PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Non-specific low back pain: cross-sectional study of 11,423 children and youth and the association with the perception of heaviness in carrying of schoolbags
items: Braincase anatomy of the Paleocene crocodyliform Rhabdognathus revealed through high resolution computed tomography
items: Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion
items: Taphonomy and taxonomy of a juvenile lambeosaurine (Ornithischia: Hadrosauridae) bonebed from the late Campanian Wapiti Formation of northwestern Alberta, Canada
items: The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia
items: Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice
items: The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings
items: Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment
items: Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer
items: Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program

Non-specific low back pain: cross-sectional study of 11,423 children and youth and the association with the perception of heaviness in carrying of schoolbags
type: item
type: AcademicArticle
description: Background Carrying a schoolbag is a daily activity for most children and adolescents.The perception of a schoolbag’s weight depends upon the individual and is a relevant theme in schoolchildren. Describing the association between the perception of heaviness in carrying a schoolbag and NLBP can facilitate the planning of preventive programs, quite different from those based on specific weight limits for schoolbags in children and youth. Objective To determine the prevalence of non-specific low back pain (NLBP) and to analyse the association between the perception of heaviness in carrying of schoolbags and NLBP in Polish children and youth aged 10–19. Methods This study included 11,423 children and youth (6,252 girls and 5,171 boys) from Poland. An original questionnaire was used to assess NLBP prevalence. Results Among 11,423 of the respondents, 41.5% of the respondents admitted that they had experienced NLBP in the period of the last 12 months. The percentage of individuals reporting NLBP increased with age of participants, p < 0.001. Girls reported NLBP more often than boys (p < 0.001). Students with NLBP declared that their school backpack was heavy more often than students without LBP. Students who thought that their backpacks weighed too much manifested a 1.44 (95% Cl [1.33–1.55]) times higher probability to experience NLBP. Conclusion In the examined group of schoolchildren a frequent occurrence of NLBP (41.5%) was noted. Its occurrence was related to female sex and age. Students who thought that their backpacks weighed too much manifested higher probability to develop NLBP.
format: application/pdf
format: text/html
creator: Agnieszka Kędra
creator: Magdalena Plandowska
creator: Przemysław Kędra
creator: Dariusz Czaprowski
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.11220
publisher: PeerJ Inc.
rights: © 2021 Kędra et al.
abstract: Background Carrying a schoolbag is a daily activity for most children and adolescents.The perception of a schoolbag’s weight depends upon the individual and is a relevant theme in schoolchildren. Describing the association between the perception of heaviness in carrying a schoolbag and NLBP can facilitate the planning of preventive programs, quite different from those based on specific weight limits for schoolbags in children and youth. Objective To determine the prevalence of non-specific low back pain (NLBP) and to analyse the association between the perception of heaviness in carrying of schoolbags and NLBP in Polish children and youth aged 10–19. Methods This study included 11,423 children and youth (6,252 girls and 5,171 boys) from Poland. An original questionnaire was used to assess NLBP prevalence. Results Among 11,423 of the respondents, 41.5% of the respondents admitted that they had experienced NLBP in the period of the last 12 months. The percentage of individuals reporting NLBP increased with age of participants, p < 0.001. Girls reported NLBP more often than boys (p < 0.001). Students with NLBP declared that their school backpack was heavy more often than students without LBP. Students who thought that their backpacks weighed too much manifested a 1.44 (95% Cl [1.33–1.55]) times higher probability to experience NLBP. Conclusion In the examined group of schoolchildren a frequent occurrence of NLBP (41.5%) was noted. Its occurrence was related to female sex and age. Students who thought that their backpacks weighed too much manifested higher probability to develop NLBP.
bibliographic citation: Kędra et al. (2021) Non-specific low back pain: cross-sectional study of 11,423 children and youth and the association with the perception of heaviness in carrying of schoolbags. PeerJ 9:e11220 https://doi.org/10.7717/peerj.11220
date submitted: 2020-12-24
date accepted: 2021-03-15
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kędra
  given name: Agnieszka
author list: Agent
  family name: Plandowska
  given name: Magdalena
author list: Agent
  family name: Kędra
  given name: Przemysław
author list: Agent
  family name: Czaprowski
  given name: Dariusz
doi: 10.7717/peerj.11220
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Kędra et al.
attribution name: Kędra et al.

