PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bioeffects of Prunus spinosa L. fruit ethanol extract on reproduction and phenotypic plasticity of Trichoplax adhaerens Schulze, 1883 (Placozoa)
items: Selection of reference genes for quantitative real-time PCR analysis in cucumber (Cucumis sativus L.), pumpkin (Cucurbita moschata Duch.) and cucumber–pumpkin grafted plants
items: The coast of giants: an anthropometric survey of high schoolers on the Adriatic coast of Croatia
items: Boto (Inia geoffrensis—Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River—Amazonas, Brazil: are they related?
items: Validation of Plasmodium falciparum deoxyhypusine synthase as an antimalarial target
items: Comparisons of WUE in twelve genotypes of winter wheat and the relationship between δ13C and WUE
items: Understanding the NaCl-dependent behavior of hydrogen production of a marine bacterium, Vibrio tritonius
items: Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study
items: Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico
items: Assessment on latitudinal tree species richness using environmental factors in the southeastern United States

Bioeffects of Prunus spinosa L. fruit ethanol extract on reproduction and phenotypic plasticity of Trichoplax adhaerens Schulze, 1883 (Placozoa)
type: item
type: AcademicArticle
description: The aim of this work was to test and analyse the bioeffects of Prunus spinosa L. (Rosacaee) fruit ethanol extract on Trichoplax adhaerens Schulze, 1883 (Placozoa) laboratory cultures which—for the first time—were employed as in vivo biological model to assess the bioactivity of a natural extract. The ethanol extract of P. spinosa was administrated during a 46 day experimental period; ultrastructural (by optical, confocal, TEM and SEM microscopy) and morphometric analyses indicated that treated Trichoplax adhaerens showed significant differences in viability, reproductive modalities, body shape and colour with respect to the control group. Finally, P. spinosa bioactive compounds seem to exert profound protective effects on T. adhaerens reproduction and phenotype. Our results may support additional investigations related to other bioactive compounds properties useful for nutraceutical preparations to be used as food supplements.
format: application/pdf
format: text/html
creator: Maria Cristina Albertini
creator: Daniele Fraternale
creator: Federica Semprucci
creator: Silvio Cecchini
creator: Mariastella Colomba
creator: Marco B.L. Rocchi
creator: Davide Sisti
creator: Barbara Di Giacomo
creator: Michele Mari
creator: Luigia Sabatini
creator: Lucia Cesaroni
creator: Maria Balsamo
creator: Loretta Guidi
subject: Animal Behavior
subject: Food Science and Technology
subject: Toxicology
subject: Nutrition
description: doi:10.7717/peerj.6789
publisher: PeerJ Inc.
rights: © 2019 Albertini et al.
abstract: The aim of this work was to test and analyse the bioeffects of Prunus spinosa L. (Rosacaee) fruit ethanol extract on Trichoplax adhaerens Schulze, 1883 (Placozoa) laboratory cultures which—for the first time—were employed as in vivo biological model to assess the bioactivity of a natural extract. The ethanol extract of P. spinosa was administrated during a 46 day experimental period; ultrastructural (by optical, confocal, TEM and SEM microscopy) and morphometric analyses indicated that treated Trichoplax adhaerens showed significant differences in viability, reproductive modalities, body shape and colour with respect to the control group. Finally, P. spinosa bioactive compounds seem to exert profound protective effects on T. adhaerens reproduction and phenotype. Our results may support additional investigations related to other bioactive compounds properties useful for nutraceutical preparations to be used as food supplements.
bibliographic citation: Albertini et al. (2019) Bioeffects of Prunus spinosa L. fruit ethanol extract on reproduction and phenotypic plasticity of Trichoplax adhaerens Schulze, 1883 (Placozoa). PeerJ 7:e6789 https://doi.org/10.7717/peerj.6789
date submitted: 2018-11-25
date accepted: 2019-03-14
issued: 2019-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albertini
  given name: Maria Cristina
author list: Agent
  family name: Fraternale
  given name: Daniele
author list: Agent
  family name: Semprucci
  given name: Federica
author list: Agent
  family name: Cecchini
  given name: Silvio
author list: Agent
  family name: Colomba
  given name: Mariastella
author list: Agent
  family name: Rocchi
  given name: Marco B.L.
author list: Agent
  family name: Sisti
  given name: Davide
author list: Agent
  family name: Di Giacomo
  given name: Barbara
author list: Agent
  family name: Mari
  given name: Michele
author list: Agent
  family name: Sabatini
  given name: Luigia
author list: Agent
  family name: Cesaroni
  given name: Lucia
author list: Agent
  family name: Balsamo
  given name: Maria
author list: Agent
  family name: Guidi
  given name: Loretta
doi: 10.7717/peerj.6789
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-18
copyright: ©2019 Albertini et al.
attribution name: Albertini et al.

