PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Changes of cellular stress response related hsp70 and abcb1 transcript and Hsp70 protein levels in Siberian freshwater amphipods upon exposure to cadmium chloride in the lethal concentration range
items: Predictive modelling of the distribution of Clematis sect. Fruticella s. str. under climate change reveals a range expansion during the Last Glacial Maximum
items: Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer
items: Conjuring cognition: a review of educational magic-based interventions
items: Relationship between healthcare seeking and pain expansion in patients with nonspecific chronic low back pain
items: Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction
items: The altered gut microbiota of high-purine-induced hyperuricemia rats and its correlation with hyperuricemia
items: Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid Lonicera japonica
items: Effects of resistance training with controlled versus self-selected repetition duration on muscle mass and strength in untrained men
items: Captorhinid reptiles from the lower Permian Pedra de Fogo Formation, Piauí, Brazil: the earliest herbivorous tetrapods in Gondwana

Changes of cellular stress response related hsp70 and abcb1 transcript and Hsp70 protein levels in Siberian freshwater amphipods upon exposure to cadmium chloride in the lethal concentration range
type: item
type: AcademicArticle
description: The induction of cellular stress response systems, heat shock protein hsp70/Hsp70 and multixenobiotic transporter abcb1, by cadmium chloride (CdCl2) was explored in amphipod species with different stress adaptation strategies from the Lake Baikal area. Based on the lethal concentrations (LC) of CdCl2, the sensitivities of the different species to CdCl2 were ranked (24 hr LC50 in mg/L CdCl2 (mean/95% confidence interval)): Gammarus lacustris (1.7/1.3–2.4) < Eulimnogammarus cyaneus (2.9/2.1–4.0) < Eulimnogammarus verrucosus (5.7/3.8–8.7) < Eulimnogammarus vittatus (18.1/12.4–26.6). Conjugated dienes, indicating lipid peroxidation, were significantly increased after 24 hr exposures to 5 mg/L CdCl2 only in the more CdCl2-sensitive species G. lacustris and E. cyaneus. Upon treatment with 0.54 to 5.8 mg/L CdCl2 for 1, 6 and 24 hrs, hsp70 transcript levels were generally more increased after the longer exposure times and in the more CdCl2-sensitive species. Relating the CdCl2 exposure concentrations to LCx values revealed that across the species the increases of hsp70 transcript levels were comparatively low (up to 2.6-fold) at CdCl2 concentrations ≤LC50. Relative hsp70 transcript levels were maximally increased in E. cyaneus by 5 mg/L CdCl2 ( $\hat {=}$ = ˆ LC70) at 24 hrs (9.1-fold increase above the respective control). When G. lacustris was exposed to 5 mg/L CdCl2 ( $\hat {=}$ = ˆ LC90) for 24 hrs, the increase in hsp70 was in comparison to E. cyaneus considerably less pronounced (3.0-fold increase in hsp70 levels relative to control). Upon exposure of amphipods to 5 mg/L CdCl2, increases in Hsp70 protein levels compared to untreated controls were highest in E. cyaneus at 1 and 6 hrs (5 mg/L CdCl2 $\hat {=}$ = ˆ LC70) and in E. verrucosus at 24 hrs (5 mg/L CdCl2 $\hat {=}$ = ˆ LC45). Thus, when the fold increases in Hsp70 protein levels in the different amphipod species were related to the respective species-specific LCx values a similar bell-shaped trend as for hsp70 …
format: application/pdf
format: text/html
creator: Marina V. Protopopova
creator: Vasiliy V. Pavlichenko
creator: Till Luckenbach
subject: Molecular Biology
subject: Ecotoxicology
subject: Freshwater Biology
description: doi:10.7717/peerj.8635
publisher: PeerJ Inc.
rights: © 2020 Protopopova et al.