Braincase anatomy of the Paleocene crocodyliform Rhabdognathus revealed through high resolution computed tomography
type: item
type: AcademicArticle
description: Dyrosaurids were highly specialized, largely marine, relatives of living crocodylians, and one of the few archosaur lineages to survive the K-Pg extinction. Dyrosaurids lived during the Cretaceous to the Eocene and represent a unique combination of morphology and ecology not seen in living crocodylians. Little is known about their endocranial anatomy, leaving many questions about their neurosensory adaptations unaddressed. Recently, µCT (micro-computed tomography) scans were made of a well-preserved skull of Rhabdognathus, a Paleocene dyrosaurid from Mali. This marks the first time the braincase and neurosensory features of a dyrosaurid have been examined using CT. We focus our attention to three specific internal structures: the cranial endocast; the inner ear; and the paratympanic sinuses. The cranial endocast of Rhabdognathus revealed novel features including a unique conformation of its paratympanic system, a prominent dorsal venous system that communicates with the external skull table, extremely enlarged tympanic vestibules that meet at the midline of the endocranium, a prominent spherical cerebrum, and elongate olfactory tracts accounting for half the total endocast length. The bizarre laterally facing lateral Eustachian foramen of dyrosaurids is now understood to be a complex fossa including both a ventrally directed lateral Eustachian foramen and a laterally directed foramen for the basioccipital diverticulum. A novel median pterygopharyngeal canal was discovered connecting the pharynx to the adductor chamber. These revelations require a reinterpretation of the associated external foramina visible on the posterior of the skull in dyrosaurids and potentially their close relatives the pholidosaurids. The olfactory tract terminates in an enlarged olfactory region possessing complex bony projections—a unique morphology perhaps serving to increase surface area for olfaction. The inner ear of Rhabdognathus exhibits characteristics seen in both Pelagosaurus and Ga…
format: application/pdf
format: text/html
creator: Arthur Erb
creator: Alan H. Turner
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11253
publisher: PeerJ Inc.
rights: © 2021 Erb and Turner
abstract: Dyrosaurids were highly specialized, largely marine, relatives of living crocodylians, and one of the few archosaur lineages to survive the K-Pg extinction. Dyrosaurids lived during the Cretaceous to the Eocene and represent a unique combination of morphology and ecology not seen in living crocodylians. Little is known about their endocranial anatomy, leaving many questions about their neurosensory adaptations unaddressed. Recently, µCT (micro-computed tomography) scans were made of a well-preserved skull of Rhabdognathus, a Paleocene dyrosaurid from Mali. This marks the first time the braincase and neurosensory features of a dyrosaurid have been examined using CT. We focus our attention to three specific internal structures: the cranial endocast; the inner ear; and the paratympanic sinuses. The cranial endocast of Rhabdognathus revealed novel features including a unique conformation of its paratympanic system, a prominent dorsal venous system that communicates with the external skull table, extremely enlarged tympanic vestibules that meet at the midline of the endocranium, a prominent spherical cerebrum, and elongate olfactory tracts accounting for half the total endocast length. The bizarre laterally facing lateral Eustachian foramen of dyrosaurids is now understood to be a complex fossa including both a ventrally directed lateral Eustachian foramen and a laterally directed foramen for the basioccipital diverticulum. A novel median pterygopharyngeal canal was discovered connecting the pharynx to the adductor chamber. These revelations require a reinterpretation of the associated external foramina visible on the posterior of the skull in dyrosaurids and potentially their close relatives the pholidosaurids. The olfactory tract terminates in an enlarged olfactory region possessing complex bony projections—a unique morphology perhaps serving to increase surface area for olfaction. The inner ear of Rhabdognathus exhibits characteristics seen in both Pelagosaurus and Ga…
bibliographic citation: Erb et al. (2021) Braincase anatomy of the Paleocene crocodyliform Rhabdognathus revealed through high resolution computed tomography. PeerJ 9:e11253 https://doi.org/10.7717/peerj.11253
date submitted: 2020-09-11
date accepted: 2021-03-20
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erb
  given name: Arthur
author list: Agent
  family name: Turner
  given name: Alan H.
