PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A horizon scan of future threats and opportunities for pollinators and pollination
items: A study of institutional spending on open access publication fees in Germany
items: Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking
items: Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development
items: An optimized approach to germ-free rearing in the jewel wasp Nasonia
items: An investigation into the bilateral functional differences of the lower limb muscles in standing and walking
items: The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons
items: A comparison of blood gases, biochemistry, and hematology to ecomorphology in a health assessment of pinfish (Lagodon rhomboides)
items: Systematic relationships of five newly sequenced cervid species
items: Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster

A horizon scan of future threats and opportunities for pollinators and pollination
type: item
type: AcademicArticle
description: Background. Pollinators, which provide the agriculturally and ecologically essential service of pollination, are under threat at a global scale. Habitat loss and homogenisation, pesticides, parasites and pathogens, invasive species, and climate change have been identified as past and current threats to pollinators. Actions to mitigate these threats, e.g., agri-environment schemes and pesticide-use moratoriums, exist, but have largely been applied post-hoc. However, future sustainability of pollinators and the service they provide requires anticipation of potential threats and opportunities before they occur, enabling timely implementation of policy and practice to prevent, rather than mitigate, further pollinator declines. Methods.Using a horizon scanning approach we identified issues that are likely to impact pollinators, either positively or negatively, over the coming three decades. Results.Our analysis highlights six high priority, and nine secondary issues. High priorities are: (1) corporate control of global agriculture, (2) novel systemic pesticides, (3) novel RNA viruses, (4) the development of new managed pollinators, (5) more frequent heatwaves and drought under climate change, and (6) the potential positive impact of reduced chemical use on pollinators in non-agricultural settings. Discussion. While current pollinator management approaches are largely driven by mitigating past impacts, we present opportunities for pre-emptive practice, legislation, and policy to sustainably manage pollinators for future generations.
format: application/pdf
format: text/html
creator: Mark J.F. Brown
creator: Lynn V. Dicks
creator: Robert J. Paxton
creator: Katherine C.R. Baldock
creator: Andrew B. Barron
creator: Marie-Pierre Chauzat
creator: Breno M. Freitas
creator: Dave Goulson
creator: Sarina Jepsen
creator: Claire Kremen
creator: Jilian Li
creator: Peter Neumann
creator: David E. Pattemore
creator: Simon G. Potts
creator: Oliver Schweiger
creator: Colleen L. Seymour
creator: Jane C. Stout
subject: Biosphere Interactions
subject: Climate Change Biology
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.2249
publisher: PeerJ Inc.
rights: © 2016 Brown et al.
abstract: Background. Pollinators, which provide the agriculturally and ecologically essential service of pollination, are under threat at a global scale. Habitat loss and homogenisation, pesticides, parasites and pathogens, invasive species, and climate change have been identified as past and current threats to pollinators. Actions to mitigate these threats, e.g., agri-environment schemes and pesticide-use moratoriums, exist, but have largely been applied post-hoc. However, future sustainability of pollinators and the service they provide requires anticipation of potential threats and opportunities before they occur, enabling timely implementation of policy and practice to prevent, rather than mitigate, further pollinator declines. Methods.Using a horizon scanning approach we identified issues that are likely to impact pollinators, either positively or negatively, over the coming three decades. Results.Our analysis highlights six high priority, and nine secondary issues. High priorities are: (1) corporate control of global agriculture, (2) novel systemic pesticides, (3) novel RNA viruses, (4) the development of new managed pollinators, (5) more frequent heatwaves and drought under climate change, and (6) the potential positive impact of reduced chemical use on pollinators in non-agricultural settings. Discussion. While current pollinator management approaches are largely driven by mitigating past impacts, we present opportunities for pre-emptive practice, legislation, and policy to sustainably manage pollinators for future generations.
bibliographic citation: Brown et al. (2016) A horizon scan of future threats and opportunities for pollinators and pollination. PeerJ 4:e2249 https://doi.org/10.7717/peerj.2249
date submitted: 2016-04-22
date accepted: 2016-06-22
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Mark J.F.
author list: Agent
  family name: Dicks
  given name: Lynn V.
author list: Agent
  family name: Paxton
  given name: Robert J.
author list: Agent
  family name: Baldock
  given name: Katherine C.R.
author list: Agent
  family name: Barron
  given name: Andrew B.
author list: Agent
  family name: Chauzat
  given name: Marie-Pierre
author list: Agent
  family name: Freitas
  given name: Breno M.
author list: Agent
  family name: Goulson
  given name: Dave
author list: Agent
  family name: Jepsen
  given name: Sarina
author list: Agent
  family name: Kremen
  given name: Claire
author list: Agent
  family name: Li
  given name: Jilian
author list: Agent
  family name: Neumann
  given name: Peter
author list: Agent
  family name: Pattemore
  given name: David E.
author list: Agent
  family name: Potts
  given name: Simon G.
author list: Agent
  family name: Schweiger
  given name: Oliver
author list: Agent
  family name: Seymour
  given name: Colleen L.
author list: Agent
  family name: Stout
  given name: Jane C.
doi: 10.7717/peerj.2249
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Brown et al.
attribution name: Brown et al.

