PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Antithrombin deficiency is associated with mortality and impaired organ function in septic pediatric patients: a retrospective study
items: Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP
items: Shrub encroachment into grasslands: end of an era?
items: Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients
items: Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids
items: Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis
items: Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species
items: Effect of vineyard soil variability on chlorophyll fluorescence, yield and quality of table grape as influenced by soil moisture, grown under double cropping system in protected condition
items: An LED-based multi-actinic illumination system for the high throughput study of photosynthetic light responses
items: Translational effects of robot-mediated therapy in subacute stroke patients: an experimental evaluation of upper limb motor recovery

Antithrombin deficiency is associated with mortality and impaired organ function in septic pediatric patients: a retrospective study
type: item
type: AcademicArticle
description: Background Sepsis remains a major problem in intensive care medicine. It is often accompanied by coagulopathies, leading to thrombotic occlusion of small vessels with subsequent organ damage and even fatal multi-organ failure. Prediction of the clinical course and outcome—especially in the heterogeneous group of pediatric patients—is difficult. Antithrombin, as an endogenous anticoagulant enzyme with anti-inflammatory properties, plays a central role in controling coagulation and infections. We investigated the relationship between antithrombin levels and organ failure as well as mortality in pediatric patients with sepsis. Methods Data from 164 patients under the age of 18, diagnosed with sepsis, were retrospectively reviewed. Antithrombin levels were recorded three days before to three days after peak C-reactive protein to correlate antithrombin levels with inflammatory activity. Using the concept of developmental haemostasis, patients were divided into groups <1 yr and ≥1 yr of age. Results In both age groups, survivors had significantly higher levels of antithrombin than did deceased patients. An optimal threshold level for antithrombin was calculated by ROC analysis for survival: 41.5% (<1 yr) and 67.5% (≥1 yr). The mortality rate above this level was 3.3% (<1 yr) and 9.5% (≥1 yr), and below this level 41.7% (<1 yr) and 32.2% (≥1 yr); OR 18.8 (1.74 to 1005.02), p = 0.0047, and OR 4.46 (1.54 to 14.89), p = 0.003. In children <1 yr with antithrombin levels <41.5% the rate of respiratory failure (66.7%) was significantly higher than in patients with antithrombin levels above this threshold level (23.3%), OR 6.23 (1.23 to 37.81), p = 0.0132. In children ≥1 yr, both liver failure (20.3% vs 1.6%, OR 15.55 (2.16 to 685.01), p = 0.0008) and a dysfunctional intestinal tract (16.9% vs 4.8%, OR 4.04 (0.97 to 24.08), p = 0.0395) occurred more frequently above the antithrombin threshold level of 67.5%. Conclusion In pediatric septic patients, significantly increased mortali…
format: application/pdf
format: text/html
creator: Christian Niederwanger
creator: Tobias Hell
creator: Sophie Hofer
creator: Christina Salvador
creator: Miriam Michel
creator: Bettina Schenk
creator: Benedikt Treml
creator: Mirjam Bachler
subject: Emergency and Critical Care
subject: Pediatrics
description: doi:10.7717/peerj.5538
publisher: PeerJ Inc.
rights: © 2018 Niederwanger et al.
