PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Sports training enhances visuo-spatial cognition regardless of open-closed typology
items: pathVar: a new method for pathway-based interpretation of gene expression variability
items: Comparison in antioxidant and antitumor activities of pine polyphenols and its seven biotransformation extracts by fungi
items: A mixed methods study of multiple health behaviors among individuals with stroke
items: A comparison of freezing-damage during isochoric and isobaric freezing of the potato
items: StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
items: Exoskeleton may influence the internal body temperatures of Neotropical dung beetles (Col. Scarabaeinae)
items: Atorvastatin alters the expression of genes related to bile acid metabolism and circadian clock in livers of mice
items: Predictive ability of the Mini Nutritional Assessment Short Form (MNA-SF) in a free-living elderly population: a cross-sectional study
items: Comparative transcriptome analyses of a late-maturing mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit maturation

Sports training enhances visuo-spatial cognition regardless of open-closed typology
type: item
type: AcademicArticle
description: The aim of this study was to investigate the effects of open and closed sport participation on visuo-spatial attention and memory performance among young adults. Forty-eight young adults—16 open-skill athletes, 16 closed-skill athletes, and 16 non-athletes controls—were recruited for the study. Both behavioral performance and event-related potential (ERP) measurement were assessed when participants performed non-delayed and delayed match-to-sample task that tested visuo-spatial attention and memory processing. Results demonstrated that regardless of training typology, the athlete groups exhibited shorter reaction times in both the visuo-spatial attention and memory conditions than the control group with no existence of speed-accuracy trade-off. Similarly, a larger P3 amplitudes were observed in both athlete groups than in the control group for the visuo-spatial memory condition. These findings suggest that sports training, regardless of typology, are associated with superior visuo-spatial attention and memory performance, and more efficient neural resource allocation in memory processing.
format: application/pdf
format: text/html
creator: Ting-Yu Chueh
creator: Chung-Ju Huang
creator: Shu-Shih Hsieh
creator: Kuan-Fu Chen
creator: Yu-Kai Chang
creator: Tsung-Min Hung
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3336
publisher: PeerJ Inc.
rights: © 2017 Chueh et al.
abstract: The aim of this study was to investigate the effects of open and closed sport participation on visuo-spatial attention and memory performance among young adults. Forty-eight young adults—16 open-skill athletes, 16 closed-skill athletes, and 16 non-athletes controls—were recruited for the study. Both behavioral performance and event-related potential (ERP) measurement were assessed when participants performed non-delayed and delayed match-to-sample task that tested visuo-spatial attention and memory processing. Results demonstrated that regardless of training typology, the athlete groups exhibited shorter reaction times in both the visuo-spatial attention and memory conditions than the control group with no existence of speed-accuracy trade-off. Similarly, a larger P3 amplitudes were observed in both athlete groups than in the control group for the visuo-spatial memory condition. These findings suggest that sports training, regardless of typology, are associated with superior visuo-spatial attention and memory performance, and more efficient neural resource allocation in memory processing.
bibliographic citation: Chueh et al. (2017) Sports training enhances visuo-spatial cognition regardless of open-closed typology. PeerJ 5:e3336 https://doi.org/10.7717/peerj.3336
date submitted: 2017-01-04
date accepted: 2017-04-19
issued: 2017-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chueh
  given name: Ting-Yu
author list: Agent
  family name: Huang
  given name: Chung-Ju
author list: Agent
  family name: Hsieh
  given name: Shu-Shih
author list: Agent
  family name: Chen
  given name: Kuan-Fu
author list: Agent
  family name: Chang
  given name: Yu-Kai
author list: Agent
  family name: Hung
  given name: Tsung-Min
doi: 10.7717/peerj.3336
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-23
copyright: ©2017 Chueh et al.
attribution name: Chueh et al.

pathVar: a new method for pathway-based interpretation of gene expression variability
type: item
type: AcademicArticle
description: Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression can highlight important genes that are under different degrees of regulatory control. Simple statistical tests exist to identify differentially-variable genes; however, methods for investigating how changes in gene expression variability in the context of pathways and gene sets are under-explored. Here we present pathVar, a new method that provides functional interpretation of gene expression variability changes at the level of pathways and gene sets. pathVar is based on a multinomial exact test, or an asymptotic Chi-squared test as a more computationally-efficient alternative. The method can be used for gene expression studies from any technology platform in all biological settings either with a single phenotypic group, or two-group comparisons. To demonstrate its utility, we applied the method to a diverse set of diseases, species and samples. Results from pathVar are benchmarked against analyses based on average expression and two methods of GSEA, and demonstrate that analyses using both statistics are useful for understanding transcriptional regulation. We also provide recommendations for the choice of variability statistic that have been informed through analyses on simulations and real data. Based on the datasets selected, we show how pathVar can be used to gain insight into expression variability of single cell versus bulk samples, different stem cell populations, and cancer versus normal tissue comparisons.