A study of institutional spending on open access publication fees in Germany
type: item
type: AcademicArticle
description: Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK reve…
format: application/pdf
format: text/html
creator: Najko Jahn
creator: Marco Tullney
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.2323
publisher: PeerJ Inc.
rights: © 2016 Jahn et al.
abstract: Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK reve…
bibliographic citation: Jahn et al. (2016) A study of institutional spending on open access publication fees in Germany. PeerJ 4:e2323 https://doi.org/10.7717/peerj.2323
date submitted: 2016-04-08
date accepted: 2016-07-13
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jahn
  given name: Najko
author list: Agent
  family name: Tullney
  given name: Marco
doi: 10.7717/peerj.2323
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Jahn et al.
attribution name: Jahn et al.

Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking
type: item
type: AcademicArticle
description: Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R2, ${Q}_{\mathrm{CV }}^{2}$ Q CV 2 and ${Q}_{\mathrm{Ext}}^{2}$ Q Ext 2 values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R2, ${Q}_{\mathrm{CV }}^{2}$ Q CV 2 and ${Q}_{\mathrm{Ext}}^{2}$ Q Ext 2 values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing…
format: application/pdf
format: text/html
creator: Saw Simeon
creator: Nuttapat Anuwongcharoen
creator: Watshara Shoombuatong
creator: Aijaz Ahmad Malik
creator: Virapong Prachayasittikul
creator: Jarl E.S. Wikberg
creator: Chanin Nantasenamat
subject: Bioinformatics
subject: Computational Biology
subject: Drugs and Devices
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.2322
publisher: PeerJ Inc.
rights: © 2016 Simeon et al.
abstract: Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R2, ${Q}_{\mathrm{CV }}^{2}$ Q CV 2 and ${Q}_{\mathrm{Ext}}^{2}$ Q Ext 2 values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R2, ${Q}_{\mathrm{CV }}^{2}$ Q CV 2 and ${Q}_{\mathrm{Ext}}^{2}$ Q Ext 2 values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing…
bibliographic citation: Simeon et al. (2016) Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking. PeerJ 4:e2322 https://doi.org/10.7717/peerj.2322
date submitted: 2016-05-09
date accepted: 2016-07-13
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simeon
  given name: Saw
author list: Agent
  family name: Anuwongcharoen
  given name: Nuttapat
author list: Agent
  family name: Shoombuatong
  given name: Watshara
author list: Agent
  family name: Malik
  given name: Aijaz Ahmad
author list: Agent
  family name: Prachayasittikul
  given name: Virapong
author list: Agent
  family name: Wikberg
  given name: Jarl E.S.
author list: Agent
  family name: Nantasenamat
  given name: Chanin
doi: 10.7717/peerj.2322
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Simeon et al.
attribution name: Simeon et al.

Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development
type: item
type: AcademicArticle
description: To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org…
format: application/pdf
format: text/html
creator: Kyle J. Beauchemin
creator: Julie M. Wells
creator: Alvin T. Kho
creator: Vivek M. Philip
creator: Daniela Kamir
creator: Isaac S. Kohane
creator: Joel H. Graber
creator: Carol J. Bult
subject: Bioinformatics
subject: Developmental Biology
subject: Genomics
subject: Respiratory Medicine
description: doi:10.7717/peerj.2318
publisher: PeerJ Inc.
rights: © 2016 Beauchemin et al.
abstract: To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org…
bibliographic citation: Beauchemin et al. (2016) Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PeerJ 4:e2318 https://doi.org/10.7717/peerj.2318
date submitted: 2016-05-13
date accepted: 2016-07-12
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beauchemin
  given name: Kyle J.
author list: Agent
  family name: Wells
  given name: Julie M.
author list: Agent
  family name: Kho
  given name: Alvin T.
author list: Agent
  family name: Philip
  given name: Vivek M.
author list: Agent
  family name: Kamir
  given name: Daniela
author list: Agent
  family name: Kohane
  given name: Isaac S.
author list: Agent
  family name: Graber
  given name: Joel H.
author list: Agent
  family name: Bult
  given name: Carol J.
doi: 10.7717/peerj.2318
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Beauchemin et al.
attribution name: Beauchemin et al.