Selection of reference genes for quantitative real-time PCR analysis in cucumber (Cucumis sativus L.), pumpkin (Cucurbita moschata Duch.) and cucumber–pumpkin grafted plants
type: item
type: AcademicArticle
description: Background Quantitative real-time PCR (qRT-PCR) is a commonly used high-throughput technique to measure mRNA transcript levels. The accuracy of this evaluation of gene expression depends on the use of optimal reference genes. Cucumber–pumpkin grafted plants, made by grafting a cucumber scion onto pumpkin rootstock, are superior to either parent plant, as grafting conveys many advantages. However, although many reliable reference genes have been identified in both cucumber and pumpkin, none have been obtained for cucumber–pumpkin grafted plants. Methods In this work, 12 candidate reference genes, including eight traditional genes and four novel genes identified from our transcriptome data, were selected to assess their expression stability. Their expression levels in 25 samples, including three cucumber and three pumpkin samples from different organs, and 19 cucumber–pumpkin grafted samples from different organs, conditions, and varieties, were analyzed by qRT-PCR, and the stability of their expression was assessed by the comparative ΔCt method, geNorm, NormFinder, BestKeeper, and RefFinder. Results The results showed that the most suitable reference gene varied dependent on the organs, conditions, and varieties. CACS and 40SRPS8 were the most stable reference genes for all samples in our research. TIP41 and CACS showed the most stable expression in different cucumber organs, TIP41 and PP2A were the optimal reference genes in pumpkin organs, and CACS and 40SRPS8 were the most stable genes in all grafted cucumber samples. However, the optimal reference gene varied under different conditions. CACS and 40SRPS8 were the best combination of genes in different organs of cucumber–pumpkin grafted plants, TUA and RPL36Aa were the most stable in the graft union under cold stress, LEA26 and ARF showed the most stable expression in the graft union during the healing process, and TIP41 and PP2A were the most stable across different varieties of cucumber–pumpkin grafted plants. Th…
format: application/pdf
format: text/html
creator: Li Miao
creator: Xing Qin
creator: Lihong Gao
creator: Qing Li
creator: Shuzhen Li
creator: Chaoxing He
creator: Yansu Li
creator: Xianchang Yu
subject: Agricultural Science
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6536
publisher: PeerJ Inc.
rights: © 2019 Miao et al.
abstract: Background Quantitative real-time PCR (qRT-PCR) is a commonly used high-throughput technique to measure mRNA transcript levels. The accuracy of this evaluation of gene expression depends on the use of optimal reference genes. Cucumber–pumpkin grafted plants, made by grafting a cucumber scion onto pumpkin rootstock, are superior to either parent plant, as grafting conveys many advantages. However, although many reliable reference genes have been identified in both cucumber and pumpkin, none have been obtained for cucumber–pumpkin grafted plants. Methods In this work, 12 candidate reference genes, including eight traditional genes and four novel genes identified from our transcriptome data, were selected to assess their expression stability. Their expression levels in 25 samples, including three cucumber and three pumpkin samples from different organs, and 19 cucumber–pumpkin grafted samples from different organs, conditions, and varieties, were analyzed by qRT-PCR, and the stability of their expression was assessed by the comparative ΔCt method, geNorm, NormFinder, BestKeeper, and RefFinder. Results The results showed that the most suitable reference gene varied dependent on the organs, conditions, and varieties. CACS and 40SRPS8 were the most stable reference genes for all samples in our research. TIP41 and CACS showed the most stable expression in different cucumber organs, TIP41 and PP2A were the optimal reference genes in pumpkin organs, and CACS and 40SRPS8 were the most stable genes in all grafted cucumber samples. However, the optimal reference gene varied under different conditions. CACS and 40SRPS8 were the best combination of genes in different organs of cucumber–pumpkin grafted plants, TUA and RPL36Aa were the most stable in the graft union under cold stress, LEA26 and ARF showed the most stable expression in the graft union during the healing process, and TIP41 and PP2A were the most stable across different varieties of cucumber–pumpkin grafted plants. Th…
bibliographic citation: Miao et al. (2019) Selection of reference genes for quantitative real-time PCR analysis in cucumber (Cucumis sativus L.), pumpkin (Cucurbita moschata Duch.) and cucumber–pumpkin grafted plants. PeerJ 7:e6536 https://doi.org/10.7717/peerj.6536
date submitted: 2018-10-29
date accepted: 2019-01-29
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miao
  given name: Li
author list: Agent
  family name: Qin
  given name: Xing
author list: Agent
  family name: Gao
  given name: Lihong
author list: Agent
  family name: Li
  given name: Qing
author list: Agent
  family name: Li
  given name: Shuzhen
author list: Agent
  family name: He
  given name: Chaoxing
author list: Agent
  family name: Li
  given name: Yansu
author list: Agent
  family name: Yu
  given name: Xianchang
doi: 10.7717/peerj.6536
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Miao et al.
attribution name: Miao et al.

