PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Coastal fish assemblages and predation pressure in northern-central Chilean Lessonia trabeculata kelp forests and barren grounds
items: Relative and absolute within-session reliability of the modified Star Excursion Balance Test in healthy elite athletes
items: Fine-root traits of allelopathic rice at the seedling stage and their relationship with allelopathic potential
items: Water regime and osmotic adjustment under warming conditions on wheat in the Yaqui Valley, Mexico
items: Identification and characterization of PsDREB2 promoter involved in tissue-specific expression and abiotic stress response from Paeonia suffruticosa
items: Sex- and tissue-specific expression of odorant-binding proteins and chemosensory proteins in adults of the scarab beetle Hylamorpha elegans (Burmeister) (Coleoptera: Scarabaeidae)
items: Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
items: Estimating biological accuracy of DSM for attention deficit/hyperactivity disorder based on multivariate analysis for small samples
items: Genetic diversity of gliadin-coding alleles in bread wheat (Triticum aestivum L.) from Northern Kazakhstan
items: T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection

Coastal fish assemblages and predation pressure in northern-central Chilean Lessonia trabeculata kelp forests and barren grounds
type: item
type: AcademicArticle
description: Kelp forests are declining in many parts of the globe, which can lead to the spreading of barren grounds. Increased abundances of grazers, mainly due to reduction of their predators, are among the causes of this development. Here, we compared the species richness (SR), frequency of occurrence (FO), and maximum abundance (MaxN) of predatory fish and their predation pressure between kelp forest and barren ground habitats of northern-central Chile. Sampling was done using baited underwater cameras with vertical and horizontal orientation. Two prey organisms were used as tethered baits, the black sea urchin Tetrapygus niger and the porcelanid crab Petrolisthes laevigatus. SR did not show major differences between habitats, while FO and MaxN were higher on barren grounds in vertical videos, with no major differences between habitats in horizontal videos. Predation pressure did not differ between habitats, but after 24 h consumption of porcelanid crabs was significantly higher than that of sea urchins. Scartichthys viridis/gigas was the main predator, accounting for 82% of the observed predation events on Petrolisthes laevigatus. Most of these attacks occurred on barren grounds. Scartichthys viridis/gigas was the only fish observed attacking (but not consuming) tethered sea urchins. High abundances of opportunistic predators (Scartichthys viridis/gigas) are probably related to low abundances of large predatory fishes. These results suggest that intense fishing activity on large predators, and their resulting low abundances, could result in low predation pressure on sea urchins, thereby contributing to the increase of T. niger abundances in subtidal rocky habitats.
format: application/pdf
format: text/html
creator: Nicolás Riquelme-Pérez
creator: Catalina A. Musrri
creator: Wolfgang B. Stotz
creator: Osvaldo Cerda
creator: Oscar Pino-Olivares
creator: Martin Thiel
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6964
publisher: PeerJ Inc.
rights: © 2019 Riquelme-Pérez et al.
abstract: Kelp forests are declining in many parts of the globe, which can lead to the spreading of barren grounds. Increased abundances of grazers, mainly due to reduction of their predators, are among the causes of this development. Here, we compared the species richness (SR), frequency of occurrence (FO), and maximum abundance (MaxN) of predatory fish and their predation pressure between kelp forest and barren ground habitats of northern-central Chile. Sampling was done using baited underwater cameras with vertical and horizontal orientation. Two prey organisms were used as tethered baits, the black sea urchin Tetrapygus niger and the porcelanid crab Petrolisthes laevigatus. SR did not show major differences between habitats, while FO and MaxN were higher on barren grounds in vertical videos, with no major differences between habitats in horizontal videos. Predation pressure did not differ between habitats, but after 24 h consumption of porcelanid crabs was significantly higher than that of sea urchins. Scartichthys viridis/gigas was the main predator, accounting for 82% of the observed predation events on Petrolisthes laevigatus. Most of these attacks occurred on barren grounds. Scartichthys viridis/gigas was the only fish observed attacking (but not consuming) tethered sea urchins. High abundances of opportunistic predators (Scartichthys viridis/gigas) are probably related to low abundances of large predatory fishes. These results suggest that intense fishing activity on large predators, and their resulting low abundances, could result in low predation pressure on sea urchins, thereby contributing to the increase of T. niger abundances in subtidal rocky habitats.
bibliographic citation: Riquelme-Pérez et al. (2019) Coastal fish assemblages and predation pressure in northern-central Chilean Lessonia trabeculata kelp forests and barren grounds. PeerJ 7:e6964 https://doi.org/10.7717/peerj.6964
date submitted: 2019-02-13
date accepted: 2019-04-15
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Riquelme-Pérez
  given name: Nicolás
author list: Agent
  family name: Musrri
  given name: Catalina A.
author list: Agent
  family name: Stotz
  given name: Wolfgang B.
author list: Agent
  family name: Cerda
  given name: Osvaldo
author list: Agent
  family name: Pino-Olivares
  given name: Oscar
author list: Agent
  family name: Thiel
  given name: Martin
doi: 10.7717/peerj.6964
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: © 2019 Riquelme-Pérez et al.
attribution name: Riquelme-Pérez et al.