abstract: The induction of cellular stress response systems, heat shock protein hsp70/Hsp70 and multixenobiotic transporter abcb1, by cadmium chloride (CdCl2) was explored in amphipod species with different stress adaptation strategies from the Lake Baikal area. Based on the lethal concentrations (LC) of CdCl2, the sensitivities of the different species to CdCl2 were ranked (24 hr LC50 in mg/L CdCl2 (mean/95% confidence interval)): Gammarus lacustris (1.7/1.3–2.4) < Eulimnogammarus cyaneus (2.9/2.1–4.0) < Eulimnogammarus verrucosus (5.7/3.8–8.7) < Eulimnogammarus vittatus (18.1/12.4–26.6). Conjugated dienes, indicating lipid peroxidation, were significantly increased after 24 hr exposures to 5 mg/L CdCl2 only in the more CdCl2-sensitive species G. lacustris and E. cyaneus. Upon treatment with 0.54 to 5.8 mg/L CdCl2 for 1, 6 and 24 hrs, hsp70 transcript levels were generally more increased after the longer exposure times and in the more CdCl2-sensitive species. Relating the CdCl2 exposure concentrations to LCx values revealed that across the species the increases of hsp70 transcript levels were comparatively low (up to 2.6-fold) at CdCl2 concentrations ≤LC50. Relative hsp70 transcript levels were maximally increased in E. cyaneus by 5 mg/L CdCl2 ( $\hat {=}$ = ˆ LC70) at 24 hrs (9.1-fold increase above the respective control). When G. lacustris was exposed to 5 mg/L CdCl2 ( $\hat {=}$ = ˆ LC90) for 24 hrs, the increase in hsp70 was in comparison to E. cyaneus considerably less pronounced (3.0-fold increase in hsp70 levels relative to control). Upon exposure of amphipods to 5 mg/L CdCl2, increases in Hsp70 protein levels compared to untreated controls were highest in E. cyaneus at 1 and 6 hrs (5 mg/L CdCl2 $\hat {=}$ = ˆ LC70) and in E. verrucosus at 24 hrs (5 mg/L CdCl2 $\hat {=}$ = ˆ LC45). Thus, when the fold increases in Hsp70 protein levels in the different amphipod species were related to the respective species-specific LCx values a similar bell-shaped trend as for hsp70 …
bibliographic citation: Protopopova et al. (2020) Changes of cellular stress response related hsp70 and abcb1 transcript and Hsp70 protein levels in Siberian freshwater amphipods upon exposure to cadmium chloride in the lethal concentration range. PeerJ 8:e8635 https://doi.org/10.7717/peerj.8635
date submitted: 2019-06-17
date accepted: 2020-01-26
issued: 2020-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Protopopova
  given name: Marina V.
author list: Agent
  family name: Pavlichenko
  given name: Vasiliy V.
author list: Agent
  family name: Luckenbach
  given name: Till
doi: 10.7717/peerj.8635
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-09
copyright: ©2020 Protopopova et al.
attribution name: Protopopova et al.

Predictive modelling of the distribution of Clematis sect. Fruticella s. str. under climate change reveals a range expansion during the Last Glacial Maximum
type: item
type: AcademicArticle
description: Background The knowledge of distributional dynamics of living organisms is a prerequisite for protecting biodiversity and for the sustainable use of biotic resources. Clematis sect. Fruticella s. str. is a small group of shrubby, yellow-flowered species distributed mainly in arid and semi-arid areas of China. Plants in this section are both horticulturally and ecologically important. Methods Using past, present, and future environmental variables and data with Maximum Entropy (Maxent) modeling, we evaluated the importance of the environmental variables on the section’s estimated distributions, thus simulating its distributional dynamics over time. The contractions and expansions of suitable habitat between the past and future scenarios and the present were then compared. Results and Discussion The models revealed that the areas with high and moderate suitability currently encompass about 725,110 km2. The distribution centroid location varies between points in Ningxia and Inner Mongolia during the different scenarios. Elevation, Mean UV-B of Lowest Month, Precipitation of Coldest Quarter, and Mean Temperature of Driest Quarter were major factors determining the section’s distribution. Our modeling indicated that Clematis sect. Fruticella underwent a significant range contraction during the last interglacial period, and then expanded during the last glacial maximum (LGM) to amounts like those of the present. Cold, dry, and relatively stable climate, as well as steppe or desert steppe environments may have facilitated range expansion of this cold-adapted, drought-resistant plant taxon during the LGM. Predicted future scenarios show little change in the amounts of suitable habitat for Clematis sect. Fruticella. This study aids understanding of the distributional dynamics of Clematis sect. Fruticella, and the results will help the conservation and sustainable use of these important woody plants in Chinese arid and semiarid areas.
format: application/pdf
format: text/html
creator: Mingyu Li
creator: Jian He
creator: Zhe Zhao
creator: Rudan Lyu
creator: Min Yao
creator: Jin Cheng
creator: Lei Xie
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.8729
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background The knowledge of distributional dynamics of living organisms is a prerequisite for protecting biodiversity and for the sustainable use of biotic resources. Clematis sect. Fruticella s. str. is a small group of shrubby, yellow-flowered species distributed mainly in arid and semi-arid areas of China. Plants in this section are both horticulturally and ecologically important. Methods Using past, present, and future environmental variables and data with Maximum Entropy (Maxent) modeling, we evaluated the importance of the environmental variables on the section’s estimated distributions, thus simulating its distributional dynamics over time. The contractions and expansions of suitable habitat between the past and future scenarios and the present were then compared. Results and Discussion The models revealed that the areas with high and moderate suitability currently encompass about 725,110 km2. The distribution centroid location varies between points in Ningxia and Inner Mongolia during the different scenarios. Elevation, Mean UV-B of Lowest Month, Precipitation of Coldest Quarter, and Mean Temperature of Driest Quarter were major factors determining the section’s distribution. Our modeling indicated that Clematis sect. Fruticella underwent a significant range contraction during the last interglacial period, and then expanded during the last glacial maximum (LGM) to amounts like those of the present. Cold, dry, and relatively stable climate, as well as steppe or desert steppe environments may have facilitated range expansion of this cold-adapted, drought-resistant plant taxon during the LGM. Predicted future scenarios show little change in the amounts of suitable habitat for Clematis sect. Fruticella. This study aids understanding of the distributional dynamics of Clematis sect. Fruticella, and the results will help the conservation and sustainable use of these important woody plants in Chinese arid and semiarid areas.