abstract: Background Sepsis remains a major problem in intensive care medicine. It is often accompanied by coagulopathies, leading to thrombotic occlusion of small vessels with subsequent organ damage and even fatal multi-organ failure. Prediction of the clinical course and outcome—especially in the heterogeneous group of pediatric patients—is difficult. Antithrombin, as an endogenous anticoagulant enzyme with anti-inflammatory properties, plays a central role in controling coagulation and infections. We investigated the relationship between antithrombin levels and organ failure as well as mortality in pediatric patients with sepsis. Methods Data from 164 patients under the age of 18, diagnosed with sepsis, were retrospectively reviewed. Antithrombin levels were recorded three days before to three days after peak C-reactive protein to correlate antithrombin levels with inflammatory activity. Using the concept of developmental haemostasis, patients were divided into groups <1 yr and ≥1 yr of age. Results In both age groups, survivors had significantly higher levels of antithrombin than did deceased patients. An optimal threshold level for antithrombin was calculated by ROC analysis for survival: 41.5% (<1 yr) and 67.5% (≥1 yr). The mortality rate above this level was 3.3% (<1 yr) and 9.5% (≥1 yr), and below this level 41.7% (<1 yr) and 32.2% (≥1 yr); OR 18.8 (1.74 to 1005.02), p = 0.0047, and OR 4.46 (1.54 to 14.89), p = 0.003. In children <1 yr with antithrombin levels <41.5% the rate of respiratory failure (66.7%) was significantly higher than in patients with antithrombin levels above this threshold level (23.3%), OR 6.23 (1.23 to 37.81), p = 0.0132. In children ≥1 yr, both liver failure (20.3% vs 1.6%, OR 15.55 (2.16 to 685.01), p = 0.0008) and a dysfunctional intestinal tract (16.9% vs 4.8%, OR 4.04 (0.97 to 24.08), p = 0.0395) occurred more frequently above the antithrombin threshold level of 67.5%. Conclusion In pediatric septic patients, significantly increased mortali…
bibliographic citation: Niederwanger et al. (2018) Antithrombin deficiency is associated with mortality and impaired organ function in septic pediatric patients: a retrospective study. PeerJ 6:e5538 https://doi.org/10.7717/peerj.5538
date submitted: 2018-03-11
date accepted: 2018-08-08
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niederwanger
  given name: Christian
author list: Agent
  family name: Hell
  given name: Tobias
author list: Agent
  family name: Hofer
  given name: Sophie
author list: Agent
  family name: Salvador
  given name: Christina
author list: Agent
  family name: Michel
  given name: Miriam
author list: Agent
  family name: Schenk
  given name: Bettina
author list: Agent
  family name: Treml
  given name: Benedikt
author list: Agent
  family name: Bachler
  given name: Mirjam
doi: 10.7717/peerj.5538
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: ©2018 Niederwanger et al.
attribution name: Niederwanger et al.

Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP
type: item
type: AcademicArticle
description: The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over several orders of magnitude. For example, the ATP synthases from thermophilic Bacillus PS3 and Escherichia coli exhibit affinities of 4 µM and 22 mM, respectively. The recently reported R103A/R115A double mutant of Bacillus PS3 ATP synthase demonstrated an increased binding affinity by two orders of magnitude with respect to the wild type. Here, we used atomic-resolution molecular dynamics simulations to determine the role of the R103A and R115A single mutations. These lead us to predict that both single mutations also cause an increased ATP binding affinity. Evolutionary analysis reveals R103 and R115 substitutions in the ε subunit from other bacillic organisms, leading us to predict they likely have a higher ATP binding affinity than previously expected.
format: application/pdf
format: text/html
creator: Alexander Krah
creator: Peter J. Bond
subject: Biophysics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.5505
publisher: PeerJ Inc.
rights: © 2018 Krah and Bond
abstract: The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over several orders of magnitude. For example, the ATP synthases from thermophilic Bacillus PS3 and Escherichia coli exhibit affinities of 4 µM and 22 mM, respectively. The recently reported R103A/R115A double mutant of Bacillus PS3 ATP synthase demonstrated an increased binding affinity by two orders of magnitude with respect to the wild type. Here, we used atomic-resolution molecular dynamics simulations to determine the role of the R103A and R115A single mutations. These lead us to predict that both single mutations also cause an increased ATP binding affinity. Evolutionary analysis reveals R103 and R115 substitutions in the ε subunit from other bacillic organisms, leading us to predict they likely have a higher ATP binding affinity than previously expected.
bibliographic citation: Krah et al. (2018) Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP. PeerJ 6:e5505 https://doi.org/10.7717/peerj.5505
date submitted: 2018-04-24
date accepted: 2018-08-02
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krah
  given name: Alexander
author list: Agent
  family name: Bond
  given name: Peter J.
doi: 10.7717/peerj.5505
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: ©2018 Krah and Bond
attribution name: Krah and Bond

Shrub encroachment into grasslands: end of an era?
type: item
type: AcademicArticle
description: Shifts in the abundance of grasses and woody plants in drylands have occurred several times during the Holocene. However, our understanding of the rates and dynamics of this state-change in recent decades is limited to scattered studies conducted at disparate spatial and temporal scales; the potential misperceptions of shrub cover change could be remedied using cross spatiotemporal scale analyses that link field observations, repeat ground-level photography and remote sensing perspectives. The study was conducted across a semi-arid landscape in southern Arizona. Local data from long-term transects revealed three distinct chronological phases of shrub cover change: expansion (1961–1991, 0.7% y−1), decline (1992–1997, −2.3% y−1) and stabilization (1998–2012, 22–25% with no net cover change). Twenty-eight years (1984–2011) of broad-scale Landsat Thematic Mapper assessments confirm that shrub cover has been relatively stable in recent decades regardless of grazing regimes and landforms with the exception of the proliferation of succulents at lower elevations (verified by repeat photography acquired in 1987 and 2015) where the physical environment is the harshest, reflecting elevated temperature and winter precipitation deficit. Warmer, drier future climates are predicted to reduce woody plant carrying capacity and promote a shift to xerophytic succulents.