Relative and absolute within-session reliability of the modified Star Excursion Balance Test in healthy elite athletes
type: item
type: AcademicArticle
description: Background The Star Excursion Balance Test (SEBT) is commonly used to assess dynamic postural balance both in clinical practice and research. The aim of our study was to assess the within-session relative and absolute reliability of participants’ performance of the modified SEBT (mSEBT) using a single practice trial in healthy elite athletes who were familiar with the test. Methods An intra-session repeated-measures design was used to investigate the relative and absolute reliability of participants’ (healthy athletes partaking in sports at a high-risk of ankle sprain injury) performance of the mSEBT. A total of 122 healthy elite athletes from soccer (n = 73), basketball (n = 15), and volleyball (n = 34) performed one practice trial and three test trials within one session, in three directions (anterior, postero-medial, and postero-lateral), for both legs. Intraclass correlation coefficient (ICC), standard error of measurement (SEM), and smallest detectable change at a 95% confidence were calculated. Results We found a good to excellent relative within-session intra-rater reliability between the three trials on specified directions, with an ICC (3,1) from 0.90 to 0.95. SEM and SDC95 for normalized and composite scores, for both legs ranged from 0.91 to 2.86, and 2.54 to 7.94, respectively. Conclusions In conclusion, we report good to excellent within-session reliability for the mSEBT. Our results confirm that the test can be reliably used with only one practice trial in healthy elite athletes familiar with the test.
format: application/pdf
format: text/html
creator: Roxana R. Onofrei
creator: Elena Amaricai
creator: Radu Petroman
creator: Oana Suciu
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.6999
publisher: PeerJ Inc.
rights: © 2019 Onofrei et al.
abstract: Background The Star Excursion Balance Test (SEBT) is commonly used to assess dynamic postural balance both in clinical practice and research. The aim of our study was to assess the within-session relative and absolute reliability of participants’ performance of the modified SEBT (mSEBT) using a single practice trial in healthy elite athletes who were familiar with the test. Methods An intra-session repeated-measures design was used to investigate the relative and absolute reliability of participants’ (healthy athletes partaking in sports at a high-risk of ankle sprain injury) performance of the mSEBT. A total of 122 healthy elite athletes from soccer (n = 73), basketball (n = 15), and volleyball (n = 34) performed one practice trial and three test trials within one session, in three directions (anterior, postero-medial, and postero-lateral), for both legs. Intraclass correlation coefficient (ICC), standard error of measurement (SEM), and smallest detectable change at a 95% confidence were calculated. Results We found a good to excellent relative within-session intra-rater reliability between the three trials on specified directions, with an ICC (3,1) from 0.90 to 0.95. SEM and SDC95 for normalized and composite scores, for both legs ranged from 0.91 to 2.86, and 2.54 to 7.94, respectively. Conclusions In conclusion, we report good to excellent within-session reliability for the mSEBT. Our results confirm that the test can be reliably used with only one practice trial in healthy elite athletes familiar with the test.
bibliographic citation: Onofrei et al. (2019) Relative and absolute within-session reliability of the modified Star Excursion Balance Test in healthy elite athletes. PeerJ 7:e6999 https://doi.org/10.7717/peerj.6999
date submitted: 2018-11-15
date accepted: 2019-04-22
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Onofrei
  given name: Roxana R.
author list: Agent
  family name: Amaricai
  given name: Elena
author list: Agent
  family name: Petroman
  given name: Radu
author list: Agent
  family name: Suciu
  given name: Oana
doi: 10.7717/peerj.6999
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: © 2019 Onofrei et al.
attribution name: Onofrei et al.