bibliographic citation: Li et al. (2020) Predictive modelling of the distribution of Clematis sect. Fruticella s. str. under climate change reveals a range expansion during the Last Glacial Maximum. PeerJ 8:e8729 https://doi.org/10.7717/peerj.8729
date submitted: 2019-11-26
date accepted: 2020-02-11
issued: 2020-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Mingyu
author list: Agent
  family name: He
  given name: Jian
author list: Agent
  family name: Zhao
  given name: Zhe
author list: Agent
  family name: Lyu
  given name: Rudan
author list: Agent
  family name: Yao
  given name: Min
author list: Agent
  family name: Cheng
  given name: Jin
author list: Agent
  family name: Xie
  given name: Lei
doi: 10.7717/peerj.8729
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-09
copyright: ©2020 Li et al.
attribution name: Li et al.

Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer
type: item
type: AcademicArticle
description: Although lung cancer is one of the greatest threats to human health, its signaling pathway and related genes are still unknown. This study integrates data from three groups of people to study potential key candidate genes and pathways related to lung cancer. Expression profiles (GSE18842, GSE19188 and GSE27262), including 162 tumor tissue and 135 adjacent normal lung tissue samples, were integrated and analyzed. Differentially expressed genes (DEGs) and candidate genes were identified, their expression pathways were analyzed, and the diethylene glycol-related protein–protein interaction (PPI) network was analyzed. We identified 232 shared DEGs (40 upregulated and 192 down-regulated) from the three GSE datasets. The DEGs were clustered according to function and signaling pathway for significant enrichment analysis. In total, 129 nodes/DEGs were identified from the DEG PPI network complex. An improved prognosis was associated with increased Helicase, Lymphoid-Specific (HELLS) and decreased Intercellular adhesion molecule 1 (ICAM1) mRNA expression in lung cancer patients. In conclusion, we used integrated bioinformatics analysis to identify candidate genes and pathways in lung cancer to show that HELLS and ICAM1 might be the key genes related to tumorigenesis or tumor progression in lung cancer. Additional studies are needed to further explore the involved functional mechanisms.
format: application/pdf
format: text/html
creator: Wei Zhu
creator: Lin Lin Li
creator: Yiyan Songyang
creator: Zhan Shi
creator: Dejia Li
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.8731
publisher: PeerJ Inc.
rights: © 2020 Zhu et al.
abstract: Although lung cancer is one of the greatest threats to human health, its signaling pathway and related genes are still unknown. This study integrates data from three groups of people to study potential key candidate genes and pathways related to lung cancer. Expression profiles (GSE18842, GSE19188 and GSE27262), including 162 tumor tissue and 135 adjacent normal lung tissue samples, were integrated and analyzed. Differentially expressed genes (DEGs) and candidate genes were identified, their expression pathways were analyzed, and the diethylene glycol-related protein–protein interaction (PPI) network was analyzed. We identified 232 shared DEGs (40 upregulated and 192 down-regulated) from the three GSE datasets. The DEGs were clustered according to function and signaling pathway for significant enrichment analysis. In total, 129 nodes/DEGs were identified from the DEG PPI network complex. An improved prognosis was associated with increased Helicase, Lymphoid-Specific (HELLS) and decreased Intercellular adhesion molecule 1 (ICAM1) mRNA expression in lung cancer patients. In conclusion, we used integrated bioinformatics analysis to identify candidate genes and pathways in lung cancer to show that HELLS and ICAM1 might be the key genes related to tumorigenesis or tumor progression in lung cancer. Additional studies are needed to further explore the involved functional mechanisms.
bibliographic citation: Zhu et al. (2020) Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer. PeerJ 8:e8731 https://doi.org/10.7717/peerj.8731
date submitted: 2019-11-13
date accepted: 2020-02-11
issued: 2020-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Wei
author list: Agent
  family name: Li
  given name: Lin Lin
author list: Agent
  family name: Songyang
  given name: Yiyan
author list: Agent
  family name: Shi
  given name: Zhan
author list: Agent
  family name: Li
  given name: Dejia
doi: 10.7717/peerj.8731
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-09
copyright: © 2020 Zhu et al.
attribution name: Zhu et al.