format: application/pdf
format: text/html
creator: Cho-ying Huang
creator: Steven R. Archer
creator: Mitchel P. McClaran
creator: Stuart E. Marsh
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
subject: Biogeochemistry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5474
publisher: PeerJ Inc.
rights: © 2018 Huang et al.
abstract: Shifts in the abundance of grasses and woody plants in drylands have occurred several times during the Holocene. However, our understanding of the rates and dynamics of this state-change in recent decades is limited to scattered studies conducted at disparate spatial and temporal scales; the potential misperceptions of shrub cover change could be remedied using cross spatiotemporal scale analyses that link field observations, repeat ground-level photography and remote sensing perspectives. The study was conducted across a semi-arid landscape in southern Arizona. Local data from long-term transects revealed three distinct chronological phases of shrub cover change: expansion (1961–1991, 0.7% y−1), decline (1992–1997, −2.3% y−1) and stabilization (1998–2012, 22–25% with no net cover change). Twenty-eight years (1984–2011) of broad-scale Landsat Thematic Mapper assessments confirm that shrub cover has been relatively stable in recent decades regardless of grazing regimes and landforms with the exception of the proliferation of succulents at lower elevations (verified by repeat photography acquired in 1987 and 2015) where the physical environment is the harshest, reflecting elevated temperature and winter precipitation deficit. Warmer, drier future climates are predicted to reduce woody plant carrying capacity and promote a shift to xerophytic succulents.
bibliographic citation: Huang et al. (2018) Shrub encroachment into grasslands: end of an era?. PeerJ 6:e5474 https://doi.org/10.7717/peerj.5474
date submitted: 2018-02-28
date accepted: 2018-07-15
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Cho-ying
author list: Agent
  family name: Archer
  given name: Steven R.
author list: Agent
  family name: McClaran
  given name: Mitchel P.
author list: Agent
  family name: Marsh
  given name: Stuart E.
doi: 10.7717/peerj.5474
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: ©2018 Huang et al.
attribution name: Huang et al.

Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients
type: item
type: AcademicArticle
description: Background Avian influenza viruses (AIVs) have been endemic in Egypt since 2006, and the co-circulation of high-pathogenic avian influenza H5N1 and low-pathogenic avian influenza H9N2 subtypes in poultry has been reported; therefore, Egypt is considered a hotspot for the generation of new subtypes and genotypes. We aimed to characterize AIVs circulating on commercial farms and in live bird markets (LBMs) during the winters of 2015 and 2016 in the study area and to identify H5N1 and H9N2 viruses in respiratory patients. Methods In total, 159 samples were collected from ducks, pigeons and quails on farms (n = 59) and in LBMs (n = 100) and screened by real-time RT-PCR for H5N1 and H9N2 subtypes. Clinical and postmortem examination was carried out on birds from the farms. Positive H5N1 samples were sequenced and analysed for mutations. Tracheal swabs were also collected from 89 respiratory patients admitted to respiratory hospitals in the same study area. Results Overall, H5N1 was identified in 13.6% of birds from farms, while it was detected in 17% of birds in LBMs. Subtype H9N2 was only identified from pigeons on farms (6.5%) and LBMs (11.4%). Sequencing of the haemagglutination gene (HA) in nine representative H5N1 isolates revealed a multi-basic amino acid motif at the cleavage site (321-PQGEKRRKKR/GLF-333), which is characteristic of highly pathogenic AIV, in five of our isolates, while the other four isolates showed an amino acid substitution (Q322K) at this cleavage site to make it (321-P K GEKRRKKR/GLF-333). All the isolates belonged to clade 2.2.1.2, and a comparison of HA sequences at the amino acid level showed 98.8–100% homology among the nine isolates, while they showed 94.1–96.1% identity with reference strains and the commonly used vaccine strain in Egypt. Out of 89 respiratory patients, 3.4% were positive for H5N1 and no patients were positive for H9N2. Discussion Our results indicated the circulation of the endemic H5N1 and H9N2 viruses among poultry in…
format: application/pdf
format: text/html
creator: Hala M.N. Tolba
creator: Rasha M.M. Abou Elez
creator: Ibrahim Elsohaby
creator: Heba A. Ahmed
subject: Veterinary Medicine
subject: Virology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.5473
publisher: PeerJ Inc.