doi: 10.7717/peerj.11253
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Erb and Turner
attribution name: Erb and Turner

Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion
type: item
type: AcademicArticle
description: Background Cotton bollworm, Helicoverpa armigera is a widely distributed, devastating pest of over 200 crop plants that mainly consist of some cellulosic materials. Despite its economic importance as a pest, little is known about the diversity and community structure of gut symbiotic bacteria potentially functioned in cellulose digestion in different gut-sections of H. armigera. In view of this lacuna, we attempted to evaluate and characterize cellulose-degrading bacteria (CDB) from foregut, midgut, and hindgut -regions of H. armigera by using a culture-dependent approach. Methodology The symbiotic bacteria were isolated from different gut-systems of H. armigera by enrichment techniques using Carboxymethyl cellulose sodium salt (CMC) as carbon source. The isolated bacteria were purified and subsequently screened for cellulose-degradation by plate-based method to display the zones of CMC clearance around the colonies. The identification and phylogeny of the gut-bacteria were reconstructed by using 16S rRNA gene sequencing. Different enzymes such as endoglucanase, exoglucanase, β-glucosidase, and xylanase were assayed to determine the cellulolytic repertoire of the isolated bacteria. Results The enrichment of CDB and subsequent plate based screening methods resulted in isolation of 71 bacteria among which 54% of the bacteria were obtained from foregut. Among the isolated bacteria, 25 isolates showed discernible cellulose-degradation potential on CMC-agar plates. The phylogenetic analysis based on 16S rRNA gene amplification and sequencing affiliated these cellulolytic bacteria to two major phyla viz., Firmicutes and Proteobacteria. The members of the genus Klebsiella accounted for 39.43% of the total isolated bacteria while 31% of the Bacillus strains were enriched from hindgut region. The principal component analysis (PCA) further suggested that the members of Bacillus and Klebsiella together dominated the foregut and hindgut regions as they accounted for 68% of the …
format: application/pdf
format: text/html
creator: Mudasir A. Dar
creator: Afrin F. Shaikh
creator: Kiran D. Pawar
creator: Rongrong Xie
creator: Jianzhong Sun
creator: Sabariswaran Kandasamy
creator: Radhakrishna S. Pandit
subject: Agricultural Science
subject: Biotechnology
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.11254
publisher: PeerJ Inc.
rights: © 2021 Dar et al.
abstract: Background Cotton bollworm, Helicoverpa armigera is a widely distributed, devastating pest of over 200 crop plants that mainly consist of some cellulosic materials. Despite its economic importance as a pest, little is known about the diversity and community structure of gut symbiotic bacteria potentially functioned in cellulose digestion in different gut-sections of H. armigera. In view of this lacuna, we attempted to evaluate and characterize cellulose-degrading bacteria (CDB) from foregut, midgut, and hindgut -regions of H. armigera by using a culture-dependent approach. Methodology The symbiotic bacteria were isolated from different gut-systems of H. armigera by enrichment techniques using Carboxymethyl cellulose sodium salt (CMC) as carbon source. The isolated bacteria were purified and subsequently screened for cellulose-degradation by plate-based method to display the zones of CMC clearance around the colonies. The identification and phylogeny of the gut-bacteria were reconstructed by using 16S rRNA gene sequencing. Different enzymes such as endoglucanase, exoglucanase, β-glucosidase, and xylanase were assayed to determine the cellulolytic repertoire of the isolated bacteria. Results The enrichment of CDB and subsequent plate based screening methods resulted in isolation of 71 bacteria among which 54% of the bacteria were obtained from foregut. Among the isolated bacteria, 25 isolates showed discernible cellulose-degradation potential on CMC-agar plates. The phylogenetic analysis based on 16S rRNA gene amplification and sequencing affiliated these cellulolytic bacteria to two major phyla viz., Firmicutes and Proteobacteria. The members of the genus Klebsiella accounted for 39.43% of the total isolated bacteria while 31% of the Bacillus strains were enriched from hindgut region. The principal component analysis (PCA) further suggested that the members of Bacillus and Klebsiella together dominated the foregut and hindgut regions as they accounted for 68% of the …
bibliographic citation: Dar et al. (2021) Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion. PeerJ 9:e11254 https://doi.org/10.7717/peerj.11254
date submitted: 2020-12-11
date accepted: 2021-03-21
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dar
  given name: Mudasir A.