Conjuring cognition: a review of educational magic-based interventions
type: item
type: AcademicArticle
description: For hundreds of years, magic tricks have been employed within a variety of pedagogic contexts, including promoting science and mathematics, delivering educational messaging, enhancing scepticism about the paranormal, and boosting creative thinking for product design. This review examines this diverse body of work, focusing on studies that have assessed the impact of such interventions. Although the studies tended to yield positive outcomes, much of the work suffered from methodological shortcomings, including measuring the impact of interventions over a relatively short period of time, focusing on self-report measures and failing to employ control groups. The paper makes several recommendations for future study in the area, including assessing the longer-term impact of magic-based interventions, comparing these interventions to other types of pedagogic techniques, focussing on knowledge retention and behavioural outcomes, and collaborating with magicians to develop more impactful interventions.
format: application/pdf
format: text/html
creator: Richard Wiseman
creator: Caroline Watt
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.8747
publisher: PeerJ Inc.
rights: © 2020 Wiseman and Watt
abstract: For hundreds of years, magic tricks have been employed within a variety of pedagogic contexts, including promoting science and mathematics, delivering educational messaging, enhancing scepticism about the paranormal, and boosting creative thinking for product design. This review examines this diverse body of work, focusing on studies that have assessed the impact of such interventions. Although the studies tended to yield positive outcomes, much of the work suffered from methodological shortcomings, including measuring the impact of interventions over a relatively short period of time, focusing on self-report measures and failing to employ control groups. The paper makes several recommendations for future study in the area, including assessing the longer-term impact of magic-based interventions, comparing these interventions to other types of pedagogic techniques, focussing on knowledge retention and behavioural outcomes, and collaborating with magicians to develop more impactful interventions.
bibliographic citation: Wiseman et al. (2020) Conjuring cognition: a review of educational magic-based interventions. PeerJ 8:e8747 https://doi.org/10.7717/peerj.8747
date submitted: 2019-12-18
date accepted: 2020-02-14
issued: 2020-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiseman
  given name: Richard
author list: Agent
  family name: Watt
  given name: Caroline
doi: 10.7717/peerj.8747
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-09
copyright: ©2020 Wiseman and Watt
attribution name: Wiseman and Watt

Relationship between healthcare seeking and pain expansion in patients with nonspecific chronic low back pain
type: item
type: AcademicArticle
description: Objectives Low back pain (LBP) is the most prevalent musculoskeletal problem, which implies a high rate of chronicity. The chronicity of symptoms can lead to pain expansion. The main objective of this study was to assess whether there were differences between patients with nonspecific chronic LBP (CLBP) who sought healthcare compared to those who did not in terms of pain expansion. Methods Ninety individuals participated in the study and were divided into three groups: 30 patients who sought care; 30 patients who did not seek care; and 30 asymptomatic individuals. The primary variable analyzed was pain expansion. Secondary physical and psychological variables were assessed later, and a regression analysis was performed. Results Patients who sought help showed significant differences in pain expansion and pain intensity compared with the group who did not seek help, with a medium effect size (0.50–0.79). The regression model for the care-seeking group showed that dynamic balance with the left leg and depression were predictors of percentage pain surface area (34.6%). The combination of dynamic balance, range of movement in flexoextension and depression were predictors of widespread pain (48.5%). Conclusion Patients who soughtcare presented greater pain expansion than patients whodidnot. A combination of functional and psychological variables can significantly predict pain expansion in patients with nonspecific CLBP who seek help.
format: application/pdf
format: text/html
creator: Mónica Grande-Alonso
creator: Daniel Muñoz-García
creator: Ferran Cuenca-Martínez
creator: Laura Delgado-Sanz
creator: María Prieto-Aldana
creator: Roy La Touche
creator: Alfonso Gil-Martínez
subject: Anesthesiology and Pain Management
subject: Orthopedics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8756
publisher: PeerJ Inc.
rights: © 2020 Grande-Alonso et al.
abstract: Objectives Low back pain (LBP) is the most prevalent musculoskeletal problem, which implies a high rate of chronicity. The chronicity of symptoms can lead to pain expansion. The main objective of this study was to assess whether there were differences between patients with nonspecific chronic LBP (CLBP) who sought healthcare compared to those who did not in terms of pain expansion. Methods Ninety individuals participated in the study and were divided into three groups: 30 patients who sought care; 30 patients who did not seek care; and 30 asymptomatic individuals. The primary variable analyzed was pain expansion. Secondary physical and psychological variables were assessed later, and a regression analysis was performed. Results Patients who sought help showed significant differences in pain expansion and pain intensity compared with the group who did not seek help, with a medium effect size (0.50–0.79). The regression model for the care-seeking group showed that dynamic balance with the left leg and depression were predictors of percentage pain surface area (34.6%). The combination of dynamic balance, range of movement in flexoextension and depression were predictors of widespread pain (48.5%). Conclusion Patients who soughtcare presented greater pain expansion than patients whodidnot. A combination of functional and psychological variables can significantly predict pain expansion in patients with nonspecific CLBP who seek help.