An optimized approach to germ-free rearing in the jewel wasp Nasonia
type: item
type: AcademicArticle
description: Development of a Nasonia in vitrogerm-free rearing system in 2012 enabled investigation of Nasonia-microbiota interactions and real-time visualization of parasitoid metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed.
format: application/pdf
format: text/html
creator: J. Dylan Shropshire
creator: Edward J. van Opstal
creator: Seth R. Bordenstein
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.2316
publisher: PeerJ Inc.
rights: © 2016 Shropshire et al.
abstract: Development of a Nasonia in vitrogerm-free rearing system in 2012 enabled investigation of Nasonia-microbiota interactions and real-time visualization of parasitoid metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed.
bibliographic citation: Shropshire et al. (2016) An optimized approach to germ-free rearing in the jewel wasp Nasonia. PeerJ 4:e2316 https://doi.org/10.7717/peerj.2316
date submitted: 2016-05-30
date accepted: 2016-07-12
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shropshire
  given name: J. Dylan
author list: Agent
  family name: van Opstal
  given name: Edward J.
author list: Agent
  family name: Bordenstein
  given name: Seth R.
doi: 10.7717/peerj.2316
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Shropshire et al.
attribution name: Shropshire et al.

An investigation into the bilateral functional differences of the lower limb muscles in standing and walking
type: item
type: AcademicArticle
description: To date, most studies use surface electromyographic (sEMG) signals as the control source on active rehabilitation robots, and unilateral data are collected based on the gait symmetry hypothesis, which has caused much controversy. The purpose of this study is to quantitatively evaluate the sEMG activity asymmetry of bilateral muscles in lower extremities during functional tasks. Nine participants were instructed to perform static and dynamic steady state tests. sEMG signals from the tibialis anterior, soleus, medial gastrocnemius and lateral gastrocnemius muscles of bilateral lower extremities were recorded in the experiments. Muscle activities are quantified in terms of sEMG amplitude. We investigated whether characteristics of left limb and the one of the right limb have the same statistical characteristics during functional tasks using The Wilcoxon rank-sum test, and studied dynamic signal irregularity degree for sEMG activities via sample entropy. The total of muscle activities showed significant differences between left limb and right limb during the static steady state (p = 0.000). For dynamic steady states, there were significant differences for most muscle activities between left limb and right limb at different speeds (p = 0.000). Nevertheless, there was no difference between the lateral gastrocnemius for bilateral limb at 2.0 kilometers per hour (p = 0.060). For medial gastrocnemius, differences were not found between left limb and right limb at 1.0 and 3.0 kilometers per hours (p = 0.390 and p = 0.085, respectively). Similarly, there was no difference for soleus at 3.0 kilometers per hour (p = 0.115). The importance of the differences in muscle activities between left limb and right limb were found. These results can potentially be used for evaluating lower limb extremity function of special populations (elderly people or stroke patients) in an objective and simple method.
format: application/pdf
format: text/html
creator: Shengyun Liang
creator: Jiali Xu
creator: Lei wang
creator: Guoru Zhao
subject: Bioengineering
subject: Computational Biology
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.2315
publisher: PeerJ Inc.
rights: © 2016 Liang et al.
abstract: To date, most studies use surface electromyographic (sEMG) signals as the control source on active rehabilitation robots, and unilateral data are collected based on the gait symmetry hypothesis, which has caused much controversy. The purpose of this study is to quantitatively evaluate the sEMG activity asymmetry of bilateral muscles in lower extremities during functional tasks. Nine participants were instructed to perform static and dynamic steady state tests. sEMG signals from the tibialis anterior, soleus, medial gastrocnemius and lateral gastrocnemius muscles of bilateral lower extremities were recorded in the experiments. Muscle activities are quantified in terms of sEMG amplitude. We investigated whether characteristics of left limb and the one of the right limb have the same statistical characteristics during functional tasks using The Wilcoxon rank-sum test, and studied dynamic signal irregularity degree for sEMG activities via sample entropy. The total of muscle activities showed significant differences between left limb and right limb during the static steady state (p = 0.000). For dynamic steady states, there were significant differences for most muscle activities between left limb and right limb at different speeds (p = 0.000). Nevertheless, there was no difference between the lateral gastrocnemius for bilateral limb at 2.0 kilometers per hour (p = 0.060). For medial gastrocnemius, differences were not found between left limb and right limb at 1.0 and 3.0 kilometers per hours (p = 0.390 and p = 0.085, respectively). Similarly, there was no difference for soleus at 3.0 kilometers per hour (p = 0.115). The importance of the differences in muscle activities between left limb and right limb were found. These results can potentially be used for evaluating lower limb extremity function of special populations (elderly people or stroke patients) in an objective and simple method.
bibliographic citation: Liang et al. (2016) An investigation into the bilateral functional differences of the lower limb muscles in standing and walking. PeerJ 4:e2315 https://doi.org/10.7717/peerj.2315
date submitted: 2016-05-03
date accepted: 2016-07-12
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Shengyun
author list: Agent
  family name: Xu
  given name: Jiali
author list: Agent
  family name: wang
  given name: Lei
author list: Agent
  family name: Zhao
  given name: Guoru
doi: 10.7717/peerj.2315
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Liang et al.
attribution name: Liang et al.