The coast of giants: an anthropometric survey of high schoolers on the Adriatic coast of Croatia
type: item
type: AcademicArticle
description: The aim of this anthropometric survey was to map regional differences in height and body proportions in eight counties adjacent to the Adriatic coast of Croatia. Body height was measured in 1,803 males and 782 females aged 17–20 years at 66 schools in 23 towns. When corrected for population size in regions, mean male height is 182.6 cm in all eight counties, 182.8 cm in seven counties of Adriatic Croatia, and 183.7 cm in four counties of Dalmatia proper. Regional variation is considerable: from 180.6 cm in the county of Karlovac to 184.1 cm in the county of Split-Dalmacija. The mean height of females is based on more limited data (168.0 cm in seven counties). These results show that young men from Dalmatia are currently the tallest in the world in the age category of 18 years, and the north-to-south gradient of increasing stature on the Adriatic coast largely mirrors that in neighbouring Bosnia and Herzegovina (BiH). The extraordinary values of height in Croatia and BiH can most likely be explained by unique genetic predispositions that are shared by the local populations of the Dinaric Alps.
format: application/pdf
format: text/html
creator: Pavel Grasgruber
creator: Stipan Prce
creator: Nikola Stračárová
creator: Eduard Hrazdíra
creator: Jan Cacek
creator: Stevo Popović
creator: Sylva Hřebíčková
creator: Predrag Potpara
creator: Ivan Davidovič
creator: Tomáš Kalina
subject: Anthropology
subject: Nutrition
subject: Pediatrics
description: doi:10.7717/peerj.6598
publisher: PeerJ Inc.
rights: © 2019 Grasgruber et al.
abstract: The aim of this anthropometric survey was to map regional differences in height and body proportions in eight counties adjacent to the Adriatic coast of Croatia. Body height was measured in 1,803 males and 782 females aged 17–20 years at 66 schools in 23 towns. When corrected for population size in regions, mean male height is 182.6 cm in all eight counties, 182.8 cm in seven counties of Adriatic Croatia, and 183.7 cm in four counties of Dalmatia proper. Regional variation is considerable: from 180.6 cm in the county of Karlovac to 184.1 cm in the county of Split-Dalmacija. The mean height of females is based on more limited data (168.0 cm in seven counties). These results show that young men from Dalmatia are currently the tallest in the world in the age category of 18 years, and the north-to-south gradient of increasing stature on the Adriatic coast largely mirrors that in neighbouring Bosnia and Herzegovina (BiH). The extraordinary values of height in Croatia and BiH can most likely be explained by unique genetic predispositions that are shared by the local populations of the Dinaric Alps.
bibliographic citation: Grasgruber et al. (2019) The coast of giants: an anthropometric survey of high schoolers on the Adriatic coast of Croatia. PeerJ 7:e6598 https://doi.org/10.7717/peerj.6598
date submitted: 2017-10-30
date accepted: 2019-02-11
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grasgruber
  given name: Pavel
author list: Agent
  family name: Prce
  given name: Stipan
author list: Agent
  family name: Stračárová
  given name: Nikola
author list: Agent
  family name: Hrazdíra
  given name: Eduard
author list: Agent
  family name: Cacek
  given name: Jan
author list: Agent
  family name: Popović
  given name: Stevo
author list: Agent
  family name: Hřebíčková
  given name: Sylva
author list: Agent
  family name: Potpara
  given name: Predrag
author list: Agent
  family name: Davidovič
  given name: Ivan
author list: Agent
  family name: Kalina
  given name: Tomáš
doi: 10.7717/peerj.6598
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Grasgruber et al.
attribution name: Grasgruber et al.

Boto (Inia geoffrensis—Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River—Amazonas, Brazil: are they related?
type: item
type: AcademicArticle
description: The Negro River currently has seven floating houses where tourists can feed and interact with botos, each with its own history of how these aggregations were formed. Some keepers say these groups are familial, even reporting individuals being born into the group. However, behavioral studies have shown that botos are solitary, only forming groups at feeding areas and during the mating season. In the present study we used 12 microsatellite and molecular sex markers to characterize relationships within and between two boto aggregations (ten and seven botos each) in the lower Negro River. Molecular sexing revealed that all botos sampled from both aggregations were males. This may be explained by habitat preference, as male botos are primarily found in the main channels of large rivers, whereas females prefer more protected areas, such as flooded forests and its channels and lakes. Most of the animals were unrelated within each aggregation, demonstrating that these aggregations are not normally formed due to kinship bonds, but are exclusively for feeding, as botos learn that these places provide easy access to food. This study provides important information that helps us understand how human interaction is affecting the social structure and behavior of these animals.
format: application/pdf
format: text/html
creator: Waleska Gravena
creator: Tomas Hrbek
creator: Vera Maria Ferreira da Silva
creator: Izeni Pires Farias
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6692
publisher: PeerJ Inc.
rights: © 2019 Gravena et al.
abstract: The Negro River currently has seven floating houses where tourists can feed and interact with botos, each with its own history of how these aggregations were formed. Some keepers say these groups are familial, even reporting individuals being born into the group. However, behavioral studies have shown that botos are solitary, only forming groups at feeding areas and during the mating season. In the present study we used 12 microsatellite and molecular sex markers to characterize relationships within and between two boto aggregations (ten and seven botos each) in the lower Negro River. Molecular sexing revealed that all botos sampled from both aggregations were males. This may be explained by habitat preference, as male botos are primarily found in the main channels of large rivers, whereas females prefer more protected areas, such as flooded forests and its channels and lakes. Most of the animals were unrelated within each aggregation, demonstrating that these aggregations are not normally formed due to kinship bonds, but are exclusively for feeding, as botos learn that these places provide easy access to food. This study provides important information that helps us understand how human interaction is affecting the social structure and behavior of these animals.