bibliographic citation: Grande-Alonso et al. (2020) Relationship between healthcare seeking and pain expansion in patients with nonspecific chronic low back pain. PeerJ 8:e8756 https://doi.org/10.7717/peerj.8756
date submitted: 2019-08-29
date accepted: 2020-02-16
issued: 2020-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grande-Alonso
  given name: Mónica
author list: Agent
  family name: Muñoz-García
  given name: Daniel
author list: Agent
  family name: Cuenca-Martínez
  given name: Ferran
author list: Agent
  family name: Delgado-Sanz
  given name: Laura
author list: Agent
  family name: Prieto-Aldana
  given name: María
author list: Agent
  family name: La Touche
  given name: Roy
author list: Agent
  family name: Gil-Martínez
  given name: Alfonso
doi: 10.7717/peerj.8756
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-09
copyright: ©2020 Grande-Alonso et al.
attribution name: Grande-Alonso et al.

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction
type: item
type: AcademicArticle
description: Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
format: application/pdf
format: text/html
creator: Akhila Melarkode Vattekatte
creator: Nicolas Ken Shinada
creator: Tarun J. Narwani
creator: Floriane Noël
creator: Olivier Bertrand
creator: Jean-Philippe Meyniel
creator: Alain Malpertuy
creator: Jean-Christophe Gelly
creator: Frédéric Cadet
creator: Alexandre G. de Brevern
subject: Biochemistry
subject: Bioinformatics
description: doi:10.7717/peerj.8408
publisher: PeerJ Inc.
rights: © 2020 Melarkode Vattekatte et al.
abstract: Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
bibliographic citation: Melarkode Vattekatte et al. (2020) Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction. PeerJ 8:e8408 https://doi.org/10.7717/peerj.8408
date submitted: 2019-06-06
date accepted: 2019-12-16
issued: 2020-03-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Melarkode Vattekatte
  given name: Akhila
author list: Agent
  family name: Shinada
  given name: Nicolas Ken
author list: Agent
  family name: Narwani
  given name: Tarun J.
author list: Agent
  family name: Noël
  given name: Floriane
author list: Agent
  family name: Bertrand
  given name: Olivier
author list: Agent
  family name: Meyniel
  given name: Jean-Philippe
author list: Agent
  family name: Malpertuy
  given name: Alain
author list: Agent
  family name: Gelly
  given name: Jean-Christophe
author list: Agent
  family name: Cadet
  given name: Frédéric
author list: Agent
  family name: de Brevern
  given name: Alexandre G.
doi: 10.7717/peerj.8408
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-06
copyright: ©2020 Melarkode Vattekatte et al.
attribution name: Melarkode Vattekatte et al.

The altered gut microbiota of high-purine-induced hyperuricemia rats and its correlation with hyperuricemia
type: item
type: AcademicArticle
description: Some studies on the hyperuricemia (HUA) have focused on intestinal bacteria. To better understand the correlation between gut microbiota and HUA, we established a HUA rat model with high-purine diet, and used 16S rRNA genes sequencing to analyze gut microbiota changes in HUA rats. To analyze the potential role played by gut microbiota in HUA, we altered the gut microbiota of HUA rats with antibiotics, and compared the degree of uric acid elevation between HUA and antibiotic-fed HUA rats (Ab+HUA). Finally, we established a recipient rat model, in which we transplanted fecal microbiota of HUA and normal rats into recipient rats. Three weeks later, we compared the uric acid content of recipient rats. As a result, the diversity and abundance of the gut microbiota had changed in HUA rats. The Ab-fed HUA rats had significantly lower uric acid content compared to the HUA rats, and gut microbiota from HUA rats increased uric acid content of recipient rats. The genera Vallitalea, Christensenella and Insolitispirillum may associate with HUA. Our findings highlight the association between gut microbiota and HUA, and the potential role played by gut microbiota in HUA. We hope that this finding will promote the isolation and culture of HUA-related bacteria and orient HUA-related studies from being correlational to mechanistic. These steps will therefore make it possible for us to treat HUA using gut microbiota as the target.
format: application/pdf
format: text/html
creator: Xiu Liu
creator: Qiulan Lv
creator: Hongyan Ren
creator: Liu Gao
creator: Peng Zhao
creator: Xiaomin Yang
creator: Guanpin Yang
creator: Daxing Xu
creator: Guangtao Wang
creator: Wan Yang
creator: Pengjun Wang
creator: Zenglan Wang
creator: Shichao Xing
subject: Microbiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.8664
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Some studies on the hyperuricemia (HUA) have focused on intestinal bacteria. To better understand the correlation between gut microbiota and HUA, we established a HUA rat model with high-purine diet, and used 16S rRNA genes sequencing to analyze gut microbiota changes in HUA rats. To analyze the potential role played by gut microbiota in HUA, we altered the gut microbiota of HUA rats with antibiotics, and compared the degree of uric acid elevation between HUA and antibiotic-fed HUA rats (Ab+HUA). Finally, we established a recipient rat model, in which we transplanted fecal microbiota of HUA and normal rats into recipient rats. Three weeks later, we compared the uric acid content of recipient rats. As a result, the diversity and abundance of the gut microbiota had changed in HUA rats. The Ab-fed HUA rats had significantly lower uric acid content compared to the HUA rats, and gut microbiota from HUA rats increased uric acid content of recipient rats. The genera Vallitalea, Christensenella and Insolitispirillum may associate with HUA. Our findings highlight the association between gut microbiota and HUA, and the potential role played by gut microbiota in HUA. We hope that this finding will promote the isolation and culture of HUA-related bacteria and orient HUA-related studies from being correlational to mechanistic. These steps will therefore make it possible for us to treat HUA using gut microbiota as the target.