The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons
type: item
type: AcademicArticle
description: The brain’s biological clock, the suprachiasmatic nucleus (SCN), exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping.
format: application/pdf
format: text/html
creator: Jeff R. Jones
creator: Douglas G. McMahon
subject: Biotechnology
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.2297
publisher: PeerJ Inc.
rights: © 2016 Jones and McMahon
abstract: The brain’s biological clock, the suprachiasmatic nucleus (SCN), exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping.
bibliographic citation: Jones et al. (2016) The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons. PeerJ 4:e2297 https://doi.org/10.7717/peerj.2297
date submitted: 2016-04-20
date accepted: 2016-07-06
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jones
  given name: Jeff R.
author list: Agent
  family name: McMahon
  given name: Douglas G.
doi: 10.7717/peerj.2297
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Jones and McMahon
attribution name: Jones and McMahon

A comparison of blood gases, biochemistry, and hematology to ecomorphology in a health assessment of pinfish (Lagodon rhomboides)
type: item
type: AcademicArticle
description: Despite the promise of hematological parameters and blood chemistry in monitoring the health of marine fishes, baseline data is often lacking for small fishes that comprise central roles in marine food webs. This study establishes blood chemistry and hematological baseline parameters for the pinfish Lagodon rhomboides, a small marine teleost that is among the most dominant members of near-shore estuarine communities of the Atlantic Ocean and Gulf of Mexico. Given their prominence, pinfishes are an ideal candidate species to use as a model for monitoring changes across a wide range of near-shore marine communities. However, pinfishes exhibit substantial morphological differences associated with a preference for feeding in primarily sea-grass or sand dominated habitats, suggesting that differences in the foraging ecology of individuals could confound health assessments. Here we collect baseline data on the blood physiology of pinfish while assessing the relationship between blood parameters and measured aspects of feeding morphology using data collected from 37 individual fish. Our findings provide new baseline health data for this important near shore fish species and find no evidence for a strong linkage between blood physiology and either sex or measured aspects of feeding morphology. Comparing our hematological and biochemical data to published results from other marine teleost species suggests that analyses of trends in blood value variation correlated with major evolutionary transitions in ecology will shed new light on the physiological changes that underlie the successful diversification of fishes.
format: application/pdf
format: text/html
creator: Sara Collins
creator: Alex Dornburg
creator: Joseph M. Flores
creator: Daniel S. Dombrowski
creator: Gregory A. Lewbart
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Marine Biology
subject: Veterinary Medicine
subject: Hematology
description: doi:10.7717/peerj.2262
publisher: PeerJ Inc.
rights: © 2016 Collins et al.
abstract: Despite the promise of hematological parameters and blood chemistry in monitoring the health of marine fishes, baseline data is often lacking for small fishes that comprise central roles in marine food webs. This study establishes blood chemistry and hematological baseline parameters for the pinfish Lagodon rhomboides, a small marine teleost that is among the most dominant members of near-shore estuarine communities of the Atlantic Ocean and Gulf of Mexico. Given their prominence, pinfishes are an ideal candidate species to use as a model for monitoring changes across a wide range of near-shore marine communities. However, pinfishes exhibit substantial morphological differences associated with a preference for feeding in primarily sea-grass or sand dominated habitats, suggesting that differences in the foraging ecology of individuals could confound health assessments. Here we collect baseline data on the blood physiology of pinfish