format: application/pdf
format: text/html
creator: Laurence de Torrente
creator: Samuel Zimmerman
creator: Deanne Taylor
creator: Yu Hasegawa
creator: Christine A. Wells
creator: Jessica C. Mar
subject: Bioinformatics
subject: Cell Biology
subject: Statistics
description: doi:10.7717/peerj.3334
publisher: PeerJ Inc.
rights: © 2017 de Torrente et al.
abstract: Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression can highlight important genes that are under different degrees of regulatory control. Simple statistical tests exist to identify differentially-variable genes; however, methods for investigating how changes in gene expression variability in the context of pathways and gene sets are under-explored. Here we present pathVar, a new method that provides functional interpretation of gene expression variability changes at the level of pathways and gene sets. pathVar is based on a multinomial exact test, or an asymptotic Chi-squared test as a more computationally-efficient alternative. The method can be used for gene expression studies from any technology platform in all biological settings either with a single phenotypic group, or two-group comparisons. To demonstrate its utility, we applied the method to a diverse set of diseases, species and samples. Results from pathVar are benchmarked against analyses based on average expression and two methods of GSEA, and demonstrate that analyses using both statistics are useful for understanding transcriptional regulation. We also provide recommendations for the choice of variability statistic that have been informed through analyses on simulations and real data. Based on the datasets selected, we show how pathVar can be used to gain insight into expression variability of single cell versus bulk samples, different stem cell populations, and cancer versus normal tissue comparisons.
bibliographic citation: de Torrente et al. (2017) pathVar: a new method for pathway-based interpretation of gene expression variability. PeerJ 5:e3334 https://doi.org/10.7717/peerj.3334
date submitted: 2016-09-30
date accepted: 2017-04-18
issued: 2017-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Torrente
  given name: Laurence
author list: Agent
  family name: Zimmerman
  given name: Samuel
author list: Agent
  family name: Taylor
  given name: Deanne
author list: Agent
  family name: Hasegawa
  given name: Yu
author list: Agent
  family name: Wells
  given name: Christine A.
author list: Agent
  family name: Mar
  given name: Jessica C.
doi: 10.7717/peerj.3334
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-23
copyright: ©2017 de Torrente et al.
attribution name: de Torrente et al.

Comparison in antioxidant and antitumor activities of pine polyphenols and its seven biotransformation extracts by fungi
type: item
type: AcademicArticle
description: Microbial transformation can strengthen the antioxidant and antitumor activities of polyphenols. Polyphenols contents, antioxidant and antitumor activities of pine polyphenols and its biotransformation extracts by Aspergillus niger, Aspergillus oryzae, Aspergillus carbonarius, Aspergillus candidus, Trichodermas viride, Mucor wutungkiao and Rhizopus sp were studied. Significant differences were noted in antioxidant and antitumor activities. The highest antioxidant activities in Trolox equivalent antioxidant capacity (TEAC), DPPH radical scavenging activity, superoxide anion radical scavenging activity, hydroxyl radical scavenging activity, reducing power assay and antitumor activity against LoVo cells were biotransformation extract of Aspergillus carbonarius (BAC), biotransformation extract of Mucor wutungkiao (BMW), biotransformation extract of Aspergillus carbonarius (BAC), biotransformation extract of Aspergillus niger (BAN), biotransformation extract of Aspergillus oryzae (BAO) and BMW, respectively. Correlation analysis found that antioxidant and antitumor activities were associated with polyphenols contents and types of free radicals and tumors. A. carbonarius can make polyphenol oxidation, hydroxylation and methylation, and form new polyphenols. In conclusion, A. carbonarius, A. niger and M. wutungkiao are valuable microorganisms used for polyphenols biotransformation and enhance the antioxidant and antitumor activities of polyphenols.
format: application/pdf
format: text/html
creator: Hui Li
creator: Zhenyu Wang
subject: Agricultural Science
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.3264
publisher: PeerJ Inc.
rights: © 2017 Li and Wang
abstract: Microbial transformation can strengthen the antioxidant and antitumor activities of polyphenols. Polyphenols contents, antioxidant and antitumor activities of pine polyphenols and its biotransformation extracts by Aspergillus niger, Aspergillus oryzae, Aspergillus carbonarius, Aspergillus candidus, Trichodermas viride, Mucor wutungkiao and Rhizopus sp were studied. Significant differences were noted in antioxidant and antitumor activities. The highest antioxidant activities in Trolox equivalent antioxidant capacity (TEAC), DPPH radical scavenging activity, superoxide anion radical scavenging activity, hydroxyl radical scavenging activity, reducing power assay and antitumor activity against LoVo cells were biotransformation extract of Aspergillus carbonarius (BAC), biotransformation extract of Mucor wutungkiao (BMW), biotransformation extract of Aspergillus carbonarius (BAC), biotransformation extract of Aspergillus niger (BAN), biotransformation extract of Aspergillus oryzae (BAO) and BMW, respectively. Correlation analysis found that antioxidant and antitumor activities were associated with polyphenols contents and types of free radicals and tumors. A. carbonarius can make polyphenol oxidation, hydroxylation and methylation, and form new polyphenols. In conclusion, A. carbonarius, A. niger and M. wutungkiao are valuable microorganisms used for polyphenols biotransformation and enhance the antioxidant and antitumor activities of polyphenols.