bibliographic citation: Gravena et al. (2019) Boto (Inia geoffrensis—Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River—Amazonas, Brazil: are they related?. PeerJ 7:e6692 https://doi.org/10.7717/peerj.6692
date submitted: 2018-03-20
date accepted: 2019-02-28
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gravena
  given name: Waleska
author list: Agent
  family name: Hrbek
  given name: Tomas
author list: Agent
  family name: da Silva
  given name: Vera Maria Ferreira
author list: Agent
  family name: Farias
  given name: Izeni Pires
doi: 10.7717/peerj.6692
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Gravena et al.
attribution name: Gravena et al.

Validation of Plasmodium falciparum deoxyhypusine synthase as an antimalarial target
type: item
type: AcademicArticle
description: Background Hypusination is an essential post-translational modification in eukaryotes. The two enzymes required for this modification, namely deoxyhypusine synthase (DHS) and deoxyhypusine hydrolase are also conserved. Plasmodium falciparum human malaria parasites possess genes for both hypusination enzymes, which are hypothesized to be targets of antimalarial drugs. Methods Transgenic P. falciparum parasites with modification of the PF3D7_1412600 gene encoding PfDHS enzyme were created by insertion of the glmS riboswitch or the M9 inactive variant. The PfDHS protein was studied in transgenic parasites by confocal microscopy and Western immunoblotting. The biochemical function of PfDHS enzyme in parasites was assessed by hypusination and nascent protein synthesis assays. Gene essentiality was assessed by competitive growth assays and chemogenomic profiling. Results Clonal transgenic parasites with integration of glmS riboswitch downstream of the PfDHS gene were established. PfDHS protein was present in the cytoplasm of transgenic parasites in asexual stages. The PfDHS protein could be attenuated fivefold in transgenic parasites with an active riboswitch, whereas PfDHS protein expression was unaffected in control transgenic parasites with insertion of the riboswitch-inactive sequence. Attenuation of PfDHS expression for 72 h led to a significant reduction of hypusinated protein; however, global protein synthesis was unaffected. Parasites with attenuated PfDHS expression showed a significant growth defect, although their decline was not as rapid as parasites with attenuated dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) expression. PfDHS-attenuated parasites showed increased sensitivity to N1-guanyl-1,7-diaminoheptane, a structural analog of spermidine, and a known inhibitor of DHS enzymes. Discussion Loss of PfDHS function leads to reduced hypusination, which may be important for synthesis of some essential proteins. The growth defect in parasites with atte…
format: application/pdf
format: text/html
creator: Aiyada Aroonsri
creator: Navaporn Posayapisit
creator: Jindaporn Kongsee
creator: Onsiri Siripan
creator: Danoo Vitsupakorn
creator: Sugunya Utaida
creator: Chairat Uthaipibull
creator: Sumalee Kamchonwongpaisan
creator: Philip J. Shaw
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.6713
publisher: PeerJ Inc.
rights: © 2019 Aroonsri et al.
abstract: Background Hypusination is an essential post-translational modification in eukaryotes. The two enzymes required for this modification, namely deoxyhypusine synthase (DHS) and deoxyhypusine hydrolase are also conserved. Plasmodium falciparum human malaria parasites possess genes for both hypusination enzymes, which are hypothesized to be targets of antimalarial drugs. Methods Transgenic P. falciparum parasites with modification of the PF3D7_1412600 gene encoding PfDHS enzyme were created by insertion of the glmS riboswitch or the M9 inactive variant. The PfDHS protein was studied in transgenic parasites by confocal microscopy and Western immunoblotting. The biochemical function of PfDHS enzyme in parasites was assessed by hypusination and nascent protein synthesis assays. Gene essentiality was assessed by competitive growth assays and chemogenomic profiling. Results Clonal transgenic parasites with integration of glmS riboswitch downstream of the PfDHS gene were established. PfDHS protein was present in the cytoplasm of transgenic parasites in asexual stages. The PfDHS protein could be attenuated fivefold in transgenic parasites with an active riboswitch, whereas PfDHS protein expression was unaffected in control transgenic parasites with insertion of the riboswitch-inactive sequence. Attenuation of PfDHS expression for 72 h led to a significant reduction of hypusinated protein; however, global protein synthesis was unaffected. Parasites with attenuated PfDHS expression showed a significant growth defect, although their decline was not as rapid as parasites with attenuated dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) expression. PfDHS-attenuated parasites showed increased sensitivity to N1-guanyl-1,7-diaminoheptane, a structural analog of spermidine, and a known inhibitor of DHS enzymes. Discussion Loss of PfDHS function leads to reduced hypusination, which may be important for synthesis of some essential proteins. The growth defect in parasites with atte…
bibliographic citation: Aroonsri et al. (2019) Validation of Plasmodium falciparum deoxyhypusine synthase as an antimalarial target. PeerJ 7:e6713 https://doi.org/10.7717/peerj.6713
date submitted: 2018-08-09
date accepted: 2019-03-05
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aroonsri
  given name: Aiyada
author list: Agent
  family name: Posayapisit
  given name: Navaporn
author list: Agent
  family name: Kongsee
  given name: Jindaporn
author list: Agent
  family name: Siripan
  given name: Onsiri
author list: Agent
  family name: Vitsupakorn
  given name: Danoo
author list: Agent
  family name: Utaida
  given name: Sugunya
author list: Agent
  family name: Uthaipibull
  given name: Chairat
author list: Agent
  family name: Kamchonwongpaisan
  given name: Sumalee
author list: Agent
  family name: Shaw
  given name: Philip J.