Fine-root traits of allelopathic rice at the seedling stage and their relationship with allelopathic potential
type: item
type: AcademicArticle
description: Background Allelopathic rice releases allelochemicals through its root systems, thereby exerting a negative effect on paddy weeds. This research aimed to evaluate the relationship between fine-root traits and the rice allelopathic potential at the seedling stage. Methods Two allelopathic rice cultivars, ‘PI312777’ and ‘Taichung Native1,’ and one non-allelopathic rice cultivar, ‘Lemont,’ were grown to the 3–6 leaf stage in a hydroponic system. Their fine roots were collected for morphological trait (root length, root surface area, root volume, and root tips number) in smaller diameter cutoffs and proliferative trait (root biomass) analysis. Their root-exudates were used for quantitative analysis of phenolic acids contents and an evaluation of allelopathic potential. Correlation analysis was also used to assess whether any linear relationships existed. Results Our results showed that allelopathic rice cultivars had significantly higher fine-root length having diameters <0.2 mm, more root tips number, and greater root biomass, coupled with higher allelopathic potential and phenolic acid contents of their root exudates, comparing with non-allelopathic rice cultivar. These fine-root traits were significantly-positively correlated to allelopathic inhibition and total phenolic contents in rice root-exudates. However, there were not significant correlations among the rice allelopathic potential and total phenolic acid contents of rice root-exudates with the root length, root surface area, and root volume of fine root in diameter >0.2 mm. Discussion Our results implied that fine-root traits appears to be important in understanding rice allelopathy at the seedling stage. The high allelopathic potential of rice cultivars might be attributed to their higher length of fine roots <0.2 mm in diameter and more number of root tips of fine root, which could accumulate and release more allelochemicals to solutions, thereby resulting in high inhibition on target plants. The mechanisms …
format: application/pdf
format: text/html
creator: Jiayu Li
creator: Shunxian Lin
creator: Qingxu Zhang
creator: Qi Zhang
creator: Wenwen Hu
creator: Haibin He
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.7006
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Allelopathic rice releases allelochemicals through its root systems, thereby exerting a negative effect on paddy weeds. This research aimed to evaluate the relationship between fine-root traits and the rice allelopathic potential at the seedling stage. Methods Two allelopathic rice cultivars, ‘PI312777’ and ‘Taichung Native1,’ and one non-allelopathic rice cultivar, ‘Lemont,’ were grown to the 3–6 leaf stage in a hydroponic system. Their fine roots were collected for morphological trait (root length, root surface area, root volume, and root tips number) in smaller diameter cutoffs and proliferative trait (root biomass) analysis. Their root-exudates were used for quantitative analysis of phenolic acids contents and an evaluation of allelopathic potential. Correlation analysis was also used to assess whether any linear relationships existed. Results Our results showed that allelopathic rice cultivars had significantly higher fine-root length having diameters <0.2 mm, more root tips number, and greater root biomass, coupled with higher allelopathic potential and phenolic acid contents of their root exudates, comparing with non-allelopathic rice cultivar. These fine-root traits were significantly-positively correlated to allelopathic inhibition and total phenolic contents in rice root-exudates. However, there were not significant correlations among the rice allelopathic potential and total phenolic acid contents of rice root-exudates with the root length, root surface area, and root volume of fine root in diameter >0.2 mm. Discussion Our results implied that fine-root traits appears to be important in understanding rice allelopathy at the seedling stage. The high allelopathic potential of rice cultivars might be attributed to their higher length of fine roots <0.2 mm in diameter and more number of root tips of fine root, which could accumulate and release more allelochemicals to solutions, thereby resulting in high inhibition on target plants. The mechanisms …
bibliographic citation: Li et al. (2019) Fine-root traits of allelopathic rice at the seedling stage and their relationship with allelopathic potential. PeerJ 7:e7006 https://doi.org/10.7717/peerj.7006
date submitted: 2018-09-21
date accepted: 2019-04-22
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiayu
author list: Agent
  family name: Lin
  given name: Shunxian
author list: Agent
  family name: Zhang
  given name: Qingxu
author list: Agent
  family name: Zhang
  given name: Qi
author list: Agent
  family name: Hu
  given name: Wenwen
author list: Agent
  family name: He
  given name: Haibin
doi: 10.7717/peerj.7006
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 Li et al.
attribution name: Li et al.

Water regime and osmotic adjustment under warming conditions on wheat in the Yaqui Valley, Mexico
type: item
type: AcademicArticle
description: An experiment was carried out to evaluate the effect of increased temperature on roots and leaf water and osmotic potential, osmotic adjustment (OA) and transpiration on Triticum durum L. (CIRNO C2008 variety) during growth (seedling growth), tillering and heading phenophases. Wheat was sown under field conditions at the Experimental Technology Transfer Center (CETT-910), as a representative wheat crop area from the Yaqui Valley, Sonora México. Thermal radiators were placed at 1.20 m from the crop canopy. Treatments included warmed plots (2 °C) and ambient canopy temperature with five replicates. Temperature treatment was controlled using a (proportional, integrative, derivative) feedback control system on plots covering a circular area of r = 1.5 m. Results indicated a significant decrease in the osmotic potential of roots and leaves for the warmed plots. Water potential, under warming treatment, also experienced a significant reduction and a potential gradient was observed in both, roots and leaves, while the phenophases were delayed. Such results demonstrate that, under warmer conditions, plants increase water absorption for cooling. Hence, transpiration experienced a significant increase under warming in all phenophases that was related to the low root and leaf water potential. CIRNO C2008 also experienced OA in all phenophases with glycine betaine as the osmolyte with major contribution.
format: application/pdf
format: text/html
creator: Leandris Argentel-Martínez
creator: Jaime Garatuza-Payan
creator: Enrico A. Yepez
creator: Tulio Arredondo
creator: Sergio de los Santos-Villalobos
subject: Agricultural Science
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.7029
publisher: PeerJ Inc.
rights: © 2019 Argentel-Martínez et al.