rights: © 2018 Tolba et al.
abstract: Background Avian influenza viruses (AIVs) have been endemic in Egypt since 2006, and the co-circulation of high-pathogenic avian influenza H5N1 and low-pathogenic avian influenza H9N2 subtypes in poultry has been reported; therefore, Egypt is considered a hotspot for the generation of new subtypes and genotypes. We aimed to characterize AIVs circulating on commercial farms and in live bird markets (LBMs) during the winters of 2015 and 2016 in the study area and to identify H5N1 and H9N2 viruses in respiratory patients. Methods In total, 159 samples were collected from ducks, pigeons and quails on farms (n = 59) and in LBMs (n = 100) and screened by real-time RT-PCR for H5N1 and H9N2 subtypes. Clinical and postmortem examination was carried out on birds from the farms. Positive H5N1 samples were sequenced and analysed for mutations. Tracheal swabs were also collected from 89 respiratory patients admitted to respiratory hospitals in the same study area. Results Overall, H5N1 was identified in 13.6% of birds from farms, while it was detected in 17% of birds in LBMs. Subtype H9N2 was only identified from pigeons on farms (6.5%) and LBMs (11.4%). Sequencing of the haemagglutination gene (HA) in nine representative H5N1 isolates revealed a multi-basic amino acid motif at the cleavage site (321-PQGEKRRKKR/GLF-333), which is characteristic of highly pathogenic AIV, in five of our isolates, while the other four isolates showed an amino acid substitution (Q322K) at this cleavage site to make it (321-P K GEKRRKKR/GLF-333). All the isolates belonged to clade 2.2.1.2, and a comparison of HA sequences at the amino acid level showed 98.8–100% homology among the nine isolates, while they showed 94.1–96.1% identity with reference strains and the commonly used vaccine strain in Egypt. Out of 89 respiratory patients, 3.4% were positive for H5N1 and no patients were positive for H9N2. Discussion Our results indicated the circulation of the endemic H5N1 and H9N2 viruses among poultry in…
bibliographic citation: Tolba et al. (2018) Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. PeerJ 6:e5473 https://doi.org/10.7717/peerj.5473
date submitted: 2018-02-27
date accepted: 2018-07-28
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tolba
  given name: Hala M.N.
author list: Agent
  family name: Abou Elez
  given name: Rasha M.M.
author list: Agent
  family name: Elsohaby
  given name: Ibrahim
author list: Agent
  family name: Ahmed
  given name: Heba A.
doi: 10.7717/peerj.5473
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: ©2018 Tolba et al.
attribution name: Tolba et al.

Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids
type: item
type: AcademicArticle
description: Plant growth-promoting bacteria (PGPB) and humic acids (HA) have been used as biostimulants in field conditions. The complete genomic and proteomic transcription of Herbaspirillum seropedicae and Gluconacetobacter diazotrophicus is available but interpreting and utilizing this information in the field to increase crop performance is challenging. The identification and characterization of metabolites that are induced by genomic changes may be used to improve plant responses to inoculation. The objective of this study was to describe changes in sugarcane metabolic profile that occur when HA and PGPB are used as biostimulants. Inoculum was applied to soil containing 45-day old sugarcane stalks. One week after inoculation, the methanolic extracts from leaves were obtained and analyzed by gas chromatography coupled to time-of-flight mass spectrometry; a total of 1,880 compounds were observed and 280 were identified in all samples. The application of HA significantly decreased the concentration of 15 metabolites, which generally included amino acids. HA increased the levels of 40 compounds, and these included metabolites linked to the stress response (shikimic, caffeic, hydroxycinnamic acids, putrescine, behenic acid, quinoline xylulose, galactose, lactose proline, oxyproline and valeric acid) and cellular growth (adenine and adenosine derivatives, ribose, ribonic acid and citric acid). Similarly, PGPB enhanced the level of metabolites identified in HA-treated soils; e.g., 48 metabolites were elevated and included amino acids, nucleic acids, organic acids, and lipids. Co-inoculation (HA+PGPB) boosted the level of 110 metabolites with respect to non-inoculated controls; these included amino acids, lipids and nitrogenous compounds. Changes in the metabolic profile induced by HA+PGPB influenced both glucose and pentose pathways and resulted in the accumulation of heptuloses and riboses, which are substrates in the nucleoside biosynthesis and shikimic acid pathways. The meval…
format: application/pdf
format: text/html
creator: Natalia O. Aguiar
creator: Fabio L. Olivares
creator: Etelvino H. Novotny
creator: Luciano P. Canellas
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.5445
publisher: PeerJ Inc.