doi: 10.7717/peerj.6713
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: © 2019 Aroonsri et al.
attribution name: Aroonsri et al.

Comparisons of WUE in twelve genotypes of winter wheat and the relationship between δ13C and WUE
type: item
type: AcademicArticle
description: Twelve winter wheat (Triticum aestivum) genotypes were examined for differences in grain yield, water use efficiency (WUE), and stable carbon isotope composition (δ13C) in flag leaves. The plants were subjected to rain-fed treatment and supplemental irrigation at the jointing and anthesis stages, during the 2015–2016 and 2016–2017 winter wheat growing seasons. The relationships between δ13C with grain yield and WUE were analyzed under two different water environments. The results indicated that there were significant differences in δ13C, grain yield, and WUE among wheat genotypes both under rain-fed and supplemental irrigation conditions. The δ13C values increased with grain-filling proceeding, the δ13C being lower under supplemental irrigation treatment than that under rain-fed treatment. The relationships between the average of δ13C with grain yield and WUE were significantly positive during three measurement periods (R2 = 0.5785 − 0.8258), whether under rain-fed or irrigation environments. This suggests that δ13C might be associated with the grain yield and WUE in winter wheat under rain-fed and supplemental irrigation conditions in the climate region of the northwest Huang-Huai-Hai Plain of China.
format: application/pdf
format: text/html
creator: Guirong Huang
creator: Xinying Zhang
creator: Yajing Wang
creator: Fu Feng
creator: Xurong Mei
creator: Xiuli Zhong
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6767
publisher: PeerJ Inc.
rights: © 2019 Huang et al.
abstract: Twelve winter wheat (Triticum aestivum) genotypes were examined for differences in grain yield, water use efficiency (WUE), and stable carbon isotope composition (δ13C) in flag leaves. The plants were subjected to rain-fed treatment and supplemental irrigation at the jointing and anthesis stages, during the 2015–2016 and 2016–2017 winter wheat growing seasons. The relationships between δ13C with grain yield and WUE were analyzed under two different water environments. The results indicated that there were significant differences in δ13C, grain yield, and WUE among wheat genotypes both under rain-fed and supplemental irrigation conditions. The δ13C values increased with grain-filling proceeding, the δ13C being lower under supplemental irrigation treatment than that under rain-fed treatment. The relationships between the average of δ13C with grain yield and WUE were significantly positive during three measurement periods (R2 = 0.5785 − 0.8258), whether under rain-fed or irrigation environments. This suggests that δ13C might be associated with the grain yield and WUE in winter wheat under rain-fed and supplemental irrigation conditions in the climate region of the northwest Huang-Huai-Hai Plain of China.
bibliographic citation: Huang et al. (2019) Comparisons of WUE in twelve genotypes of winter wheat and the relationship between δ13C and WUE. PeerJ 7:e6767 https://doi.org/10.7717/peerj.6767
date submitted: 2018-11-21
date accepted: 2019-03-08
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Guirong
author list: Agent
  family name: Zhang
  given name: Xinying
author list: Agent
  family name: Wang
  given name: Yajing
author list: Agent
  family name: Feng
  given name: Fu
author list: Agent
  family name: Mei
  given name: Xurong
author list: Agent
  family name: Zhong
  given name: Xiuli
doi: 10.7717/peerj.6767
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Huang et al.
attribution name: Huang et al.

Understanding the NaCl-dependent behavior of hydrogen production of a marine bacterium, Vibrio tritonius
type: item
type: AcademicArticle
description: Biohydrogen is one of the most suitable clean energy sources for sustaining a fossil fuel independent society. The use of both land and ocean bioresources as feedstocks show great potential in maximizing biohydrogen production, but sodium ion is one of the main obstacles in efficient bacterial biohydrogen production. Vibrio tritonius strain AM2 can perform efficient hydrogen production with a molar yield of 1.7 mol H2/mol mannitol, which corresponds to 85% theoretical molar yield of H2 production, under saline conditions. With a view to maximizing the hydrogen production using marine biomass, it is important to accumulate knowledge on the effects of salts on the hydrogen production kinetics. Here, we show the kinetics in batch hydrogen production of V. tritonius strain AM2 to investigate the response to various NaCl concentrations. The modified Han–Levenspiel model reveals that salt inhibition in hydrogen production using V. tritonius starts precisely at the point where 10.2 g/L of NaCl is added, and is critically inhibited at 46 g/L. NaCl concentration greatly affects the substrate consumption which in turn affects both growth and hydrogen production. The NaCl-dependent behavior of fermentative hydrogen production of V. tritonius compared to that of Escherichia coli JCM 1649 reveals the marine-adapted fermentative hydrogen production system in V. tritonius. V. tritonius AM2 is capable of producing hydrogen from seaweed carbohydrate under a wide range of NaCl concentrations (5 to 46 g/L). The optimal salt concentration producing the highest levels of hydrogen, optimal substrate consumption and highest molar hydrogen yield is at 10 g/L NaCl (1.0% (w/v)).