author list: Agent
  family name: Shaikh
  given name: Afrin F.
author list: Agent
  family name: Pawar
  given name: Kiran D.
author list: Agent
  family name: Xie
  given name: Rongrong
author list: Agent
  family name: Sun
  given name: Jianzhong
author list: Agent
  family name: Kandasamy
  given name: Sabariswaran
author list: Agent
  family name: Pandit
  given name: Radhakrishna S.
doi: 10.7717/peerj.11254
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Dar et al.
attribution name: Dar et al.

Taphonomy and taxonomy of a juvenile lambeosaurine (Ornithischia: Hadrosauridae) bonebed from the late Campanian Wapiti Formation of northwestern Alberta, Canada
type: item
type: AcademicArticle
description: Hadrosaurid (duck-billed) dinosaur bonebeds are exceedingly prevalent in upper Cretaceous (Campanian–Maastrichtian) strata from the Midwest of North America (especially Alberta, Canada, and Montana, U.S.A) but are less frequently documented from more northern regions. The Wapiti Formation (Campanian–Maastrichtian) of northwestern Alberta is a largely untapped resource of terrestrial palaeontological information missing from southern Alberta due to the deposition of the marine Bearpaw Formation. In 2018, the Boreal Alberta Dinosaur Project rediscovered the Spring Creek Bonebed, which had been lost since 2002, along the northern bank of the Wapiti River, southwest of Grande Prairie. Earlier excavations and observations of the Spring Creek Bonebed suggested that the site yielded young hadrosaurines. Continued work in 2018 and 2019 recovered ~300 specimens that included a minimum of eight individuals, based on the number of right humeri. The morphology of several recovered cranial elements unequivocally supports lambeosaurine affinities, making the Spring Creek sample the first documented occurrence of lambeosaurines in the Wapiti Formation. The overall size range and histology of the bones found at the site indicate that these animals were uniformly late juveniles, suggesting that age segregation was a life history strategy among hadrosaurids. Given the considerable size attained by the Spring Creek lambeosaurines, they were probably segregated from the breeding population during nesting or caring for young, rather than due to different diet and locomotory requirements. Dynamic aspects of life history, such as age segregation, may well have contributed to the highly diverse and cosmopolitan nature of Late Cretaceous hadrosaurids.
format: application/pdf
format: text/html
creator: Brayden Holland
creator: Phil R. Bell
creator: Federico Fanti
creator: Samantha M. Hamilton
creator: Derek W. Larson
creator: Robin Sissons
creator: Corwin Sullivan
creator: Matthew J. Vavrek
creator: Yanyin Wang
creator: Nicolás E. Campione
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11290
publisher: PeerJ Inc.
rights: © 2021 Holland et al.
abstract: Hadrosaurid (duck-billed) dinosaur bonebeds are exceedingly prevalent in upper Cretaceous (Campanian–Maastrichtian) strata from the Midwest of North America (especially Alberta, Canada, and Montana, U.S.A) but are less frequently documented from more northern regions. The Wapiti Formation (Campanian–Maastrichtian) of northwestern Alberta is a largely untapped resource of terrestrial palaeontological information missing from southern Alberta due to the deposition of the marine Bearpaw Formation. In 2018, the Boreal Alberta Dinosaur Project rediscovered the Spring Creek Bonebed, which had been lost since 2002, along the northern bank of the Wapiti River, southwest of Grande Prairie. Earlier excavations and observations of the Spring Creek Bonebed suggested that the site yielded young hadrosaurines. Continued work in 2018 and 2019 recovered ~300 specimens that included a minimum of eight individuals, based on the number of right humeri. The morphology of several recovered cranial elements unequivocally supports lambeosaurine affinities, making the Spring Creek sample the first documented occurrence of lambeosaurines in the Wapiti Formation. The overall size range and histology of the bones found at the site indicate that these animals were uniformly late juveniles, suggesting that age segregation was a life history strategy among hadrosaurids. Given the considerable size attained by the Spring Creek lambeosaurines, they were probably segregated from the breeding population during nesting or caring for young, rather than due to different diet and locomotory requirements. Dynamic aspects of life history, such as age segregation, may well have contributed to the highly diverse and cosmopolitan nature of Late Cretaceous hadrosaurids.