rights: © 2018 Aguiar et al.
abstract: Plant growth-promoting bacteria (PGPB) and humic acids (HA) have been used as biostimulants in field conditions. The complete genomic and proteomic transcription of Herbaspirillum seropedicae and Gluconacetobacter diazotrophicus is available but interpreting and utilizing this information in the field to increase crop performance is challenging. The identification and characterization of metabolites that are induced by genomic changes may be used to improve plant responses to inoculation. The objective of this study was to describe changes in sugarcane metabolic profile that occur when HA and PGPB are used as biostimulants. Inoculum was applied to soil containing 45-day old sugarcane stalks. One week after inoculation, the methanolic extracts from leaves were obtained and analyzed by gas chromatography coupled to time-of-flight mass spectrometry; a total of 1,880 compounds were observed and 280 were identified in all samples. The application of HA significantly decreased the concentration of 15 metabolites, which generally included amino acids. HA increased the levels of 40 compounds, and these included metabolites linked to the stress response (shikimic, caffeic, hydroxycinnamic acids, putrescine, behenic acid, quinoline xylulose, galactose, lactose proline, oxyproline and valeric acid) and cellular growth (adenine and adenosine derivatives, ribose, ribonic acid and citric acid). Similarly, PGPB enhanced the level of metabolites identified in HA-treated soils; e.g., 48 metabolites were elevated and included amino acids, nucleic acids, organic acids, and lipids. Co-inoculation (HA+PGPB) boosted the level of 110 metabolites with respect to non-inoculated controls; these included amino acids, lipids and nitrogenous compounds. Changes in the metabolic profile induced by HA+PGPB influenced both glucose and pentose pathways and resulted in the accumulation of heptuloses and riboses, which are substrates in the nucleoside biosynthesis and shikimic acid pathways. The meval…
bibliographic citation: Aguiar et al. (2018) Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids. PeerJ 6:e5445 https://doi.org/10.7717/peerj.5445
date submitted: 2018-02-22
date accepted: 2018-07-25
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguiar
  given name: Natalia O.
author list: Agent
  family name: Olivares
  given name: Fabio L.
author list: Agent
  family name: Novotny
  given name: Etelvino H.
author list: Agent
  family name: Canellas
  given name: Luciano P.
doi: 10.7717/peerj.5445
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: ©2018 Aguiar et al.
attribution name: Aguiar et al.

Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis
type: item
type: AcademicArticle
description: Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is r…
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format: text/html
creator: Gita Shafiee
creator: Yazdan Asgari
creator: Akbar Soltani
creator: Bagher Larijani
creator: Ramin Heshmat
subject: Bioinformatics
subject: Diabetes and Endocrinology
subject: Geriatrics
subject: Medical Genetics
description: doi:10.7717/peerj.5239
publisher: PeerJ Inc.
rights: © 2018 Shafiee et al.
abstract: Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is r…
bibliographic citation: Shafiee et al. (2018) Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis. PeerJ 6:e5239 https://doi.org/10.7717/peerj.5239
date submitted: 2018-03-09
date accepted: 2018-06-24
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shafiee
  given name: Gita
author list: Agent
  family name: Asgari
  given name: Yazdan
author list: Agent
  family name: Soltani
  given name: Akbar
author list: Agent
  family name: Larijani
  given name: Bagher
author list: Agent
  family name: Heshmat
  given name: Ramin
doi: 10.7717/peerj.5239
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: ©2018 Shafiee et al.
attribution name: Shafiee et al.

Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species
type: item
type: AcademicArticle
description: The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.
format: application/pdf
format: text/html
creator: Jinming Lu
creator: Yuan Zhang
creator: Hongwei Chen
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5160
publisher: PeerJ Inc.
rights: © 2018 Lu et al.
abstract: The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.
bibliographic citation: Lu et al. (2018) Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species. PeerJ 6:e5160 https://doi.org/10.7717/peerj.5160
date submitted: 2018-01-26
date accepted: 2018-06-14
issued: 2018-09-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Jinming
author list: Agent
  family name: Zhang
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Hongwei
doi: 10.7717/peerj.5160
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-05
copyright: © 2018 Lu et al.
attribution name: Lu et al.

Effect of vineyard soil variability on chlorophyll fluorescence, yield and quality of table grape as influenced by soil moisture, grown under double cropping system in protected condition
type: item
type: AcademicArticle
description: Environmental factors greatly influence grape quality. Among them, the effect of within-vineyard variability of soil in relation to soil moisture on table grape under protected condition has rarely been studied. In this present research, we investigated the influence of soil variability, in relation with soil moisture on chlorophyll fluorescence, yield and quality attributes of the “Summer Black” (Vitis vinifera L. × V. labruscana L.) table grape, popularly grown under double cropping system in protected covering in the southern part of China. The vineyard was divided vertically into three sites (lower, middle and upper, 192, 202 and 212 m above sea level, respectively) and data on soil moisture and other yield and quality parameters were recorded. Among the three vineyard sites, middle site resulted in higher yield compared to the upper and lower sites during winter and summer cropping cycles. However, compared to regular summer cycle, winter cycle provided grapevines with higher quality attributes. Polyphasic OJIP fluorescence transient exhibited a considerable increase in fluorescence intensity at J, I and P phase in the upper and middle sites compared to the lower site due to variation in soil moisture in both seasons. Values of fluorescence parameters including minimal fluorescence, relative variable fluorescence at phase J and I, the maximal quantum yield of photosystem II were also influenced by soil moisture in different sites. Different sites also exhibited a significant difference in total phenolics, flavonoid, antioxidant activity and individual anthocyanin which was influenced by available soil moisture. The present study shows that chlorophyll fluorescence OJIP transient can be used as a sensitive indicator to determine the moisture stress in grape grown in a varied soil. Double cropping proved to be a powerful technique to improve the fruit quality. This result may be useful for the table grape growers to better utilize the vineyard soil variability wi…
format: application/pdf
format: text/html
creator: Sangeeta Mitra
creator: Muhammad Irshad
creator: Biswojit Debnath
creator: Xiaocao Lu
creator: Min Li
creator: Chandra Kanta Dash
creator: Hafiz Muhammad Rizwan
creator: Zhipeng Qiu
creator: Dongliang Qiu
subject: Agricultural Science
subject: Food Science and Technology
description: doi:10.7717/peerj.5592
publisher: PeerJ Inc.
rights: © 2018 Mitra et al.
abstract: Environmental factors greatly influence grape quality. Among them, the effect of within-vineyard variability of soil in relation to soil moisture on table grape under protected condition has rarely been studied. In this present research, we investigated the influence of soil variability, in relation with soil moisture on chlorophyll fluorescence, yield and quality attributes of the “Summer Black” (Vitis vinifera L. × V. labruscana L.) table grape, popularly grown under double cropping system in protected covering in the southern part of China. The vineyard was divided vertically into three sites (lower, middle and upper, 192, 202 and 212 m above sea level, respectively) and data on soil moisture and other yield and quality parameters were recorded. Among the three vineyard sites, middle site resulted in higher yield compared to the upper and lower sites during winter and summer cropping cycles. However, compared to regular summer cycle, winter cycle provided grapevines with higher quality attributes. Polyphasic OJIP fluorescence transient exhibited a considerable increase in fluorescence intensity at J, I and P phase in the upper and middle sites compared to the lower site due to variation in soil moisture in both seasons. Values of fluorescence parameters including minimal fluorescence, relative variable fluorescence at phase J and I, the maximal quantum yield of photosystem II were also influenced by soil moisture in different sites. Different sites also exhibited a significant difference in total phenolics, flavonoid, antioxidant activity and individual anthocyanin which was influenced by available soil moisture. The present study shows that chlorophyll fluorescence OJIP transient can be used as a sensitive indicator to determine the moisture stress in grape grown in a varied soil. Double cropping proved to be a powerful technique to improve the fruit quality. This result may be useful for the table grape growers to better utilize the vineyard soil variability wi…
bibliographic citation: Mitra et al. (2018) Effect of vineyard soil variability on chlorophyll fluorescence, yield and quality of table grape as influenced by soil moisture, grown under double cropping system in protected condition. PeerJ 6:e5592 https://doi.org/10.7717/peerj.5592
date submitted: 2018-03-26
date accepted: 2018-08-16
issued: 2018-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitra
  given name: Sangeeta
author list: Agent
  family name: Irshad
  given name: Muhammad
author list: Agent
  family name: Debnath
  given name: Biswojit
author list: Agent
  family name: Lu
  given name: Xiaocao
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Dash
  given name: Chandra Kanta
author list: Agent
  family name: Rizwan
  given name: Hafiz Muhammad
author list: Agent
  family name: Qiu
  given name: Zhipeng
author list: Agent
  family name: Qiu
  given name: Dongliang
doi: 10.7717/peerj.5592
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-04
copyright: © 2018 Mitra et al.
