PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
items: Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry
items: Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar)
items: Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands)
items: Self-medication practices and rational drug use habits among university students: a cross-sectional study from Kahramanmaraş, Turkey
items: Mechanisms of oat (Avena sativa L.) acclimation to phosphate deficiency
items: Can 9q34.2 rs633862 polymorphism predict survival in epithelial ovarian cancer?
items: Effects of graded concentrations of supplemental lead on lead concentrations in tissues of pigs and prediction equations for estimating dietary lead intake
items: Water absorption through salivary gland type I acini in the blacklegged tick, Ixodes scapularis
items: Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa

Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
type: item
type: AcademicArticle
description: Extensive and in-depth investigations of high-altitude adaptation have been carried out at the level of morphology, anatomy, physiology and genomics, but few investigations focused on the roles of microRNA (miRNA) in high-altitude adaptation. We examined the differences in the miRNA transcriptomes of two representative hypoxia-sensitive tissues (heart and lung) between yak and cattle, two closely related species that live in high and low altitudes, respectively. In this study, we identified a total of 808 mature miRNAs, which corresponded to 715 pre-miRNAs in the two species. The further analysis revealed that both tissues showed relatively high correlation coefficient between yak and cattle, but a greater differentiation was present in lung than heart between the two species. In addition, miRNAs with significantly differentiated patterns of expression in two tissues exhibited co-operation effect in high altitude adaptation based on miRNA family and cluster. Functional analysis revealed that differentially expressed miRNAs were enriched in hypoxia-related pathways, such as the HIF-1α signaling pathway, the insulin signaling pathway, the PI3K-Akt signaling pathway, nucleotide excision repair, cell cycle, apoptosis and fatty acid metabolism, which indicated the important roles of miRNAs in high altitude adaptation. These results suggested the diverse degrees of miRNA transcriptome variation in different tissues between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation.
format: application/pdf
format: text/html
creator: Jiuqiang Guan
creator: Keren Long
creator: Jideng Ma
creator: Jinwei Zhang
creator: Dafang He
creator: Long Jin
creator: Qianzi Tang
creator: Anan Jiang
creator: Xun Wang
creator: Yaodong Hu
creator: Shilin Tian
creator: Zhi Jiang
creator: Mingzhou Li
creator: Xiaolin Luo
subject: Agricultural Science
subject: Biodiversity
subject: Molecular Biology
description: doi:10.7717/peerj.3959
publisher: PeerJ Inc.
rights: © 2017 Guan et al.
abstract: Extensive and in-depth investigations of high-altitude adaptation have been carried out at the level of morphology, anatomy, physiology and genomics, but few investigations focused on the roles of microRNA (miRNA) in high-altitude adaptation. We examined the differences in the miRNA transcriptomes of two representative hypoxia-sensitive tissues (heart and lung) between yak and cattle, two closely related species that live in high and low altitudes, respectively. In this study, we identified a total of 808 mature miRNAs, which corresponded to 715 pre-miRNAs in the two species. The further analysis revealed that both tissues showed relatively high correlation coefficient between yak and cattle, but a greater differentiation was present in lung than heart between the two species. In addition, miRNAs with significantly differentiated patterns of expression in two tissues exhibited co-operation effect in high altitude adaptation based on miRNA family and cluster. Functional analysis revealed that differentially expressed miRNAs were enriched in hypoxia-related pathways, such as the HIF-1α signaling pathway, the insulin signaling pathway, the PI3K-Akt signaling pathway, nucleotide excision repair, cell cycle, apoptosis and fatty acid metabolism, which indicated the important roles of miRNAs in high altitude adaptation. These results suggested the diverse degrees of miRNA transcriptome variation in different tissues between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation.