bibliographic citation: Li et al. (2017) Comparison in antioxidant and antitumor activities of pine polyphenols and its seven biotransformation extracts by fungi. PeerJ 5:e3264 https://doi.org/10.7717/peerj.3264
date submitted: 2016-01-13
date accepted: 2017-04-02
issued: 2017-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hui
author list: Agent
  family name: Wang
  given name: Zhenyu
doi: 10.7717/peerj.3264
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-23
copyright: ©2017 Li and Wang
attribution name: Li and Wang

A mixed methods study of multiple health behaviors among individuals with stroke
type: item
type: AcademicArticle
description: Background Individuals with stroke often have multiple cardiovascular risk factors that necessitate promoting engagement in multiple health behaviors. However, observational studies of individuals with stroke have typically focused on promoting a single health behavior. Thus, there is a poor understanding of linkages between healthy behaviors and the circumstances in which factors, such as stroke impairments, may influence a single or multiple health behaviors. Methods We conducted a mixed methods convergent parallel study of 25 individuals with stroke to examine the relationships between stroke impairments and physical activity, sleep, and nutrition. Our goal was to gain further insight into possible strategies to promote multiple health behaviors among individuals with stroke. This study focused on physical activity, sleep, and nutrition because of their importance in achieving energy balance, maintaining a healthy weight, and reducing cardiovascular risks. Qualitative and quantitative data were collected concurrently, with the former being prioritized over the latter. Qualitative data was prioritized in order to develop a conceptual model of engagement in multiple health behaviors among individuals with stroke. Qualitative and quantitative data were analyzed independently and then were integrated during the inference stage to develop meta-inferences. The 25 individuals with stroke completed closed-ended questionnaires on healthy behaviors and physical function. They also participated in face-to-face focus groups and one-to-one phone interviews. Results We found statistically significant and moderate correlations between hand function and healthy eating habits (r = 0.45), sleep disturbances and limitations in activities of daily living (r = − 0.55), BMI and limitations in activities of daily living (r = − 0.49), physical activity and limitations in activities of daily living (r = 0.41), mobility impairments and BMI (r = − 0.41), sleep disturbances and physical act…
format: application/pdf
format: text/html
creator: Matthew Plow
creator: Shirley M. Moore
creator: Martha Sajatovic
creator: Irene Katzan
subject: Neurology
subject: Nursing
subject: Nutrition
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.3210
publisher: PeerJ Inc.
rights: © 2017 Plow et al.
abstract: Background Individuals with stroke often have multiple cardiovascular risk factors that necessitate promoting engagement in multiple health behaviors. However, observational studies of individuals with stroke have typically focused on promoting a single health behavior. Thus, there is a poor understanding of linkages between healthy behaviors and the circumstances in which factors, such as stroke impairments, may influence a single or multiple health behaviors. Methods We conducted a mixed methods convergent parallel study of 25 individuals with stroke to examine the relationships between stroke impairments and physical activity, sleep, and nutrition. Our goal was to gain further insight into possible strategies to promote multiple health behaviors among individuals with stroke. This study focused on physical activity, sleep, and nutrition because of their importance in achieving energy balance, maintaining a healthy weight, and reducing cardiovascular risks. Qualitative and quantitative data were collected concurrently, with the former being prioritized over the latter. Qualitative data was prioritized in order to develop a conceptual model of engagement in multiple health behaviors among individuals with stroke. Qualitative and quantitative data were analyzed independently and then were integrated during the inference stage to develop meta-inferences. The 25 individuals with stroke completed closed-ended questionnaires on healthy behaviors and physical function. They also participated in face-to-face focus groups and one-to-one phone interviews. Results We found statistically significant and moderate correlations between hand function and healthy eating habits (r = 0.45), sleep disturbances and limitations in activities of daily living (r = − 0.55), BMI and limitations in activities of daily living (r = − 0.49), physical activity and limitations in activities of daily living (r = 0.41), mobility impairments and BMI (r = − 0.41), sleep disturbances and physical act…
bibliographic citation: Plow et al. (2017) A mixed methods study of multiple health behaviors among individuals with stroke. PeerJ 5:e3210 https://doi.org/10.7717/peerj.3210
date submitted: 2016-12-13
date accepted: 2017-03-21
issued: 2017-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Plow
  given name: Matthew
author list: Agent
  family name: Moore
  given name: Shirley M.
author list: Agent
  family name: Sajatovic
  given name: Martha
author list: Agent
  family name: Katzan
  given name: Irene
doi: 10.7717/peerj.3210
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-23
copyright: ©2017 Plow et al.
attribution name: Plow et al.