bibliographic citation: Liu et al. (2020) The altered gut microbiota of high-purine-induced hyperuricemia rats and its correlation with hyperuricemia. PeerJ 8:e8664 https://doi.org/10.7717/peerj.8664
date submitted: 2019-11-18
date accepted: 2020-01-29
issued: 2020-03-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiu
author list: Agent
  family name: Lv
  given name: Qiulan
author list: Agent
  family name: Ren
  given name: Hongyan
author list: Agent
  family name: Gao
  given name: Liu
author list: Agent
  family name: Zhao
  given name: Peng
author list: Agent
  family name: Yang
  given name: Xiaomin
author list: Agent
  family name: Yang
  given name: Guanpin
author list: Agent
  family name: Xu
  given name: Daxing
author list: Agent
  family name: Wang
  given name: Guangtao
author list: Agent
  family name: Yang
  given name: Wan
author list: Agent
  family name: Wang
  given name: Pengjun
author list: Agent
  family name: Wang
  given name: Zenglan
author list: Agent
  family name: Xing
  given name: Shichao
doi: 10.7717/peerj.8664
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-06
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid Lonicera japonica
type: item
type: AcademicArticle
description: The Flos Lonicerae Japonicae (FLJ), Lonicera japonica Thunb, belonging to the Caprifoliaceae family, is an economically important plant that is highly utilized in traditional Chinese medicine as well as in Japanese medicine. The flowers of these plants are rich in chlorogenic acid (CGA) and luteoloside. Our previous study revealed that tetraploid L. japonica has higher fresh/dry weight, phenolic acids and flavonoids contents than those of diploid plants. However, why tetraploid L. japonica can yield higher CGA and luteolosides than that in diploid and what is the difference in the molecular regulatory mechanism of these pathways between diploid and tetraploids remained unclear. Therefore, in the present study, we performed comprehensive transcriptome analyses of different flowering stages of diploid and tetraploid L. japonica. The CGA content of tetraploid was found higher than that of diploid at all the growth stages. While the luteoloside content of diploid was higher than that of tetraploid at S4 and S6 growth stages. We obtained a high-quality transcriptome assembly (N50 = 2,055 bp; Average length = 1,331 bp) compared to earlier studies. Differential expression analysis revealed that several important genes involving in plant hormone signal transduction, carbon metabolism, starch/sucrose metabolism and plant-pathogen interaction were upregulated in tetraploid compared with the diploid L. japonica, reflecting the higher adaptability and resistance of tetraploid species. Furthermore, by associating the phenotypic data and gene expression profiles, we were able to characterize the potential molecular regulatory mechanism of important biosynthetic pathways at different flowering stages. Overall, our work provides a foundation for further research on these important secondary metabolite pathways and their implications in traditional Chinese/Japanese medicine.
format: application/pdf
format: text/html
creator: Hongli Wang
creator: Yanqun Li
creator: Sibo Wang
creator: Dexin Kong
creator: Sunil Kumar Sahu
creator: Mei Bai
creator: Haoyuan Li
creator: Linzhou Li
creator: Yan Xu
creator: Hongping Liang
creator: Huan Liu
creator: Hong Wu
subject: Biochemistry
subject: Bioinformatics
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8690
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: The Flos Lonicerae Japonicae (FLJ), Lonicera japonica Thunb, belonging to the Caprifoliaceae family, is an economically important plant that is highly utilized in traditional Chinese medicine as well as in Japanese medicine. The flowers of these plants are rich in chlorogenic acid (CGA) and luteoloside. Our previous study revealed that tetraploid L. japonica has higher fresh/dry weight, phenolic acids and flavonoids contents than those of diploid plants. However, why tetraploid L. japonica can yield higher CGA and luteolosides than that in diploid and what is the difference in the molecular regulatory mechanism of these pathways between diploid and tetraploids remained unclear. Therefore, in the present study, we performed comprehensive transcriptome analyses of different flowering stages of diploid and tetraploid L. japonica. The CGA content of tetraploid was found higher than that of diploid at all the growth stages. While the luteoloside content of diploid was higher than that of tetraploid at S4 and S6 growth stages. We obtained a high-quality transcriptome assembly (N50 = 2,055 bp; Average length = 1,331 bp) compared to earlier studies. Differential expression analysis revealed that several important genes involving in plant hormone signal transduction, carbon metabolism, starch/sucrose metabolism and plant-pathogen interaction were upregulated in tetraploid compared with the diploid L. japonica, reflecting the higher adaptability and resistance of tetraploid species. Furthermore, by associating the phenotypic data and gene expression profiles, we were able to characterize the potential molecular regulatory mechanism of important biosynthetic pathways at different flowering stages. Overall, our work provides a foundation for further research on these important secondary metabolite pathways and their implications in traditional Chinese/Japanese medicine.