format: application/pdf
format: text/html
creator: Nurhidayu Al-saari
creator: Eri Amada
creator: Yuta Matsumura
creator: Mami Tanaka
creator: Sayaka Mino
creator: Tomoo Sawabe
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.6769
publisher: PeerJ Inc.
rights: © 2019 Al-saari et al.
abstract: Biohydrogen is one of the most suitable clean energy sources for sustaining a fossil fuel independent society. The use of both land and ocean bioresources as feedstocks show great potential in maximizing biohydrogen production, but sodium ion is one of the main obstacles in efficient bacterial biohydrogen production. Vibrio tritonius strain AM2 can perform efficient hydrogen production with a molar yield of 1.7 mol H2/mol mannitol, which corresponds to 85% theoretical molar yield of H2 production, under saline conditions. With a view to maximizing the hydrogen production using marine biomass, it is important to accumulate knowledge on the effects of salts on the hydrogen production kinetics. Here, we show the kinetics in batch hydrogen production of V. tritonius strain AM2 to investigate the response to various NaCl concentrations. The modified Han–Levenspiel model reveals that salt inhibition in hydrogen production using V. tritonius starts precisely at the point where 10.2 g/L of NaCl is added, and is critically inhibited at 46 g/L. NaCl concentration greatly affects the substrate consumption which in turn affects both growth and hydrogen production. The NaCl-dependent behavior of fermentative hydrogen production of V. tritonius compared to that of Escherichia coli JCM 1649 reveals the marine-adapted fermentative hydrogen production system in V. tritonius. V. tritonius AM2 is capable of producing hydrogen from seaweed carbohydrate under a wide range of NaCl concentrations (5 to 46 g/L). The optimal salt concentration producing the highest levels of hydrogen, optimal substrate consumption and highest molar hydrogen yield is at 10 g/L NaCl (1.0% (w/v)).
bibliographic citation: Al-saari et al. (2019) Understanding the NaCl-dependent behavior of hydrogen production of a marine bacterium, Vibrio tritonius. PeerJ 7:e6769 https://doi.org/10.7717/peerj.6769
date submitted: 2018-09-11
date accepted: 2019-03-12
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-saari
  given name: Nurhidayu
author list: Agent
  family name: Amada
  given name: Eri
author list: Agent
  family name: Matsumura
  given name: Yuta
author list: Agent
  family name: Tanaka
  given name: Mami
author list: Agent
  family name: Mino
  given name: Sayaka
author list: Agent
  family name: Sawabe
  given name: Tomoo
doi: 10.7717/peerj.6769
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Al-saari et al.
attribution name: Al-saari et al.

Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study
type: item
type: AcademicArticle
description: Aims and objectives To examine changes in patient-reported fatigue, over a twelve month period, in rheumatoid arthritis patients who commence biologic treatment, and to identify possible predictors for such changes. Background Fatigue is a burdensome symptom for patients with rheumatoid arthritis. Despite biologics being effective in reducing disease activity, patients still report fatigue. Design A longitudinal observational study. Methods A total of 48 patients were enrolled in the study. Fatigue was measured by the Fatigue Severity Scale. Independent samples T-tests were used to test gender differences, and paired samples T-tests were used to measure differences between repeated measures. Bivariate and multiple regression analyses were used to examine potential predictors for changes in fatigue, such as age, sex, Disease Activity Score 28, pain and physical and emotional well-being. Results Forty-seven patients completed the study. From baseline to 12-month follow-up, fatigue decreased significantly in both women and men. Analyses of predictors were performed step-wise, and the final model included sex and physical well-being. The results from this final step showed that female sex was the only significant predictor for changes in fatigue. Conclusion Patients commencing biologic therapy reported a significant reduction in fatigue. Female sex was a significant predictor of changes in fatigue. Relevance to clinical practice Despite improvements in pharmacological treatment, patients with rheumatoid arthritis still report fatigue. This is a multifaceted health problem encompassing personal and emotional factors in addition to the clinical factors directly connected to the disease.
format: application/pdf
format: text/html
creator: Hege Selheim Rinke
creator: Clara Beate Gram Gjesdal
creator: Heidi Markussen
creator: Jörg Assmus
creator: Gerd Karin Natvig
subject: Allergy and Clinical Immunology
subject: Nursing
subject: Rheumatology
description: doi:10.7717/peerj.6771
publisher: PeerJ Inc.
rights: © 2019 Rinke et al.