A comparison of freezing-damage during isochoric and isobaric freezing of the potato
type: item
type: AcademicArticle
description: Background Freezing is commonly used for food preservation. It is usually done under constant atmospheric pressure (isobaric). While extending the life of the produce, isobaric freezing has detrimental effects. It causes loss of food weight and changes in food quality. Using thermodynamic analysis, we have developed a theoretical model of the process of freezing in a constant volume system (isochoric). The mathematical model suggests that the detrimental effects associated with isobaric freezing may be reduced in an isochoric freezing system. To explore this hypothesis, we performed a preliminary study on the isochoric freezing of a produce with which our group has experience, the potato. Method Experiments were performed in an isochoric freezing device we designed. The device is robust and has no moving parts. For comparison, we used a geometrically identical isobaric freezing device. Following freezing and thawing, the samples were weighed, examined with colorimetry, and examined with microscopy. Results It was found that potatoes frozen to −5 °C in an isochoric system experienced no weight loss and limited enzymatic browning. In contrast the −5 °C isobaric frozen potato experienced substantial weight loss and substantial enzymatic browning. Microscopic analysis shows that the structural integrity of the potato is maintained after freezing in the isochoric system and impaired after freezing in the isobaric system. Discussion Tissue damage during isobaric freezing is caused by the increase in extracellular osmolality and the mechanical damage by ice crystals. Our thermodynamic analysis predicts that during isochoric freezing the intracellular osmolality remains comparable to the extracellular osmolality and that isochoric systems can be designed to eliminate the mechanical damage by ice. The results of this preliminary study seem to confirm the theoretical predictions. Conclusion This is a preliminary exploratory study on isochoric freezing of food. We have shown t…
format: application/pdf
format: text/html
creator: Chenang Lyu
creator: Gabriel Nastase
creator: Gideon Ukpai
creator: Alexandru Serban
creator: Boris Rubinsky
subject: Agricultural Science
subject: Biophysics
subject: Cell Biology
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.3322
publisher: PeerJ Inc.
rights: © 2017 Lyu et al.
abstract: Background Freezing is commonly used for food preservation. It is usually done under constant atmospheric pressure (isobaric). While extending the life of the produce, isobaric freezing has detrimental effects. It causes loss of food weight and changes in food quality. Using thermodynamic analysis, we have developed a theoretical model of the process of freezing in a constant volume system (isochoric). The mathematical model suggests that the detrimental effects associated with isobaric freezing may be reduced in an isochoric freezing system. To explore this hypothesis, we performed a preliminary study on the isochoric freezing of a produce with which our group has experience, the potato. Method Experiments were performed in an isochoric freezing device we designed. The device is robust and has no moving parts. For comparison, we used a geometrically identical isobaric freezing device. Following freezing and thawing, the samples were weighed, examined with colorimetry, and examined with microscopy. Results It was found that potatoes frozen to −5 °C in an isochoric system experienced no weight loss and limited enzymatic browning. In contrast the −5 °C isobaric frozen potato experienced substantial weight loss and substantial enzymatic browning. Microscopic analysis shows that the structural integrity of the potato is maintained after freezing in the isochoric system and impaired after freezing in the isobaric system. Discussion Tissue damage during isobaric freezing is caused by the increase in extracellular osmolality and the mechanical damage by ice crystals. Our thermodynamic analysis predicts that during isochoric freezing the intracellular osmolality remains comparable to the extracellular osmolality and that isochoric systems can be designed to eliminate the mechanical damage by ice. The results of this preliminary study seem to confirm the theoretical predictions. Conclusion This is a preliminary exploratory study on isochoric freezing of food. We have shown t…
bibliographic citation: Lyu et al. (2017) A comparison of freezing-damage during isochoric and isobaric freezing of the potato. PeerJ 5:e3322 https://doi.org/10.7717/peerj.3322
date submitted: 2017-01-18
date accepted: 2017-04-16
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lyu
  given name: Chenang
author list: Agent
  family name: Nastase
  given name: Gabriel
author list: Agent
  family name: Ukpai
  given name: Gideon
author list: Agent
  family name: Serban
  given name: Alexandru
author list: Agent
  family name: Rubinsky
  given name: Boris
doi: 10.7717/peerj.3322
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: © 2017 Lyu et al.
attribution name: Lyu et al.