abstract: An experiment was carried out to evaluate the effect of increased temperature on roots and leaf water and osmotic potential, osmotic adjustment (OA) and transpiration on Triticum durum L. (CIRNO C2008 variety) during growth (seedling growth), tillering and heading phenophases. Wheat was sown under field conditions at the Experimental Technology Transfer Center (CETT-910), as a representative wheat crop area from the Yaqui Valley, Sonora México. Thermal radiators were placed at 1.20 m from the crop canopy. Treatments included warmed plots (2 °C) and ambient canopy temperature with five replicates. Temperature treatment was controlled using a (proportional, integrative, derivative) feedback control system on plots covering a circular area of r = 1.5 m. Results indicated a significant decrease in the osmotic potential of roots and leaves for the warmed plots. Water potential, under warming treatment, also experienced a significant reduction and a potential gradient was observed in both, roots and leaves, while the phenophases were delayed. Such results demonstrate that, under warmer conditions, plants increase water absorption for cooling. Hence, transpiration experienced a significant increase under warming in all phenophases that was related to the low root and leaf water potential. CIRNO C2008 also experienced OA in all phenophases with glycine betaine as the osmolyte with major contribution.
bibliographic citation: Argentel-Martínez et al. (2019) Water regime and osmotic adjustment under warming conditions on wheat in the Yaqui Valley, Mexico. PeerJ 7:e7029 https://doi.org/10.7717/peerj.7029
date submitted: 2019-02-01
date accepted: 2019-04-26
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Argentel-Martínez
  given name: Leandris
author list: Agent
  family name: Garatuza-Payan
  given name: Jaime
author list: Agent
  family name: Yepez
  given name: Enrico A.
author list: Agent
  family name: Arredondo
  given name: Tulio
author list: Agent
  family name: de los Santos-Villalobos
  given name: Sergio
doi: 10.7717/peerj.7029
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: © 2019 Argentel-Martínez et al.
attribution name: Argentel-Martínez et al.

Identification and characterization of PsDREB2 promoter involved in tissue-specific expression and abiotic stress response from Paeonia suffruticosa
type: item
type: AcademicArticle
description: Dehydration-responsive element-binding factor 2 (DREB2) belongs to the C-repeat-binding factor (CBF)/DREB subfamily of proteins. In this study, a 2,245 bp PsDREB2 promoter fragment was isolated from the genome of Paeonia suffruticosa. The fragment was rich in A/T bases and contained TATA box sequences, abscisic acid (ABA)-response elements, and other cis-elements, such as MYB and CAAT box. The promoter was fused with the β-glucuronidase (GUS) reporter gene to generate an expression vector. Arabidopsis thaliana was transformed with a flower dipping method. Gus activity in different tissues and organs of transgenic plants was determined via histochemical staining and quantified via GUS fluorescence. The activity of promoter regulatory elements in transgenic plants under drought, low-temperature, high-salt, and ABA stresses was analyzed. The results showed that the PsDREB2 gene promoter was expressed in the roots, stems, leaves, flowers, and silique pods but not in the seeds of transgenic Arabidopsis. Furthermore, the promoter was induced by drought, low temperature, high salt, and ABA. Hence, the PsDREB2 promoter is tissue- and stress-specific and can be used in the genetic engineering of novel peony cultivars in the future.
format: application/pdf
format: text/html
creator: Huichun Liu
creator: Kaiyuan Zhu
creator: Chen Tan
creator: Jiaqiang Zhang
creator: Jianghua Zhou
creator: Liang Jin
creator: Guangying Ma
creator: Qingcheng Zou
subject: Agricultural Science
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.7052
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Dehydration-responsive element-binding factor 2 (DREB2) belongs to the C-repeat-binding factor (CBF)/DREB subfamily of proteins. In this study, a 2,245 bp PsDREB2 promoter fragment was isolated from the genome of Paeonia suffruticosa. The fragment was rich in A/T bases and contained TATA box sequences, abscisic acid (ABA)-response elements, and other cis-elements, such as MYB and CAAT box. The promoter was fused with the β-glucuronidase (GUS) reporter gene to generate an expression vector. Arabidopsis thaliana was transformed with a flower dipping method. Gus activity in different tissues and organs of transgenic plants was determined via histochemical staining and quantified via GUS fluorescence. The activity of promoter regulatory elements in transgenic plants under drought, low-temperature, high-salt, and ABA stresses was analyzed. The results showed that the PsDREB2 gene promoter was expressed in the roots, stems, leaves, flowers, and silique pods but not in the seeds of transgenic Arabidopsis. Furthermore, the promoter was induced by drought, low temperature, high salt, and ABA. Hence, the PsDREB2 promoter is tissue- and stress-specific and can be used in the genetic engineering of novel peony cultivars in the future.
bibliographic citation: Liu et al. (2019) Identification and characterization of PsDREB2 promoter involved in tissue-specific expression and abiotic stress response from Paeonia suffruticosa. PeerJ 7:e7052 https://doi.org/10.7717/peerj.7052
date submitted: 2018-12-13
date accepted: 2019-05-02
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Huichun
author list: Agent
  family name: Zhu
  given name: Kaiyuan
author list: Agent
  family name: Tan
  given name: Chen
author list: Agent
  family name: Zhang
  given name: Jiaqiang
author list: Agent
  family name: Zhou
  given name: Jianghua
author list: Agent
  family name: Jin
  given name: Liang
author list: Agent
  family name: Ma
  given name: Guangying
author list: Agent
  family name: Zou
  given name: Qingcheng
doi: 10.7717/peerj.7052
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 Liu et al.
attribution name: Liu et al.

