/peerj.1
date submitted: 2012-11-13
date accepted: 2012-11-21
issued: 2013-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Choi
  given name: Yoonjoo
author list: Agent
  family name: Agarwal
  given name: Sumeet
author list: Agent
  family name: Deane
  given name: Charlotte M.
doi: 10.7717/peerj.1
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-02-12
copyright: © 2013 Choi et al.
attribution name: Choi et al.

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