bibliographic citation: Holland et al. (2021) Taphonomy and taxonomy of a juvenile lambeosaurine (Ornithischia: Hadrosauridae) bonebed from the late Campanian Wapiti Formation of northwestern Alberta, Canada. PeerJ 9:e11290 https://doi.org/10.7717/peerj.11290
date submitted: 2020-12-08
date accepted: 2021-03-26
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holland
  given name: Brayden
author list: Agent
  family name: Bell
  given name: Phil R.
author list: Agent
  family name: Fanti
  given name: Federico
author list: Agent
  family name: Hamilton
  given name: Samantha M.
author list: Agent
  family name: Larson
  given name: Derek W.
author list: Agent
  family name: Sissons
  given name: Robin
author list: Agent
  family name: Sullivan
  given name: Corwin
author list: Agent
  family name: Vavrek
  given name: Matthew J.
author list: Agent
  family name: Wang
  given name: Yanyin
author list: Agent
  family name: Campione
  given name: Nicolás E.
doi: 10.7717/peerj.11290
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: © 2021 Holland et al.
attribution name: Holland et al.

The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia
type: item
type: AcademicArticle
description: In rural Nova Scotia (NS), many small family farms raise free-range hens that consume a varied diet that is different from that of conventionally-farmed hens in caged housing systems. However, it is not known how this varied diet impacts the quality of these eggs. The objective of the present study was to compare the chemical composition of free-range eggs obtained from a small family farm in rural NS to that of conventionally-farmed eggs purchased from a local grocery store. The values obtained from the present study were also compared to published values in the Canadian Nutrient File (CNF) and the U.S. Department of Agriculture FoodData Central database. The egg components and the amino acid compositions were evaluated, and protein concentrations were determined using the Kjeldahl method whereas the fatty acid profiles of the egg yolks were determined using gas chromatography. No difference (P = 0.3) in protein content was observed in free-range eggs (10.6 ± 1.1%) compared to conventionally-farmed eggs (9.7 ± 0.6%). Similar values were also observed for the physical properties of the two types of eggs measured except for the weights of the egg shells. Conversely, the amino acid cysteine, was in higher amounts (P = 0.05) 0.26 g/100 g in the CNF compared to the measured values of ~0.16 g/100 g. Notably, the polyunsaturated linoleic acid (C18:2n-6) was higher (P = 0.001) in the free-range eggs (45.6%) compared to (40.8%) the conventionally-farmed eggs. The cholesterol content of egg yolks was lower in free-range eggs (253.4 ± 0.01 mg/extra-large yolk or 14 mg cholesterol/g of yolk) vs. for conventionally-farmed eggs (263 ± 0.7 mg/extra-large yolk or 15.4 mg cholesterol/g of yolk), respectively. In terms of protein nutrition, free-range eggs may be a suitable alternative to conventionally-farmed eggs, moreover, the lower cholesterol content may be a favourable attribute for Canadian consumers who wish to purchase local free-range eggs.
format: application/pdf
format: text/html
creator: Marcia M. English
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
description: doi:10.7717/peerj.11357
publisher: PeerJ Inc.