Sex- and tissue-specific expression of odorant-binding proteins and chemosensory proteins in adults of the scarab beetle Hylamorpha elegans (Burmeister) (Coleoptera: Scarabaeidae)
type: item
type: AcademicArticle
description: In this study, we addressed the sex- and tissue-specific expression patterns of odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) in Hylamorpha elegans (Burmeister), an important native scarab beetle pest species from Chile. Similar to other members of its family, this scarab beetle exhibit habits that make difficult to control the pest by conventional methods. Hence, alternative ways to manage the pest populations based on chemical communication and signaling (such as disrupting mating or host finding process) are highly desirable. However, developing pest-control methods based on chemical communication requires to understand the molecular basis for pheromone recognition/chemical perception in this species. Thus, with the aim of discovering olfaction-related genes, we obtained the first reference transcriptome assembly of H. elegans. We used different tissues of adult beetles from males and females: antennae and maxillary palps, which are well known for embedded sensory organs. Then, the expression of predicted odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) was analyzed by qRT-PCR. In total, 165 transcripts related to chemoperception were predicted. Of these, 16 OBPs, including one pheromone-binding protein (PBP), and four CSPs were successfully amplified by qRT-PCR. All of these genes were differentially expressed in the sensory tissues with respect to the tibial tissue that was used as a control. The single predicted PBP found was highly expressed in the antennal tissues, particularly in males, while several OBPs and one CSP showed male-biased expression patterns, suggesting that these proteins may participate in sexual recognition process. In addition, a single CSP was expressed at higher levels in female palps than in any other studied condition, suggesting that this CSP would participate in oviposition process. Finally, all four CSPs exhibited palp-biased expression while mixed results were obtained for the expression of the OB…
format: application/pdf
format: text/html
creator: Angélica González-González
creator: María E. Rubio-Meléndez
creator: Gabriel I. Ballesteros
creator: Claudio C. Ramírez
creator: Rubén Palma-Millanao
subject: Agricultural Science
subject: Bioinformatics
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.7054
publisher: PeerJ Inc.
rights: © 2019 González-González et al.
abstract: In this study, we addressed the sex- and tissue-specific expression patterns of odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) in Hylamorpha elegans (Burmeister), an important native scarab beetle pest species from Chile. Similar to other members of its family, this scarab beetle exhibit habits that make difficult to control the pest by conventional methods. Hence, alternative ways to manage the pest populations based on chemical communication and signaling (such as disrupting mating or host finding process) are highly desirable. However, developing pest-control methods based on chemical communication requires to understand the molecular basis for pheromone recognition/chemical perception in this species. Thus, with the aim of discovering olfaction-related genes, we obtained the first reference transcriptome assembly of H. elegans. We used different tissues of adult beetles from males and females: antennae and maxillary palps, which are well known for embedded sensory organs. Then, the expression of predicted odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) was analyzed by qRT-PCR. In total, 165 transcripts related to chemoperception were predicted. Of these, 16 OBPs, including one pheromone-binding protein (PBP), and four CSPs were successfully amplified by qRT-PCR. All of these genes were differentially expressed in the sensory tissues with respect to the tibial tissue that was used as a control. The single predicted PBP found was highly expressed in the antennal tissues, particularly in males, while several OBPs and one CSP showed male-biased expression patterns, suggesting that these proteins may participate in sexual recognition process. In addition, a single CSP was expressed at higher levels in female palps than in any other studied condition, suggesting that this CSP would participate in oviposition process. Finally, all four CSPs exhibited palp-biased expression while mixed results were obtained for the expression of the OB…
bibliographic citation: González-González et al. (2019) Sex- and tissue-specific expression of odorant-binding proteins and chemosensory proteins in adults of the scarab beetle Hylamorpha elegans (Burmeister) (Coleoptera: Scarabaeidae). PeerJ 7:e7054 https://doi.org/10.7717/peerj.7054
date submitted: 2018-12-21
date accepted: 2019-05-02
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: González-González
  given name: Angélica
author list: Agent
  family name: Rubio-Meléndez
  given name: María E.
author list: Agent
  family name: Ballesteros
  given name: Gabriel I.
author list: Agent
  family name: Ramírez
  given name: Claudio C.
author list: Agent
  family name: Palma-Millanao
  given name: Rubén
doi: 10.7717/peerj.7054
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 González-González et al.
attribution name: González-González et al.