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
type: item
type: AcademicArticle
description: Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. Results A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. Conclusion StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.
format: application/pdf
format: text/html
creator: Märt Roosaare
creator: Mihkel Vaher
creator: Lauris Kaplinski
creator: Märt Möls
creator: Reidar Andreson
creator: Maarja Lepamets
creator: Triinu Kõressaar
creator: Paul Naaber
creator: Siiri Kõljalg
creator: Maido Remm
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
description: doi:10.7717/peerj.3353
publisher: PeerJ Inc.
rights: © 2017 Roosaare et al.
abstract: Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. Results A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. Conclusion StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.
bibliographic citation: Roosaare et al. (2017) StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ 5:e3353 https://doi.org/10.7717/peerj.3353
date submitted: 2017-02-24
date accepted: 2017-04-26
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roosaare
  given name: Märt
author list: Agent
  family name: Vaher
  given name: Mihkel
author list: Agent
  family name: Kaplinski
  given name: Lauris
author list: Agent
  family name: Möls
  given name: Märt
author list: Agent
  family name: Andreson
  given name: Reidar
author list: Agent
  family name: Lepamets
  given name: Maarja
author list: Agent
  family name: Kõressaar
  given name: Triinu
author list: Agent
  family name: Naaber
  given name: Paul
author list: Agent
  family name: Kõljalg
  given name: Siiri
author list: Agent
  family name: Remm
  given name: Maido
doi: 10.7717/peerj.3353
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: © 2017 Roosaare et al.
attribution name: Roosaare et al.

Exoskeleton may influence the internal body temperatures of Neotropical dung beetles (Col. Scarabaeinae)
type: item
type: AcademicArticle
description: The insect exoskeleton is a multifunctional coat with a continuum of mechanical and structural properties constituting the barrier between electromagnetic waves and the internal body parts. This paper examines the ability of beetle exoskeleton to regulate internal body temperature considering its thermal permeability or isolation to simulated solar irradiance and infrared radiation. Seven Neotropical species of dung beetles (Coleoptera, Scarabaeinae) differing in colour, surface sculptures, size, sexual dimorphism, period of activity, guild category and altitudinal distribution were studied. Specimens were repeatedly subjected to heating trials under simulated solar irradiance and infrared radiation using a halogen neodymium bulb light with a balanced daylight spectrum and a ceramic infrared heat emitter. The volume of exoskeleton and its weight per volume unit were significantly more important for the heating rate at the beginning of the heating process than for the asymptotic maximum temperature reached at the end of the trials: larger beetles with relatively thicker exoskeletons heated more slowly. The source of radiation greatly influences the asymptotic temperature reached, but has a negligible effect in determining the rate of heat gain by beetles: they reached higher temperatures under artificial sunlight than under infrared radiation. Interspecific differences were negligible in the heating rate but had a large magnitude effect on the asymptotic temperature, only detectable under simulated sun irradiance. The fact that sun irradiance is differentially absorbed dorsally and transformed into heat among species opens the possibility that differences in dorsal exoskeleton would facilitate the heat gain under restrictive environmental temperatures below the preferred ones. The findings provided by this study support the important role played by the exoskeleton in the heating process of beetles, a cuticle able to act passively in the thermal control of body temper…
format: application/pdf
format: text/html
creator: Valentina Amore
creator: Malva I.M. Hernández
creator: Luis M. Carrascal
creator: Jorge M. Lobo
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.3349
publisher: PeerJ Inc.
rights: © 2017 Amore et al.
abstract: The insect exoskeleton is a multifunctional coat with a continuum of mechanical and structural properties constituting the barrier between electromagnetic waves and the internal body parts. This paper examines the ability of beetle exoskeleton to regulate internal body temperature considering its thermal permeability or isolation to simulated solar irradiance and infrared radiation. Seven Neotropical species of dung beetles (Coleoptera, Scarabaeinae) differing in colour, surface sculptures, size, sexual dimorphism, period of activity, guild category and altitudinal distribution were studied. Specimens were repeatedly subjected to heating trials under simulated solar irradiance and infrared radiation using a halogen neodymium bulb light with a balanced daylight spectrum and a ceramic infrared heat emitter. The volume of exoskeleton and its weight per volume unit were significantly more important for the heating rate at the beginning of the heating process than for the asymptotic maximum temperature reached at the end of the trials: larger beetles with relatively thicker exoskeletons heated more slowly. The source of radiation greatly influences the asymptotic temperature reached, but has a negligible effect in determining the rate of heat gain by beetles: they reached higher temperatures under artificial sunlight than under infrared radiation. Interspecific differences were negligible in the heating rate but had a large magnitude effect on the asymptotic temperature, only detectable under simulated sun irradiance. The fact that sun irradiance is differentially absorbed dorsally and transformed into heat among species opens the possibility that differences in dorsal exoskeleton would facilitate the heat gain under restrictive environmental temperatures below the preferred ones. The findings provided by this study support the important role played by the exoskeleton in the heating process of beetles, a cuticle able to act passively in the thermal control of body temper…
bibliographic citation: Amore et al. (2017) Exoskeleton may influence the internal body temperatures of Neotropical dung beetles (Col. Scarabaeinae). PeerJ 5:e3349 https://doi.org/10.7717/peerj.3349
date submitted: 2016-12-14
date accepted: 2017-04-24
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amore
  given name: Valentina
author list: Agent
  family name: Hernández
  given name: Malva I.M.
author list: Agent
  family name: Carrascal
  given name: Luis M.
author list: Agent
  family name: Lobo
  given name: Jorge M.
doi: 10.7717/peerj.3349
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Amore et al.
attribution name: Amore et al.