bibliographic citation: Wang et al. (2020) Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid Lonicera japonica. PeerJ 8:e8690 https://doi.org/10.7717/peerj.8690
date submitted: 2019-07-30
date accepted: 2020-02-05
issued: 2020-03-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hongli
author list: Agent
  family name: Li
  given name: Yanqun
author list: Agent
  family name: Wang
  given name: Sibo
author list: Agent
  family name: Kong
  given name: Dexin
author list: Agent
  family name: Sahu
  given name: Sunil Kumar
author list: Agent
  family name: Bai
  given name: Mei
author list: Agent
  family name: Li
  given name: Haoyuan
author list: Agent
  family name: Li
  given name: Linzhou
author list: Agent
  family name: Xu
  given name: Yan
author list: Agent
  family name: Liang
  given name: Hongping
author list: Agent
  family name: Liu
  given name: Huan
author list: Agent
  family name: Wu
  given name: Hong
doi: 10.7717/peerj.8690
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-06
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Effects of resistance training with controlled versus self-selected repetition duration on muscle mass and strength in untrained men
type: item
type: AcademicArticle
description: The aim of this study was to compare the effect of self-selected repetition duration (SELF), with and without volume load (VL) equalized with controlled repetition duration (CON) on muscle strength and hypertrophy in untrained males. We used a within-subjects design in which 20 volunteers (age: 24.7 ± 2.9 years) had one leg randomly assigned to CON (i.e., 2 s concentric, 2 s eccentric) and the other to SELF or to self-selected repetition duration with equalized volume load (SELF-EV). One repetition maximum (1-RM) and muscle cross-sectional area (CSA) were measured at baseline (Pre) and after (Post) resistance training (RT; 2×/wk for 8 weeks). For the main study variables (1-RM and muscle CSA), a mixed-model analysis was performed, assuming repetition duration (SELF, SELF-EV and CON), and time (Pre and Post) as fixed factors and the subjects as random factor for each dependent variable (1-RM and CSA). All RT protocols showed significant increases in values of 1-RM from Pre (CON: 73.7 ± 17.6 kg; SELF: 75.9 ± 17.7 kg; and SELF-EV: 72.6 ± 16.9 kg) to Post (CON: 83.4 ± 19.9 kg, effect size (ES): 0.47; SELF: 84 ± 19.1 kg, ES: 0.43; and SELF-EV: 83.2 ± 19.9 kg, ES: 0.57, P < 0.0001). Muscle CSA values increased for all protocols from Pre (CON: 12.09 ± 3.14 cm2; SELF: 11.91 ± 3.71 cm2; and SELF-EV: 11.93 ± 2.32 cm2) to Post (CON: 13.03 ± 3.25 cm2, ES: 0.29; SELF: 13.2 ± 4.16 cm2, ES: 0.32; and SELF-EV: 13.2 ± 2.35 cm2, ES: 0.53, P < 0.0001). No significant differences between protocols were found for both 1-RM and CSA (P > 0.05). Performing RT with SELF, regardless of VL, was equally effective in inducing increases in muscle strength and hypertrophy compared to CON in untrained men.
format: application/pdf
format: text/html
creator: Talisson Santos Chaves
creator: Thaís Marina Pires de Campos Biazon
creator: Lucas Marcelino Eder dos Santos
creator: Cleiton Augusto Libardi
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.8697
publisher: PeerJ Inc.
rights: © 2020 Chaves et al.