abstract: Aims and objectives To examine changes in patient-reported fatigue, over a twelve month period, in rheumatoid arthritis patients who commence biologic treatment, and to identify possible predictors for such changes. Background Fatigue is a burdensome symptom for patients with rheumatoid arthritis. Despite biologics being effective in reducing disease activity, patients still report fatigue. Design A longitudinal observational study. Methods A total of 48 patients were enrolled in the study. Fatigue was measured by the Fatigue Severity Scale. Independent samples T-tests were used to test gender differences, and paired samples T-tests were used to measure differences between repeated measures. Bivariate and multiple regression analyses were used to examine potential predictors for changes in fatigue, such as age, sex, Disease Activity Score 28, pain and physical and emotional well-being. Results Forty-seven patients completed the study. From baseline to 12-month follow-up, fatigue decreased significantly in both women and men. Analyses of predictors were performed step-wise, and the final model included sex and physical well-being. The results from this final step showed that female sex was the only significant predictor for changes in fatigue. Conclusion Patients commencing biologic therapy reported a significant reduction in fatigue. Female sex was a significant predictor of changes in fatigue. Relevance to clinical practice Despite improvements in pharmacological treatment, patients with rheumatoid arthritis still report fatigue. This is a multifaceted health problem encompassing personal and emotional factors in addition to the clinical factors directly connected to the disease.
bibliographic citation: Rinke et al. (2019) Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study. PeerJ 7:e6771 https://doi.org/10.7717/peerj.6771
date submitted: 2018-07-10
date accepted: 2019-03-12
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rinke
  given name: Hege Selheim
author list: Agent
  family name: Gjesdal
  given name: Clara Beate Gram
author list: Agent
  family name: Markussen
  given name: Heidi
author list: Agent
  family name: Assmus
  given name: Jörg
author list: Agent
  family name: Natvig
  given name: Gerd Karin
doi: 10.7717/peerj.6771
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Rinke et al.
attribution name: Rinke et al.

Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico
type: item
type: AcademicArticle
description: Background The begomovirus, squash leaf curl virus (SLCuV) is one of the causal agents of squash leaf curl (SLC) disease, which is among the most destructive diseases of cucurbit crops in tropical, subtropical, and semiarid regions worldwide. This disease was originally reported in the American continent with subsequent spread to the Mediterranean basin. Up to now, SLCuV has only been detected by PCR in Mexico. This study provides the first complete sequence of a Mexican SLCuV isolate from Baja California Sur (BCS). In addition, the genome of the virus was characterized, establishing its phylogenetic relationship with other SLCuV isolates. Methods The full genome (DNA-A and DNA-B) was amplified by rolling circle amplification, cloned and sequenced and the open reading frames (ORF) were annotated. Virus identification was performed according to the International Committee on Taxonomy of Viruses (ICTV) criteria for begomovirus species demarcation. To infer evolutionary relationship with other SLCuV isolates, phylogenetic and recombination analyses were performed. Results The SLCuV-[MX-BCS-La Paz-16] genome (DNA-A and DNA-B) had 99% identity with SLCuV reference genomes. The phylogenetic analysis showed that SLCuV-[MX-BCS-La Paz-16] is closely related to SLCuV isolates from the Middle East (Egypt, Israel, Palestine and Lebanon). No evidence of interspecific recombination was determined and iterons were 100% identical in all isolates in the SLCuV clade. Conclusions SLCuV-[MX-BCS-La Paz-16] showed low genetic variability in its genome, which could be due to a local adaptation process (isolate environment), suggesting that SLCuV isolates from the Middle East could have derived from the southwestern United States of America (USA) and northwestern Mexico.
format: application/pdf
format: text/html
creator: Diana Medina-Hernández
creator: M. Goretty Caamal-Chan
creator: Mayela Vargas-Salinas
creator: Abraham Loera-Muro
creator: Aarón Barraza
creator: Ramón Jaime Holguín-Peña
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.6774
publisher: PeerJ Inc.
rights: © 2019 Medina-Hernández et al.
abstract: Background The begomovirus, squash leaf curl virus (SLCuV) is one of the causal agents of squash leaf curl (SLC) disease, which is among the most destructive diseases of cucurbit crops in tropical, subtropical, and semiarid regions worldwide. This disease was originally reported in the American continent with subsequent spread to the Mediterranean basin. Up to now, SLCuV has only been detected by PCR in Mexico. This study provides the first complete sequence of a Mexican SLCuV isolate from Baja California Sur (BCS). In addition, the genome of the virus was characterized, establishing its phylogenetic relationship with other SLCuV isolates. Methods The full genome (DNA-A and DNA-B) was amplified by rolling circle amplification, cloned and sequenced and the open reading frames (ORF) were annotated. Virus identification was performed according to the International Committee on Taxonomy of Viruses (ICTV) criteria for begomovirus species demarcation. To infer evolutionary relationship with other SLCuV isolates, phylogenetic and recombination analyses were performed. Results The SLCuV-[MX-BCS-La Paz-16] genome (DNA-A and DNA-B) had 99% identity with SLCuV reference genomes. The phylogenetic analysis showed that SLCuV-[MX-BCS-La Paz-16] is closely related to SLCuV isolates from the Middle East (Egypt, Israel, Palestine and Lebanon). No evidence of interspecific recombination was determined and iterons were 100% identical in all isolates in the SLCuV clade. Conclusions SLCuV-[MX-BCS-La Paz-16] showed low genetic variability in its genome, which could be due to a local adaptation process (isolate environment), suggesting that SLCuV isolates from the Middle East could have derived from the southwestern United States of America (USA) and northwestern Mexico.