Atorvastatin alters the expression of genes related to bile acid metabolism and circadian clock in livers of mice
type: item
type: AcademicArticle
description: Aim Atorvastatin is a HMG-CoA reductase inhibitor used for hyperlipidemia. Atorvastatin is generally safe but may induce cholestasis. The present study aimed to examine the effects of atorvastatin on hepatic gene expression related to bile acid metabolism and homeostasis, as well as the expression of circadian clock genes in livers of mice. Methods Adult male mice were given atorvastatin (10, 30, and 100 mg/kg, po) daily for 30 days, and blood biochemistry, histopathology, and gene expression were examined. Results Repeated administration of atorvastatin did not affect animal body weight gain or liver weights. Serum enzyme activities were in the normal range. Histologically, the high dose of atorvastatin produced scattered swollen hepatocytes, foci of feathery-like degeneration, together with increased expression of Egr-1 and metallothionein-1. Atorvastatin increased the expression of Cyp7a1 in the liver, along with FXR and SHP. In contract, atorvastatin decreased the expression of bile acid transporters Ntcp, Bsep, Ostα, and Ostβ. The most dramatic change was the 30-fold induction of Cyp7a1. Because Cyp7a1 is a circadian clock-controlled gene, we further examined the effect of atorvastatin on clock gene expression. Atorvastatin increased the expression of clock core master genes Bmal1 and Npas2, decreased the expression of clock feedback genes Per2, Per3, and the clock targeted genes Dbp and Tef, whereas it had no effect on Cry1 and Nr1d1 expression. Conclusion Repeated administration of atorvastatin affects bile acid metabolism and markedly increases the expression of the bile acid synthesis rate-limiting enzyme gene Cyp7a1, together with alterations in the expression of circadian clock genes.
format: application/pdf
format: text/html
creator: Wen-Kai Li
creator: Huan Li
creator: Yuan-Fu Lu
creator: Ying-Ying Li
creator: Zidong Donna Fu
creator: Jie Liu
subject: Toxicology
subject: Pharmacology
description: doi:10.7717/peerj.3348
publisher: PeerJ Inc.
rights: © 2017 Li et al.
abstract: Aim Atorvastatin is a HMG-CoA reductase inhibitor used for hyperlipidemia. Atorvastatin is generally safe but may induce cholestasis. The present study aimed to examine the effects of atorvastatin on hepatic gene expression related to bile acid metabolism and homeostasis, as well as the expression of circadian clock genes in livers of mice. Methods Adult male mice were given atorvastatin (10, 30, and 100 mg/kg, po) daily for 30 days, and blood biochemistry, histopathology, and gene expression were examined. Results Repeated administration of atorvastatin did not affect animal body weight gain or liver weights. Serum enzyme activities were in the normal range. Histologically, the high dose of atorvastatin produced scattered swollen hepatocytes, foci of feathery-like degeneration, together with increased expression of Egr-1 and metallothionein-1. Atorvastatin increased the expression of Cyp7a1 in the liver, along with FXR and SHP. In contract, atorvastatin decreased the expression of bile acid transporters Ntcp, Bsep, Ostα, and Ostβ. The most dramatic change was the 30-fold induction of Cyp7a1. Because Cyp7a1 is a circadian clock-controlled gene, we further examined the effect of atorvastatin on clock gene expression. Atorvastatin increased the expression of clock core master genes Bmal1 and Npas2, decreased the expression of clock feedback genes Per2, Per3, and the clock targeted genes Dbp and Tef, whereas it had no effect on Cry1 and Nr1d1 expression. Conclusion Repeated administration of atorvastatin affects bile acid metabolism and markedly increases the expression of the bile acid synthesis rate-limiting enzyme gene Cyp7a1, together with alterations in the expression of circadian clock genes.
bibliographic citation: Li et al. (2017) Atorvastatin alters the expression of genes related to bile acid metabolism and circadian clock in livers of mice. PeerJ 5:e3348 https://doi.org/10.7717/peerj.3348
date submitted: 2017-01-17
date accepted: 2017-04-23
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wen-Kai
author list: Agent
  family name: Li
  given name: Huan
author list: Agent
  family name: Lu
  given name: Yuan-Fu
author list: Agent
  family name: Li
  given name: Ying-Ying
author list: Agent
  family name: Fu
  given name: Zidong Donna
author list: Agent
  family name: Liu
  given name: Jie
doi: 10.7717/peerj.3348
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Li et al.
attribution name: Li et al.