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
type: item
type: AcademicArticle
description: Background Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic analysis of transcriptomic data, especially in cases with cSVs, is a complex and challenging task, and the development of proper bioinformatic tools for transcriptome studies is necessary. Methods We designed a bioinformatic workflow for the analysis of total RNA-Seq data consisting of two separate parts (pipelines): The first pipeline incorporates a statistical solution for differential gene expression analysis in a biologically heterogeneous sample set. We utilized results from transcriptomic arrays which were carried out in parallel to increase the precision of the analysis. The second pipeline is used for the identification of de novo fusion genes. Special attention was given to the filtering of false positives (FPs), which was achieved through consensus fusion calling with several fusion gene callers. We applied the workflow to the data obtained from ten patients with chronic lymphocytic leukemia (CLL) to describe the consequences of their cSVs in detail. The fusion genes identified by our pipeline were correlated with genomic break-points detected by genomic arrays. Results We set up a novel solution for differential gene expression analysis of individual samples and de novo fusion gene detection from total RNA-Seq data. The results of the differential gene expression analysis were concordant with results obtained by transcriptomic arrays, which demonstrates the analytica…
format: application/pdf
format: text/html
creator: Jakub Hynst
creator: Karla Plevova
creator: Lenka Radova
creator: Vojtech Bystry
creator: Karol Pal
creator: Sarka Pospisilova
subject: Bioinformatics
subject: Genomics
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.7071
publisher: PeerJ Inc.
rights: © 2019 Hynst et al.
abstract: Background Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic analysis of transcriptomic data, especially in cases with cSVs, is a complex and challenging task, and the development of proper bioinformatic tools for transcriptome studies is necessary. Methods We designed a bioinformatic workflow for the analysis of total RNA-Seq data consisting of two separate parts (pipelines): The first pipeline incorporates a statistical solution for differential gene expression analysis in a biologically heterogeneous sample set. We utilized results from transcriptomic arrays which were carried out in parallel to increase the precision of the analysis. The second pipeline is used for the identification of de novo fusion genes. Special attention was given to the filtering of false positives (FPs), which was achieved through consensus fusion calling with several fusion gene callers. We applied the workflow to the data obtained from ten patients with chronic lymphocytic leukemia (CLL) to describe the consequences of their cSVs in detail. The fusion genes identified by our pipeline were correlated with genomic break-points detected by genomic arrays. Results We set up a novel solution for differential gene expression analysis of individual samples and de novo fusion gene detection from total RNA-Seq data. The results of the differential gene expression analysis were concordant with results obtained by transcriptomic arrays, which demonstrates the analytica…
bibliographic citation: Hynst et al. (2019) Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants. PeerJ 7:e7071 https://doi.org/10.7717/peerj.7071
date submitted: 2018-12-30
date accepted: 2019-05-06
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hynst
  given name: Jakub
author list: Agent
  family name: Plevova
  given name: Karla
author list: Agent
  family name: Radova
  given name: Lenka
author list: Agent
  family name: Bystry
  given name: Vojtech
author list: Agent
  family name: Pal
  given name: Karol
author list: Agent
  family name: Pospisilova
  given name: Sarka
doi: 10.7717/peerj.7071
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 Hynst et al.
attribution name: Hynst et al.

Estimating biological accuracy of DSM for attention deficit/hyperactivity disorder based on multivariate analysis for small samples
type: item
type: AcademicArticle
description: Objective To estimate whether the “Diagnostic and Statistical Manual of Mental Disorders” (DSM) is biologically accurate for the diagnosis of Attention Deficit/ Hyperactivity Disorder (ADHD) using a biological-based classifier built by a special method of multivariate analysis of a large dataset of a small sample (much more variables than subjects), holding neurophysiological, behavioral, and psychological variables. Methods Twenty typically developing boys and 19 boys diagnosed with ADHD, aged 10–13 years, were examined using the Attentional Network Test (ANT) with recordings of event-related potentials (ERPs). From 774 variables, a reduced number of latent variables (LVs) were extracted with a clustering of variables method (CLV), for further reclassification of subjects using the k-means method. This approach allowed a multivariate analysis to be applied to a significantly larger number of variables than the number of cases. Results From datasets including ERPs from the mid-frontal, mid-parietal, right frontal, and central scalp areas, we found 82% of agreement between DSM and biological-based classifications. The kappa index between DSM and behavioral/psychological/neurophysiological data was 0.75, which is regarded as a “substantial level of agreement”. Discussion The CLV is a useful method for multivariate analysis of datasets with much less subjects than variables. In this study, a correlation is found between the biological-based classifier and the DSM outputs for the classification of subjects as either ADHD or not. This result suggests that DSM clinically describes a biological condition, supporting its validity for ADHD diagnostics.
format: application/pdf
format: text/html
creator: Dimitri M. Abramov
creator: Vladimir V. Lazarev
creator: Saint Clair Gomes Junior
creator: Carlos Alberto Mourao-Junior
creator: Monique Castro-Pontes
creator: Carla Q. Cunha
creator: Leonardo C. deAzevedo
creator: Evelyne Vigneau
subject: Neuroscience
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7074
publisher: PeerJ Inc.
rights: © 2019 Abramov et al.