abstract: The aim of this study was to compare the effect of self-selected repetition duration (SELF), with and without volume load (VL) equalized with controlled repetition duration (CON) on muscle strength and hypertrophy in untrained males. We used a within-subjects design in which 20 volunteers (age: 24.7 ± 2.9 years) had one leg randomly assigned to CON (i.e., 2 s concentric, 2 s eccentric) and the other to SELF or to self-selected repetition duration with equalized volume load (SELF-EV). One repetition maximum (1-RM) and muscle cross-sectional area (CSA) were measured at baseline (Pre) and after (Post) resistance training (RT; 2×/wk for 8 weeks). For the main study variables (1-RM and muscle CSA), a mixed-model analysis was performed, assuming repetition duration (SELF, SELF-EV and CON), and time (Pre and Post) as fixed factors and the subjects as random factor for each dependent variable (1-RM and CSA). All RT protocols showed significant increases in values of 1-RM from Pre (CON: 73.7 ± 17.6 kg; SELF: 75.9 ± 17.7 kg; and SELF-EV: 72.6 ± 16.9 kg) to Post (CON: 83.4 ± 19.9 kg, effect size (ES): 0.47; SELF: 84 ± 19.1 kg, ES: 0.43; and SELF-EV: 83.2 ± 19.9 kg, ES: 0.57, P < 0.0001). Muscle CSA values increased for all protocols from Pre (CON: 12.09 ± 3.14 cm2; SELF: 11.91 ± 3.71 cm2; and SELF-EV: 11.93 ± 2.32 cm2) to Post (CON: 13.03 ± 3.25 cm2, ES: 0.29; SELF: 13.2 ± 4.16 cm2, ES: 0.32; and SELF-EV: 13.2 ± 2.35 cm2, ES: 0.53, P < 0.0001). No significant differences between protocols were found for both 1-RM and CSA (P > 0.05). Performing RT with SELF, regardless of VL, was equally effective in inducing increases in muscle strength and hypertrophy compared to CON in untrained men.
bibliographic citation: Chaves et al. (2020) Effects of resistance training with controlled versus self-selected repetition duration on muscle mass and strength in untrained men. PeerJ 8:e8697 https://doi.org/10.7717/peerj.8697
date submitted: 2019-09-03
date accepted: 2020-02-06
issued: 2020-03-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chaves
  given name: Talisson Santos
author list: Agent
  family name: Pires de Campos Biazon
  given name: Thaís Marina
author list: Agent
  family name: Marcelino Eder dos Santos
  given name: Lucas
author list: Agent
  family name: Libardi
  given name: Cleiton Augusto
doi: 10.7717/peerj.8697
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-06
copyright: © 2020 Chaves et al.
attribution name: Chaves et al.

Captorhinid reptiles from the lower Permian Pedra de Fogo Formation, Piauí, Brazil: the earliest herbivorous tetrapods in Gondwana
type: item
type: AcademicArticle
description: The Pedra de Fogo Formation in the Parnaíba Basin of northeastern Brazil hosts a recently discovered lacustrine fauna and provides the only known record of the Captorhinidae in South America. Here, new captorhinid remains from this unit are described. Two partial mandibles, including one formerly ascribed to the genus Captorhinus, are here referred to Captorhinikos sp. a genus previously described from North America. The natural mould of a large mandible probably represents a new taxon within the captorhinid subclade Moradisaurinae, and a small skull roof is regarded as Captorhinidae indet. Captorhinids are generally considered to have been herbivores or omnivores. The Pedra de Fogo captorhinids likely played an important ecological role as primary consumers in the palaeoenvironment of this geological unit, which is also known for its extensive record of petrified forests. The new finds reinforce the close relationships between the continental faunas of palaeotropical western Gondwana and palaeoequatorial North America during the Cisuralian.
format: application/pdf
format: text/html
creator: Juan C. Cisneros
creator: Kenneth Angielczyk
creator: Christian F. Kammerer
creator: Roger M.H. Smith
creator: Jörg Fröbisch
creator: Claudia A. Marsicano
creator: Martha Richter
subject: Biogeography
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.8719
publisher: PeerJ Inc.
rights: © 2020 Cisneros et al.
abstract: The Pedra de Fogo Formation in the Parnaíba Basin of northeastern Brazil hosts a recently discovered lacustrine fauna and provides the only known record of the Captorhinidae in South America. Here, new captorhinid remains from this unit are described. Two partial mandibles, including one formerly ascribed to the genus Captorhinus, are here referred to Captorhinikos sp. a genus previously described from North America. The natural mould of a large mandible probably represents a new taxon within the captorhinid subclade Moradisaurinae, and a small skull roof is regarded as Captorhinidae indet. Captorhinids are generally considered to have been herbivores or omnivores. The Pedra de Fogo captorhinids likely played an important ecological role as primary consumers in the palaeoenvironment of this geological unit, which is also known for its extensive record of petrified forests. The new finds reinforce the close relationships between the continental faunas of palaeotropical western Gondwana and palaeoequatorial North America during the Cisuralian.
bibliographic citation: Cisneros et al. (2020) Captorhinid reptiles from the lower Permian Pedra de Fogo Formation, Piauí, Brazil: the earliest herbivorous tetrapods in Gondwana. PeerJ 8:e8719 https://doi.org/10.7717/peerj.8719
date submitted: 2019-11-20
date accepted: 2020-02-10
issued: 2020-03-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cisneros
  given name: Juan C.
author list: Agent
  family name: Angielczyk
  given name: Kenneth
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Smith
  given name: Roger M.H.
author list: Agent
  family name: Fröbisch
  given name: Jörg
author list: Agent
  family name: Marsicano
  given name: Claudia A.
author list: Agent
  family name: Richter
  given name: Martha
doi: 10.7717/peerj.8719
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-06
copyright: © 2020 Cisneros et al.
attribution name: Cisneros et al.

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