rights: © 2021 English
abstract: In rural Nova Scotia (NS), many small family farms raise free-range hens that consume a varied diet that is different from that of conventionally-farmed hens in caged housing systems. However, it is not known how this varied diet impacts the quality of these eggs. The objective of the present study was to compare the chemical composition of free-range eggs obtained from a small family farm in rural NS to that of conventionally-farmed eggs purchased from a local grocery store. The values obtained from the present study were also compared to published values in the Canadian Nutrient File (CNF) and the U.S. Department of Agriculture FoodData Central database. The egg components and the amino acid compositions were evaluated, and protein concentrations were determined using the Kjeldahl method whereas the fatty acid profiles of the egg yolks were determined using gas chromatography. No difference (P = 0.3) in protein content was observed in free-range eggs (10.6 ± 1.1%) compared to conventionally-farmed eggs (9.7 ± 0.6%). Similar values were also observed for the physical properties of the two types of eggs measured except for the weights of the egg shells. Conversely, the amino acid cysteine, was in higher amounts (P = 0.05) 0.26 g/100 g in the CNF compared to the measured values of ~0.16 g/100 g. Notably, the polyunsaturated linoleic acid (C18:2n-6) was higher (P = 0.001) in the free-range eggs (45.6%) compared to (40.8%) the conventionally-farmed eggs. The cholesterol content of egg yolks was lower in free-range eggs (253.4 ± 0.01 mg/extra-large yolk or 14 mg cholesterol/g of yolk) vs. for conventionally-farmed eggs (263 ± 0.7 mg/extra-large yolk or 15.4 mg cholesterol/g of yolk), respectively. In terms of protein nutrition, free-range eggs may be a suitable alternative to conventionally-farmed eggs, moreover, the lower cholesterol content may be a favourable attribute for Canadian consumers who wish to purchase local free-range eggs.
bibliographic citation: English (2021) The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia. PeerJ 9:e11357 https://doi.org/10.7717/peerj.11357
date submitted: 2020-07-20
date accepted: 2021-04-05
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: English
  given name: Marcia M.
doi: 10.7717/peerj.11357
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: © 2021 English
attribution name: English

Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice
type: item
type: AcademicArticle
description: Rice protein has attracted considerable attention recently due to its physiological effects. This study extracted the proteins from paddy rice (PR) and germinated paddy rice (GPR) using three methods i.e., alkaline, sodium dodecyl sulfate (SDS) reagent and enzymatic extractions. The extracted proteins or protein fractions were assessed for their properties using various techniques. Data were analyzed by 2′3 factorial design experiment. It was found that germination and extraction methods significantly affected the concentration of protein fractions when analyzed by Bradford assay. Average protein fraction concentration of the GPR was lower than that of PR. SDS-PAGE patterns of protein fractions obtained from PR and GPR using any extraction method displayed similar protein profiles. Three major protein bands at about 13 kDa (prolamin), 22–23 kDa (basic glutelin) and 37–39 kDa (acidic glutelin) with small amount of 57 kDa proglutelin were observed. For amino acid profile, germination increased the content of most amino acids, resulting in the higher content of amino acids in GPR, excepted for some amino acids. When processed with in vitro digestion, protein fractions from GPR exhibited a higher level of digestibility than those from PR as evidenced by the less intensity of the protein bands obtained from SDS-PAGE. Alkaline and SDS reagent extractions provided more digestible protein fractions than enzymatic extraction. Extraction methods also influenced phase transition of protein fractions as investigated by a DSC. Alkaline extraction resulted in protein fractions with higher phase transition temperature than the other methods. For antioxidant capacity, extraction methods as well as germination significantly affected antioxidant capacity of the protein fractions. Enzymatic extraction provided protein fractions with the best antioxidant capacity.
format: application/pdf
format: text/html
creator: Wirot Likittrakulwong
creator: Pisit Poolprasert
creator: Khongsak Srikaeo
subject: Agricultural Science
subject: Food Science and Technology
description: doi:10.7717/peerj.11365
publisher: PeerJ Inc.
rights: © 2021 Likittrakulwong et al.