abstract: Objective To estimate whether the “Diagnostic and Statistical Manual of Mental Disorders” (DSM) is biologically accurate for the diagnosis of Attention Deficit/ Hyperactivity Disorder (ADHD) using a biological-based classifier built by a special method of multivariate analysis of a large dataset of a small sample (much more variables than subjects), holding neurophysiological, behavioral, and psychological variables. Methods Twenty typically developing boys and 19 boys diagnosed with ADHD, aged 10–13 years, were examined using the Attentional Network Test (ANT) with recordings of event-related potentials (ERPs). From 774 variables, a reduced number of latent variables (LVs) were extracted with a clustering of variables method (CLV), for further reclassification of subjects using the k-means method. This approach allowed a multivariate analysis to be applied to a significantly larger number of variables than the number of cases. Results From datasets including ERPs from the mid-frontal, mid-parietal, right frontal, and central scalp areas, we found 82% of agreement between DSM and biological-based classifications. The kappa index between DSM and behavioral/psychological/neurophysiological data was 0.75, which is regarded as a “substantial level of agreement”. Discussion The CLV is a useful method for multivariate analysis of datasets with much less subjects than variables. In this study, a correlation is found between the biological-based classifier and the DSM outputs for the classification of subjects as either ADHD or not. This result suggests that DSM clinically describes a biological condition, supporting its validity for ADHD diagnostics.
bibliographic citation: Abramov et al. (2019) Estimating biological accuracy of DSM for attention deficit/hyperactivity disorder based on multivariate analysis for small samples. PeerJ 7:e7074 https://doi.org/10.7717/peerj.7074
date submitted: 2018-11-15
date accepted: 2019-05-02
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abramov
  given name: Dimitri M.
author list: Agent
  family name: Lazarev
  given name: Vladimir V.
author list: Agent
  family name: Gomes Junior
  given name: Saint Clair
author list: Agent
  family name: Mourao-Junior
  given name: Carlos Alberto
author list: Agent
  family name: Castro-Pontes
  given name: Monique
author list: Agent
  family name: Cunha
  given name: Carla Q.
author list: Agent
  family name: deAzevedo
  given name: Leonardo C.
author list: Agent
  family name: Vigneau
  given name: Evelyne
doi: 10.7717/peerj.7074
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 Abramov et al.
attribution name: Abramov et al.

Genetic diversity of gliadin-coding alleles in bread wheat (Triticum aestivum L.) from Northern Kazakhstan
type: item
type: AcademicArticle
description: Background Spring bread wheat (Triticum aestivum L.) represents the main cereal crop in Northern Kazakhstan. The quality of wheat grain and flour strongly depends on the structure of gluten, comprised of gliadin and glutenin proteins. Electrophoresis spectra of gliadins are not altered by environmental conditions or plant growth, are easily reproducible and very useful for wheat germplasm identification in addition to DNA markers. Genetic polymorphism of two Gli loci encoding gliadins can be used for selection of preferable genotypes of wheat with high grain quality. Methods Polyacrylamide gel electrophoresis was used to analyse genetic diversity of gliadins in a germplasm collection of spring bread wheat from Northern Kazakhstan. Results The highest frequencies of gliadin alleles were found as follows, in Gli1: -A1f (39.3%), -B1e (71.9%), and -D1a (41.0%); and in Gli-2: -A2q (17.8%), -B2t (13.5%), and -D2q (20.4%). The combination of these alleles in a single genotype may be associated with higher quality of grain as well as better adaptation to the dry environment of Northern Kazakhstan; preferable for wheat breeding in locations with similar conditions.
format: application/pdf
format: text/html
creator: Maral Utebayev
creator: Svetlana Dashkevich
creator: Nina Bome
creator: Kulpash Bulatova
creator: Yuri Shavrukov
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.7082
publisher: PeerJ Inc.
rights: © 2019 Utebayev et al.
abstract: Background Spring bread wheat (Triticum aestivum L.) represents the main cereal crop in Northern Kazakhstan. The quality of wheat grain and flour strongly depends on the structure of gluten, comprised of gliadin and glutenin proteins. Electrophoresis spectra of gliadins are not altered by environmental conditions or plant growth, are easily reproducible and very useful for wheat germplasm identification in addition to DNA markers. Genetic polymorphism of two Gli loci encoding gliadins can be used for selection of preferable genotypes of wheat with high grain quality. Methods Polyacrylamide gel electrophoresis was used to analyse genetic diversity of gliadins in a germplasm collection of spring bread wheat from Northern Kazakhstan. Results The highest frequencies of gliadin alleles were found as follows, in Gli1: -A1f (39.3%), -B1e (71.9%), and -D1a (41.0%); and in Gli-2: -A2q (17.8%), -B2t (13.5%), and -D2q (20.4%). The combination of these alleles in a single genotype may be associated with higher quality of grain as well as better adaptation to the dry environment of Northern Kazakhstan; preferable for wheat breeding in locations with similar conditions.
bibliographic citation: Utebayev et al. (2019) Genetic diversity of gliadin-coding alleles in bread wheat (Triticum aestivum L.) from Northern Kazakhstan. PeerJ 7:e7082 https://doi.org/10.7717/peerj.7082
date submitted: 2019-03-12
date accepted: 2019-05-02
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Utebayev
  given name: Maral
author list: Agent
  family name: Dashkevich
  given name: Svetlana
author list: Agent
  family name: Bome
  given name: Nina
author list: Agent
  family name: Bulatova
  given name: Kulpash
author list: Agent
  family name: Shavrukov
  given name: Yuri
doi: 10.7717/peerj.7082
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 Utebayev et al.
attribution name: Utebayev et al.