Predictive ability of the Mini Nutritional Assessment Short Form (MNA-SF) in a free-living elderly population: a cross-sectional study
type: item
type: AcademicArticle
description: Background Various scales have been used to perform a quick and first level nutritional assessment, and the MNA is one of the most used and recommended by experts in the elderly in all areas. This scale has a short form, the MNA-SF, revised and validated in 2009, which has two versions: the BMI-MNA-SF contains the first six items of the full scale including Body Mass Index while the CC-MNA-SF includes Calf Circumference instead of BMI. Objective To evaluate the predictive ability for nutritional status of the two versions of the MNA-SF against the MNA in free-living elderly in the province of Valencia. Methods Cross-sectional study of 660 free-living elderly in the province of Valencia selected in 12 community centres using stratified sampling by blocks. Inclusion criteria: being aged 65 or over, living at home, having functional autonomy, residing in the province of study for more than one year, regularly attending community centres and voluntarily wanting to take part. Results Of the 660 subjects studied, 319 were men (48.3%) and 341 (51.7%) women with a mean age of 74.3 years (SD = 6.6). In terms of nutritional assessment, using the BMI-MNA-SF and the CC-MNA-SF we found that 26.5% and 26.2% were at risk of malnutrition and 0.9% and 1.5% were malnourished respectively. With the full MNA, 23.3% were at risk of malnutrition. Spearman’s rank correlation coefficients indicate a high association between the full MNA score and the MNA-SFs scores (BMI-MNA-SF: ρ = 0.78p < 0.001; CC-MNA-SF: ρ = 0.78p < 0.001). In addition we obtained a very high correlation between the two MNA-SFs (ρ = 0.96p < 0.001). We evaluated the agreement between the full MNA and the MNA-SFs classification in three nutritional categories (normal nutritional status, risk of malnutrition, malnutrition) with Cohen’s kappa coefficients (BMI-MNA-SF: κ = 0.54p < 0.001; CC-MNA-SF: κ = 0.52p < 0.001). These values indicate moderate agreement with the full MNA. There is very good agreement between the BMI-MNA…
format: application/pdf
format: text/html
creator: Raimunda Montejano Lozoya
creator: Nieves Martínez-Alzamora
creator: Gonzalo Clemente Marín
creator: Silamani J.A. Guirao-Goris
creator: Rosa María Ferrer-Diego
subject: Geriatrics
subject: Nursing
subject: Nutrition
description: doi:10.7717/peerj.3345
publisher: PeerJ Inc.
rights: © 2017 Montejano Lozoya et al.
abstract: Background Various scales have been used to perform a quick and first level nutritional assessment, and the MNA is one of the most used and recommended by experts in the elderly in all areas. This scale has a short form, the MNA-SF, revised and validated in 2009, which has two versions: the BMI-MNA-SF contains the first six items of the full scale including Body Mass Index while the CC-MNA-SF includes Calf Circumference instead of BMI. Objective To evaluate the predictive ability for nutritional status of the two versions of the MNA-SF against the MNA in free-living elderly in the province of Valencia. Methods Cross-sectional study of 660 free-living elderly in the province of Valencia selected in 12 community centres using stratified sampling by blocks. Inclusion criteria: being aged 65 or over, living at home, having functional autonomy, residing in the province of study for more than one year, regularly attending community centres and voluntarily wanting to take part. Results Of the 660 subjects studied, 319 were men (48.3%) and 341 (51.7%) women with a mean age of 74.3 years (SD = 6.6). In terms of nutritional assessment, using the BMI-MNA-SF and the CC-MNA-SF we found that 26.5% and 26.2% were at risk of malnutrition and 0.9% and 1.5% were malnourished respectively. With the full MNA, 23.3% were at risk of malnutrition. Spearman’s rank correlation coefficients indicate a high association between the full MNA score and the MNA-SFs scores (BMI-MNA-SF: ρ = 0.78p < 0.001; CC-MNA-SF: ρ = 0.78p < 0.001). In addition we obtained a very high correlation between the two MNA-SFs (ρ = 0.96p < 0.001). We evaluated the agreement between the full MNA and the MNA-SFs classification in three nutritional categories (normal nutritional status, risk of malnutrition, malnutrition) with Cohen’s kappa coefficients (BMI-MNA-SF: κ = 0.54p < 0.001; CC-MNA-SF: κ = 0.52p < 0.001). These values indicate moderate agreement with the full MNA. There is very good agreement between the BMI-MNA…
bibliographic citation: Montejano Lozoya et al. (2017) Predictive ability of the Mini Nutritional Assessment Short Form (MNA-SF) in a free-living elderly population: a cross-sectional study. PeerJ 5:e3345 https://doi.org/10.7717/peerj.3345
date submitted: 2016-11-04
date accepted: 2017-04-22
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montejano Lozoya
  given name: Raimunda
author list: Agent
  family name: Martínez-Alzamora
  given name: Nieves
author list: Agent
  family name: Clemente Marín
  given name: Gonzalo
author list: Agent
  family name: Guirao-Goris
  given name: Silamani J.A.
author list: Agent
  family name: Ferrer-Diego
  given name: Rosa María
doi: 10.7717/peerj.3345
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Montejano Lozoya et al.
attribution name: Montejano Lozoya et al.