abstract: Rice protein has attracted considerable attention recently due to its physiological effects. This study extracted the proteins from paddy rice (PR) and germinated paddy rice (GPR) using three methods i.e., alkaline, sodium dodecyl sulfate (SDS) reagent and enzymatic extractions. The extracted proteins or protein fractions were assessed for their properties using various techniques. Data were analyzed by 2′3 factorial design experiment. It was found that germination and extraction methods significantly affected the concentration of protein fractions when analyzed by Bradford assay. Average protein fraction concentration of the GPR was lower than that of PR. SDS-PAGE patterns of protein fractions obtained from PR and GPR using any extraction method displayed similar protein profiles. Three major protein bands at about 13 kDa (prolamin), 22–23 kDa (basic glutelin) and 37–39 kDa (acidic glutelin) with small amount of 57 kDa proglutelin were observed. For amino acid profile, germination increased the content of most amino acids, resulting in the higher content of amino acids in GPR, excepted for some amino acids. When processed with in vitro digestion, protein fractions from GPR exhibited a higher level of digestibility than those from PR as evidenced by the less intensity of the protein bands obtained from SDS-PAGE. Alkaline and SDS reagent extractions provided more digestible protein fractions than enzymatic extraction. Extraction methods also influenced phase transition of protein fractions as investigated by a DSC. Alkaline extraction resulted in protein fractions with higher phase transition temperature than the other methods. For antioxidant capacity, extraction methods as well as germination significantly affected antioxidant capacity of the protein fractions. Enzymatic extraction provided protein fractions with the best antioxidant capacity.
bibliographic citation: Likittrakulwong et al. (2021) Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice. PeerJ 9:e11365 https://doi.org/10.7717/peerj.11365
date submitted: 2021-01-15
date accepted: 2021-04-07
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Likittrakulwong
  given name: Wirot
author list: Agent
  family name: Poolprasert
  given name: Pisit
author list: Agent
  family name: Srikaeo
  given name: Khongsak
doi: 10.7717/peerj.11365
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Likittrakulwong et al.
attribution name: Likittrakulwong et al.

The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings
type: item
type: AcademicArticle
description: The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated.
format: application/pdf
format: text/html
creator: Hongzhan Liu
creator: Chaoqiong Li
creator: Lin Qiao
creator: Lizong Hu
creator: Xueqin Wang
creator: Junsheng Wang
creator: Xianle Ruan
creator: Guangyu Yang
creator: Guihong Yin
creator: Chunping Wang
creator: Zhongke Sun
creator: Keshi Ma
creator: Lili Li
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11371
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated.
bibliographic citation: Liu et al. (2021) The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings. PeerJ 9:e11371 https://doi.org/10.7717/peerj.11371
date submitted: 2020-10-04
date accepted: 2021-04-07
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hongzhan
author list: Agent
  family name: Li
  given name: Chaoqiong
author list: Agent
  family name: Qiao
  given name: Lin
author list: Agent
  family name: Hu
  given name: Lizong
author list: Agent
  family name: Wang
  given name: Xueqin
author list: Agent
  family name: Wang
  given name: Junsheng
author list: Agent
  family name: Ruan
  given name: Xianle
author list: Agent
  family name: Yang
  given name: Guangyu
author list: Agent
  family name: Yin
  given name: Guihong
author list: Agent
  family name: Wang
  given name: Chunping
author list: Agent
  family name: Sun
  given name: Zhongke
author list: Agent
  family name: Ma
  given name: Keshi
author list: Agent
  family name: Li
  given name: Lili
doi: 10.7717/peerj.11371
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment
type: item
type: AcademicArticle
description: Background Ovarian cancer is one of the leading causes of female deaths worldwide. Ovarian serous cystadenocarcinoma occupies about 90% of it. Effective and accurate biomarkers for diagnosis, outcome prediction and personalized treatment are needed urgently Methods Gene expression profile for OSC patients was obtained from the TCGA database. The ESTIMATE algorithm was used to calculate immune scores and stromal scores of expression data of ovarian serous cystadenocarcinoma samples. Survival results between high and low groups of immune and stromal score were compared and differentially expressed genes (DEGs) were screened out by limma package. The Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network analysis were performed with the g:Profiler database, the Cytoscape and Search Tool for the Retrieval of Interacting Genes (STRING-DB). Survival results between high and low immune and stromal score groups were compared. Kaplan-Meier plots based on TCGA follow up information were generated to evaluate patients’ overall survival. Results Eighty-six upregulated DEGs and one downregulated DEG were identified. Three modules, which included 49 nodes were chosen as important networks. Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were considered to be correlated with poor overall survival. Conclusion Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were correlated with poor overall survival in our study. This new set of genes can become strong predictor of survival, individually or combined. Further investigation of these genes is needed to validate the conclusion to provide novel understanding of tumor microenvironment with ovarian serous cystadenocarcinoma prognosis and treatment.