T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection
type: item
type: AcademicArticle
description: Background Respiratory syncytial virus (RSV) is the main cause of respiratory tract infection, which seriously threatens the health and life of children. This study is conducted to reveal the rehabilitation mechanisms of RSV infection. Methods E-MTAB-5195 dataset was downloaded from EBI ArrayExpress database, including 39 acute phase samples in the acute phase of infection and 21 samples in the recovery period. Using the limma package, differentially expressed RNAs (DE-RNAs) were analyzed. The significant modules were identified using WGCNA package, and the mRNAs in them were conducted with enrichment analysis using DAVID tool. Afterwards, co-expression network for the RNAs involved in the significant modules was built by Cytoscape software. Additionally, RSV-correlated pathways were searched from Comparative Toxicogenomics Database, and then the pathway network was constructed. Results There were 2,489 DE-RNAs between the two groups, including 2,386 DE-mRNAs and 103 DE-lncRNAs. The RNAs in the black, salmon, blue, tan and turquoise modules correlated with stage were taken as RNA set1. Meanwhile, the RNAs in brown, blue, magenta and pink modules related to disease severity were defined as RNA set2. In the pathway networks, CD40LG and RASGRP1 co-expressed with LINC00891/LINC00526/LINC01215 were involved in the T cell receptor signaling pathway, and IL1B, IL1R2, IL18, and IL18R1 co-expressed with BAIAP2-AS1/CRNDE/LINC01503/SMIM25 were implicated in cytokine-cytokine receptor interaction. Conclusion LINC00891/LINC00526/LINC01215 co-expressed with CD40LG and RASGRP1 might affect the rehabilitation process of RSV infection through the T cell receptor signaling pathway. Besides, BAIAP2-AS1/CRNDE/LINC01503/SMIM25 co-expressed with IL1 and IL18 families might function in the clearance process after RSV infection via cytokine-cytokine receptor interaction.
format: application/pdf
format: text/html
creator: Zuanhao Qian
creator: Zhenglei Zhang
creator: Yingying Wang
subject: Bioinformatics
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.7089
publisher: PeerJ Inc.
rights: © 2019 Qian et al.
abstract: Background Respiratory syncytial virus (RSV) is the main cause of respiratory tract infection, which seriously threatens the health and life of children. This study is conducted to reveal the rehabilitation mechanisms of RSV infection. Methods E-MTAB-5195 dataset was downloaded from EBI ArrayExpress database, including 39 acute phase samples in the acute phase of infection and 21 samples in the recovery period. Using the limma package, differentially expressed RNAs (DE-RNAs) were analyzed. The significant modules were identified using WGCNA package, and the mRNAs in them were conducted with enrichment analysis using DAVID tool. Afterwards, co-expression network for the RNAs involved in the significant modules was built by Cytoscape software. Additionally, RSV-correlated pathways were searched from Comparative Toxicogenomics Database, and then the pathway network was constructed. Results There were 2,489 DE-RNAs between the two groups, including 2,386 DE-mRNAs and 103 DE-lncRNAs. The RNAs in the black, salmon, blue, tan and turquoise modules correlated with stage were taken as RNA set1. Meanwhile, the RNAs in brown, blue, magenta and pink modules related to disease severity were defined as RNA set2. In the pathway networks, CD40LG and RASGRP1 co-expressed with LINC00891/LINC00526/LINC01215 were involved in the T cell receptor signaling pathway, and IL1B, IL1R2, IL18, and IL18R1 co-expressed with BAIAP2-AS1/CRNDE/LINC01503/SMIM25 were implicated in cytokine-cytokine receptor interaction. Conclusion LINC00891/LINC00526/LINC01215 co-expressed with CD40LG and RASGRP1 might affect the rehabilitation process of RSV infection through the T cell receptor signaling pathway. Besides, BAIAP2-AS1/CRNDE/LINC01503/SMIM25 co-expressed with IL1 and IL18 families might function in the clearance process after RSV infection via cytokine-cytokine receptor interaction.
bibliographic citation: Qian et al. (2019) T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection. PeerJ 7:e7089 https://doi.org/10.7717/peerj.7089
date submitted: 2019-01-14
date accepted: 2019-05-06
issued: 2019-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qian
  given name: Zuanhao
author list: Agent
  family name: Zhang
  given name: Zhenglei
author list: Agent
  family name: Wang
  given name: Yingying
doi: 10.7717/peerj.7089
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-12
copyright: ©2019 Qian et al.
attribution name: Qian et al.

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