while assessing the relationship between blood parameters and measured aspects of feeding morphology using data collected from 37 individual fish. Our findings provide new baseline health data for this important near shore fish species and find no evidence for a strong linkage between blood physiology and either sex or measured aspects of feeding morphology. Comparing our hematological and biochemical data to published results from other marine teleost species suggests that analyses of trends in blood value variation correlated with major evolutionary transitions in ecology will shed new light on the physiological changes that underlie the successful diversification of fishes.
bibliographic citation: Collins et al. (2016) A comparison of blood gases, biochemistry, and hematology to ecomorphology in a health assessment of pinfish (Lagodon rhomboides). PeerJ 4:e2262 https://doi.org/10.7717/peerj.2262
date submitted: 2016-02-19
date accepted: 2016-06-26
issued: 2016-08-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Collins
  given name: Sara
author list: Agent
  family name: Dornburg
  given name: Alex
author list: Agent
  family name: Flores
  given name: Joseph M.
author list: Agent
  family name: Dombrowski
  given name: Daniel S.
author list: Agent
  family name: Lewbart
  given name: Gregory A.
doi: 10.7717/peerj.2262
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-09
copyright: ©2016 Collins et al.
attribution name: Collins et al.

Systematic relationships of five newly sequenced cervid species
type: item
type: AcademicArticle
description: Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.
format: application/pdf
format: text/html
creator: Nicola S. Heckeberg
creator: Dirk Erpenbeck
creator: Gert Wörheide
creator: Gertrud E. Rössner
subject: Biodiversity
subject: Computational Biology
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2307
publisher: PeerJ Inc.
rights: © 2016 Heckeberg et al.
abstract: Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.
bibliographic citation: Heckeberg et al. (2016) Systematic relationships of five newly sequenced cervid species. PeerJ 4:e2307 https://doi.org/10.7717/peerj.2307
date submitted: 2015-09-12
date accepted: 2016-07-09
issued: 2016-08-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heckeberg
  given name: Nicola S.
author list: Agent
  family name: Erpenbeck
  given name: Dirk
author list: Agent
  family name: Wörheide
  given name: Gert
author list: Agent
  family name: Rössner
  given name: Gertrud E.
doi: 10.7717/peerj.2307
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-04
copyright: ©2016 Heckeberg et al.
attribution name: Heckeberg et al.

Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster
type: item
type: AcademicArticle
description: Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures.
format: application/pdf
format: text/html
creator: Indrikis Krams
creator: Sarah Eichler Inwood
creator: Giedrius Trakimas
creator: Ronalds Krams
creator: Gordon M. Burghardt
creator: David M. Butler
creator: Severi Luoto
creator: Tatjana Krama
subject: Animal Behavior
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.2314
publisher: PeerJ Inc.
rights: © 2016 Krams et al.
abstract: Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures.
bibliographic citation: Krams et al. (2016) Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster. PeerJ 4:e2314 https://doi.org/10.7717/peerj.2314
date submitted: 2016-04-24
date accepted: 2016-07-12
issued: 2016-08-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krams
  given name: Indrikis
author list: Agent
  family name: Eichler Inwood
  given name: Sarah
author list: Agent
  family name: Trakimas
  given name: Giedrius
author list: Agent
  family name: Krams
  given name: Ronalds
author list: Agent
  family name: Burghardt
  given name: Gordon M.
author list: Agent
  family name: Butler
  given name: David M.
author list: Agent
  family name: Luoto
  given name: Severi
author list: Agent
  family name: Krama
  given name: Tatjana
doi: 10.7717/peerj.2314
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-04
copyright: ©2016 Krams et al.
attribution name: Krams et al.

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