attribution name: Mitra et al.

An LED-based multi-actinic illumination system for the high throughput study of photosynthetic light responses
type: item
type: AcademicArticle
description: The responses of photosynthetic organisms to light stress are of interest for both fundamental and applied research. Functional traits related to the photoinhibition, the light-induced loss of photosynthetic efficiency, are particularly interesting as this process is a key limiting factor of photosynthetic productivity in algae and plants. The quantitative characterization of light responses is often time-consuming and calls for cost-effective high throughput approaches that enable the fast screening of multiple samples. Here we present a novel illumination system based on the concept of ‘multi-actinic imaging’ of in vivo chlorophyll fluorescence. The system is based on the combination of an array of individually addressable low power RGBW LEDs and custom-designed well plates, allowing for the independent illumination of 64 samples through the digital manipulation of both exposure duration and light intensity. The illumination system is inexpensive and easily fabricated, based on open source electronics, off-the-shelf components, and 3D-printed parts, and is optimized for imaging of chlorophyll fluorescence. The high-throughput potential of the system is illustrated by assessing the functional diversity in light responses of marine macroalgal species, through the fast and simultaneous determination of kinetic parameters characterizing the response to light stress of multiple samples. Although the presented illumination system was primarily designed for the measurement of phenotypic traits related to photosynthetic activity and photoinhibition, it can be potentially used for a number of alternative applications, including the measurement of chloroplast phototaxis and action spectra, or as the basis for microphotobioreactors.
format: application/pdf
format: text/html
creator: João Serôdio
creator: William Schmidt
creator: Jörg C. Frommlet
creator: Gregor Christa
creator: Matthew R. Nitschke
subject: Ecology
subject: Marine Biology
subject: Plant Science
description: doi:10.7717/peerj.5589
publisher: PeerJ Inc.
rights: © 2018 Serôdio et al.
abstract: The responses of photosynthetic organisms to light stress are of interest for both fundamental and applied research. Functional traits related to the photoinhibition, the light-induced loss of photosynthetic efficiency, are particularly interesting as this process is a key limiting factor of photosynthetic productivity in algae and plants. The quantitative characterization of light responses is often time-consuming and calls for cost-effective high throughput approaches that enable the fast screening of multiple samples. Here we present a novel illumination system based on the concept of ‘multi-actinic imaging’ of in vivo chlorophyll fluorescence. The system is based on the combination of an array of individually addressable low power RGBW LEDs and custom-designed well plates, allowing for the independent illumination of 64 samples through the digital manipulation of both exposure duration and light intensity. The illumination system is inexpensive and easily fabricated, based on open source electronics, off-the-shelf components, and 3D-printed parts, and is optimized for imaging of chlorophyll fluorescence. The high-throughput potential of the system is illustrated by assessing the functional diversity in light responses of marine macroalgal species, through the fast and simultaneous determination of kinetic parameters characterizing the response to light stress of multiple samples. Although the presented illumination system was primarily designed for the measurement of phenotypic traits related to photosynthetic activity and photoinhibition, it can be potentially used for a number of alternative applications, including the measurement of chloroplast phototaxis and action spectra, or as the basis for microphotobioreactors.
bibliographic citation: Serôdio et al. (2018) An LED-based multi-actinic illumination system for the high throughput study of photosynthetic light responses. PeerJ 6:e5589 https://doi.org/10.7717/peerj.5589
date submitted: 2018-05-22
date accepted: 2018-08-15
issued: 2018-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serôdio
  given name: João
author list: Agent
  family name: Schmidt
  given name: William
author list: Agent
  family name: Frommlet
  given name: Jörg C.
author list: Agent
  family name: Christa
  given name: Gregor
author list: Agent
  family name: Nitschke
  given name: Matthew R.
doi: 10.7717/peerj.5589
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-04
copyright: ©2018 Serôdio et al.
attribution name: Serôdio et al.