bibliographic citation: Medina-Hernández et al. (2019) Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico. PeerJ 7:e6774 https://doi.org/10.7717/peerj.6774
date submitted: 2018-10-30
date accepted: 2019-03-12
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medina-Hernández
  given name: Diana
author list: Agent
  family name: Caamal-Chan
  given name: M. Goretty
author list: Agent
  family name: Vargas-Salinas
  given name: Mayela
author list: Agent
  family name: Loera-Muro
  given name: Abraham
author list: Agent
  family name: Barraza
  given name: Aarón
author list: Agent
  family name: Holguín-Peña
  given name: Ramón Jaime
doi: 10.7717/peerj.6774
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Medina-Hernández et al.
attribution name: Medina-Hernández et al.

Assessment on latitudinal tree species richness using environmental factors in the southeastern United States
type: item
type: AcademicArticle
description: The southeastern region of the United States exhibits an unusual trend of decreasing tree species richness (TSR) from higher to lower latitudes over the Florida peninsula. This trend contradicts the widely marked latitudinal diversity gradient where species richness is highest in tropical zones and decreases towards extratropical regions. This study aims to assess the environmental factors that prompt this atypical inverse latitudinal gradient seen in TSR using the USDA Forest Service’s Forest Inventory and Analysis (FIA) database. Fifteen variables under four categories of forested area, groundwater, soil properties, and climate groups were examined to model TSR in the region. Generalized linear models (GLMs) with Poisson distributions first assessed individual variables to test explanatory power then the LASSO regularization method was utilized to extract two subsets of the most influential variables to predict TSR. Forest area and four climate variables (mean annual temperature, precipitation seasonality, mean temperature of coldest quarter, and mean precipitation of driest quarter) were the top five variables during the initial GLM assessment implying their potential individual influence in regulating TSR. Two subsets of LASSO models contained seven and three predictor variables, respectively. Frist subset includes seven predictors, presented in highest to low standardized coefficient, mean temperature of coldest quarter, forested area, precipitation seasonality, mean precipitation of driest quarter, water table depth, spodosol, and available water storage. The other subset further excluded four lowest influential variables from the first set, leaving the top three variables from the first subset. The first subset of the LASSO model predicted TSR with 63.4% explained deviance while the second subset reproduced 60.2% of deviance explained. With only three variables used, the second model outperformed the first model evaluated by the AIC value. We conclude that fo…
format: application/pdf
format: text/html
creator: Youngsang Kwon
creator: Taesoo Lee
creator: Alison Lang
creator: Dorian Burnette
subject: Biogeography
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6781
publisher: PeerJ Inc.
rights: © 2019 Kwon et al.
abstract: The southeastern region of the United States exhibits an unusual trend of decreasing tree species richness (TSR) from higher to lower latitudes over the Florida peninsula. This trend contradicts the widely marked latitudinal diversity gradient where species richness is highest in tropical zones and decreases towards extratropical regions. This study aims to assess the environmental factors that prompt this atypical inverse latitudinal gradient seen in TSR using the USDA Forest Service’s Forest Inventory and Analysis (FIA) database. Fifteen variables under four categories of forested area, groundwater, soil properties, and climate groups were examined to model TSR in the region. Generalized linear models (GLMs) with Poisson distributions first assessed individual variables to test explanatory power then the LASSO regularization method was utilized to extract two subsets of the most influential variables to predict TSR. Forest area and four climate variables (mean annual temperature, precipitation seasonality, mean temperature of coldest quarter, and mean precipitation of driest quarter) were the top five variables during the initial GLM assessment implying their potential individual influence in regulating TSR. Two subsets of LASSO models contained seven and three predictor variables, respectively. Frist subset includes seven predictors, presented in highest to low standardized coefficient, mean temperature of coldest quarter, forested area, precipitation seasonality, mean precipitation of driest quarter, water table depth, spodosol, and available water storage. The other subset further excluded four lowest influential variables from the first set, leaving the top three variables from the first subset. The first subset of the LASSO model predicted TSR with 63.4% explained deviance while the second subset reproduced 60.2% of deviance explained. With only three variables used, the second model outperformed the first model evaluated by the AIC value. We conclude that fo…
bibliographic citation: Kwon et al. (2019) Assessment on latitudinal tree species richness using environmental factors in the southeastern United States. PeerJ 7:e6781 https://doi.org/10.7717/peerj.6781
date submitted: 2018-11-08
date accepted: 2019-03-13
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kwon
  given name: Youngsang
author list: Agent
  family name: Lee
  given name: Taesoo
author list: Agent
  family name: Lang
  given name: Alison
author list: Agent
  family name: Burnette
  given name: Dorian
doi: 10.7717/peerj.6781
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Kwon et al.
attribution name: Kwon et al.

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