Comparative transcriptome analyses of a late-maturing mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit maturation
type: item
type: AcademicArticle
description: Characteristics of late maturity in fruit are good agronomic traits for extending the harvest period and marketing time. However, underlying molecular basis of the late-maturing mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-Seq) technology was used to identify differentially expressed genes (DEGs) related to late-maturing characteristics from a late-maturing mutant ‘Huawan Wuzishatangju’ (HWWZSTJ) (Citrus reticulata Blanco) and its original line ‘Wuzishatangju’ (WZSTJ). A total of approximately 17.0 Gb and 84.2 M paried-end reads were obtained. DEGs were significantly enriched in the pathway of photosynthesis, phenylpropanoid biosynthesis, carotenoid biosynthesis, chlorophyll and abscisic acid (ABA) metabolism. Thirteen candidate transcripts related to chlorophyll metabolism, carotenoid biosynthesis and ABA metabolism were analyzed using real-time quantitative PCR (qPCR) at all fruit maturing stages of HWWZSTJ and WZSTJ. Chlorophyllase (CLH) and divinyl reductase (DVR) from chlorophyll metabolism, phytoene synthase (PSY) and capsanthin/capsorubin synthase (CCS) from carotenoid biosynthesis, and abscisic acid 8′-hydroxylase (AB1) and 9-cis-epoxycarotenoid dioxygenase (NCED1) from ABA metabolism were cloned and analyzed. The expression pattern of NCED1 indicated its role in the late-maturing characteristics of HWWZSTJ. There were 270 consecutive bases missing in HWWZSTJ in comparison with full-length sequences of NCED1 cDNA from WZSTJ. Those results suggested that NCED1 might play an important role in the late maturity of HWWZSTJ. This study provides new information on complex process that results in the late maturity of Citrus fruit at the transcriptional level.
format: application/pdf
format: text/html
creator: Lu Wang
creator: Qingzhu Hua
creator: Yuewen Ma
creator: Guibing Hu
creator: Yonghua Qin
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3343
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Characteristics of late maturity in fruit are good agronomic traits for extending the harvest period and marketing time. However, underlying molecular basis of the late-maturing mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-Seq) technology was used to identify differentially expressed genes (DEGs) related to late-maturing characteristics from a late-maturing mutant ‘Huawan Wuzishatangju’ (HWWZSTJ) (Citrus reticulata Blanco) and its original line ‘Wuzishatangju’ (WZSTJ). A total of approximately 17.0 Gb and 84.2 M paried-end reads were obtained. DEGs were significantly enriched in the pathway of photosynthesis, phenylpropanoid biosynthesis, carotenoid biosynthesis, chlorophyll and abscisic acid (ABA) metabolism. Thirteen candidate transcripts related to chlorophyll metabolism, carotenoid biosynthesis and ABA metabolism were analyzed using real-time quantitative PCR (qPCR) at all fruit maturing stages of HWWZSTJ and WZSTJ. Chlorophyllase (CLH) and divinyl reductase (DVR) from chlorophyll metabolism, phytoene synthase (PSY) and capsanthin/capsorubin synthase (CCS) from carotenoid biosynthesis, and abscisic acid 8′-hydroxylase (AB1) and 9-cis-epoxycarotenoid dioxygenase (NCED1) from ABA metabolism were cloned and analyzed. The expression pattern of NCED1 indicated its role in the late-maturing characteristics of HWWZSTJ. There were 270 consecutive bases missing in HWWZSTJ in comparison with full-length sequences of NCED1 cDNA from WZSTJ. Those results suggested that NCED1 might play an important role in the late maturity of HWWZSTJ. This study provides new information on complex process that results in the late maturity of Citrus fruit at the transcriptional level.
bibliographic citation: Wang et al. (2017) Comparative transcriptome analyses of a late-maturing mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit maturation. PeerJ 5:e3343 https://doi.org/10.7717/peerj.3343
date submitted: 2017-01-20
date accepted: 2017-04-21
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lu
author list: Agent
  family name: Hua
  given name: Qingzhu
author list: Agent
  family name: Ma
  given name: Yuewen
author list: Agent
  family name: Hu
  given name: Guibing
author list: Agent
  family name: Qin
  given name: Yonghua
doi: 10.7717/peerj.3343
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Wang et al.
attribution name: Wang et al.

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