Translational effects of robot-mediated therapy in subacute stroke patients: an experimental evaluation of upper limb motor recovery
type: item
type: AcademicArticle
description: Robot-mediated therapies enhance the recovery of post-stroke patients with motor deficits. Repetitive and repeatable exercises are essential for rehabilitation following brain damage or other disorders that impact the central nervous system, as plasticity permits to reorganize its neural structure, fostering motor relearning. Despite the fact that so many studies claim the validity of robot-mediated therapy in post-stroke patient rehabilitation, it is still difficult to assess to what extent its adoption improves the efficacy of traditional therapy in daily life, and also because most of the studies involved planar robots. In this paper, we report the effects of a 20-session-rehabilitation project involving the Armeo Power robot, an assistive exoskeleton to perform 3D upper limb movements, in addition to conventional rehabilitation therapy, on 10 subacute stroke survivors. Patients were evaluated through clinical scales and a kinematic assessment of the upper limbs, both pre- and post-treatment. A set of indices based on the patients’ 3D kinematic data, gathered from an optoelectronic system, was calculated. Statistical analysis showed a remarkable difference in most parameters between pre- and post-treatment. Significant correlations between the kinematic parameters and clinical scales were found. Our findings suggest that 3D robot-mediated rehabilitation, in addition to conventional therapy, could represent an effective means for the recovery of upper limb disability. Kinematic assessment may represent a valid tool for objectively evaluating the efficacy of the rehabilitation treatment.
format: application/pdf
format: text/html
creator: Eduardo Palermo
creator: Darren Richard Hayes
creator: Emanuele Francesco Russo
creator: Rocco Salvatore Calabrò
creator: Alessandra Pacilli
creator: Serena Filoni
subject: Neurology
description: doi:10.7717/peerj.5544
publisher: PeerJ Inc.
rights: © 2018 Palermo et al.
abstract: Robot-mediated therapies enhance the recovery of post-stroke patients with motor deficits. Repetitive and repeatable exercises are essential for rehabilitation following brain damage or other disorders that impact the central nervous system, as plasticity permits to reorganize its neural structure, fostering motor relearning. Despite the fact that so many studies claim the validity of robot-mediated therapy in post-stroke patient rehabilitation, it is still difficult to assess to what extent its adoption improves the efficacy of traditional therapy in daily life, and also because most of the studies involved planar robots. In this paper, we report the effects of a 20-session-rehabilitation project involving the Armeo Power robot, an assistive exoskeleton to perform 3D upper limb movements, in addition to conventional rehabilitation therapy, on 10 subacute stroke survivors. Patients were evaluated through clinical scales and a kinematic assessment of the upper limbs, both pre- and post-treatment. A set of indices based on the patients’ 3D kinematic data, gathered from an optoelectronic system, was calculated. Statistical analysis showed a remarkable difference in most parameters between pre- and post-treatment. Significant correlations between the kinematic parameters and clinical scales were found. Our findings suggest that 3D robot-mediated rehabilitation, in addition to conventional therapy, could represent an effective means for the recovery of upper limb disability. Kinematic assessment may represent a valid tool for objectively evaluating the efficacy of the rehabilitation treatment.
bibliographic citation: Palermo et al. (2018) Translational effects of robot-mediated therapy in subacute stroke patients: an experimental evaluation of upper limb motor recovery. PeerJ 6:e5544 https://doi.org/10.7717/peerj.5544
date submitted: 2018-04-07
date accepted: 2018-08-09
issued: 2018-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palermo
  given name: Eduardo
author list: Agent
  family name: Hayes
  given name: Darren Richard
author list: Agent
  family name: Russo
  given name: Emanuele Francesco
author list: Agent
  family name: Calabrò
  given name: Rocco Salvatore
author list: Agent
  family name: Pacilli
  given name: Alessandra
author list: Agent
  family name: Filoni
  given name: Serena
doi: 10.7717/peerj.5544
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-04
copyright: © 2018 Palermo et al.
attribution name: Palermo et al.

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