format: application/pdf
format: text/html
creator: Youzheng Xu
creator: Yixin Xu
creator: Chun Wang
creator: Baoguo Xia
creator: Qingling Mu
creator: Shaohong Luan
creator: Jun Fan
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.11375
publisher: PeerJ Inc.
rights: © 2021 Xu et al.
abstract: Background Ovarian cancer is one of the leading causes of female deaths worldwide. Ovarian serous cystadenocarcinoma occupies about 90% of it. Effective and accurate biomarkers for diagnosis, outcome prediction and personalized treatment are needed urgently Methods Gene expression profile for OSC patients was obtained from the TCGA database. The ESTIMATE algorithm was used to calculate immune scores and stromal scores of expression data of ovarian serous cystadenocarcinoma samples. Survival results between high and low groups of immune and stromal score were compared and differentially expressed genes (DEGs) were screened out by limma package. The Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network analysis were performed with the g:Profiler database, the Cytoscape and Search Tool for the Retrieval of Interacting Genes (STRING-DB). Survival results between high and low immune and stromal score groups were compared. Kaplan-Meier plots based on TCGA follow up information were generated to evaluate patients’ overall survival. Results Eighty-six upregulated DEGs and one downregulated DEG were identified. Three modules, which included 49 nodes were chosen as important networks. Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were considered to be correlated with poor overall survival. Conclusion Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were correlated with poor overall survival in our study. This new set of genes can become strong predictor of survival, individually or combined. Further investigation of these genes is needed to validate the conclusion to provide novel understanding of tumor microenvironment with ovarian serous cystadenocarcinoma prognosis and treatment.
bibliographic citation: Xu et al. (2021) Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment. PeerJ 9:e11375 https://doi.org/10.7717/peerj.11375
date submitted: 2019-03-27
date accepted: 2021-04-08
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Youzheng
author list: Agent
  family name: Xu
  given name: Yixin
author list: Agent
  family name: Wang
  given name: Chun
author list: Agent
  family name: Xia
  given name: Baoguo
author list: Agent
  family name: Mu
  given name: Qingling
author list: Agent
  family name: Luan
  given name: Shaohong
author list: Agent
  family name: Fan
  given name: Jun
doi: 10.7717/peerj.11375
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Xu et al.
attribution name: Xu et al.

Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer
type: item
type: AcademicArticle
description: Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using…
format: application/pdf
format: text/html
creator: Chongyang Ren
creator: Xiaojiang Tang
creator: Haitao Lan
subject: Bioinformatics
subject: Oncology
subject: Translational Medicine
subject: Women’s Health
description: doi:10.7717/peerj.11377
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using…
bibliographic citation: Ren et al. (2021) Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer. PeerJ 9:e11377 https://doi.org/10.7717/peerj.11377
date submitted: 2020-09-16
date accepted: 2021-04-08
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Chongyang
author list: Agent
  family name: Tang
  given name: Xiaojiang
author list: Agent
  family name: Lan
  given name: Haitao
doi: 10.7717/peerj.11377
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Ren et al.
attribution name: Ren et al.

Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program
type: item
type: AcademicArticle
description: The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts.
format: application/pdf
format: text/html
creator: Jennifer F. Moore
creator: William E. Pine III
subject: Aquaculture, Fisheries and Fish Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.11378
publisher: PeerJ Inc.
rights: © 2021 Moore and Pine III
abstract: The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts.
bibliographic citation: Moore et al. (2021) Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program. PeerJ 9:e11378 https://doi.org/10.7717/peerj.11378
date submitted: 2021-01-08
date accepted: 2021-04-08
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moore
  given name: Jennifer F.
author list: Agent
  family name: Pine III
  given name: William E.
doi: 10.7717/peerj.11378
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Moore and Pine III
attribution name: Moore and Pine III

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