bibliographic citation: Guan et al. (2017) Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation. PeerJ 5:e3959 https://doi.org/10.7717/peerj.3959
date submitted: 2017-04-07
date accepted: 2017-10-04
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guan
  given name: Jiuqiang
author list: Agent
  family name: Long
  given name: Keren
author list: Agent
  family name: Ma
  given name: Jideng
author list: Agent
  family name: Zhang
  given name: Jinwei
author list: Agent
  family name: He
  given name: Dafang
author list: Agent
  family name: Jin
  given name: Long
author list: Agent
  family name: Tang
  given name: Qianzi
author list: Agent
  family name: Jiang
  given name: Anan
author list: Agent
  family name: Wang
  given name: Xun
author list: Agent
  family name: Hu
  given name: Yaodong
author list: Agent
  family name: Tian
  given name: Shilin
author list: Agent
  family name: Jiang
  given name: Zhi
author list: Agent
  family name: Li
  given name: Mingzhou
author list: Agent
  family name: Luo
  given name: Xiaolin
doi: 10.7717/peerj.3959
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Guan et al.
attribution name: Guan et al.

Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry
type: item
type: AcademicArticle
description: Background Currently, there is limited knowledge about the genetics underlying pigmentary traits in East Asian populations. Here, we report the results of the first genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. Methods We obtained quantitative skin pigmentation measures (M-index) in the inner upper arm of the participants using a portable reflectometer (N = 305). Quantitative measures of iris color (expressed as L*, a* and b* CIELab coordinates) were extracted from high-resolution iris pictures (N = 342). We also measured the color differences between the pupillary and ciliary regions of the iris (e.g., iris heterochromia). DNA samples were genotyped with Illumina’s Infinium Multi-Ethnic Global Array (MEGA) and imputed using the 1000 Genomes Phase 3 samples as reference haplotypes. Results For skin pigmentation, we did not observe any genome-wide significant signal. We followed-up in three independent Chinese samples the lead SNPs of five regions showing multiple common markers (minor allele frequency ≥ 5%) with good imputation scores and suggestive evidence of association (p-values < 10−5). One of these markers, rs2373391, which is located in an intron of the ZNF804B gene on chromosome 7, was replicated in one of the Chinese samples (p = 0.003). For iris color, we observed genome-wide signals in the OCA2 region on chromosome 15. This signal is driven by the non-synonymous rs1800414 variant, which explains 11.9%, 10.4% and 6% of the variation observed in the b*, a* and L* coordinates in our sample, respectively. However, the OCA2 region was not associated with iris heterochromia. Discussion Additional genome-wide association studies in East Asian samples will be necessary to further disentangle the genetic architecture of pigmentary traits in East Asian populations.
format: application/pdf
format: text/html
creator: Lida Rawofi
creator: Melissa Edwards
creator: S Krithika
creator: Phuong Le
creator: David Cha
creator: Zhaohui Yang
creator: Yanyun Ma
creator: Jiucun Wang
creator: Bing Su
creator: Li Jin
creator: Heather L. Norton
creator: Esteban J. Parra
subject: Anthropology
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.3951
publisher: PeerJ Inc.
rights: © 2017 Rawofi et al.
abstract: Background Currently, there is limited knowledge about the genetics underlying pigmentary traits in East Asian populations. Here, we report the results of the first genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. Methods We obtained quantitative skin pigmentation measures (M-index) in the inner upper arm of the participants using a portable reflectometer (N = 305). Quantitative measures of iris color (expressed as L*, a* and b* CIELab coordinates) were extracted from high-resolution iris pictures (N = 342). We also measured the color differences between the pupillary and ciliary regions of the iris (e.g., iris heterochromia). DNA samples were genotyped with Illumina’s Infinium Multi-Ethnic Global Array (MEGA) and imputed using the 1000 Genomes Phase 3 samples as reference haplotypes. Results For skin pigmentation, we did not observe any genome-wide significant signal. We followed-up in three independent Chinese samples the lead SNPs of five regions showing multiple common markers (minor allele frequency ≥ 5%) with good imputation scores and suggestive evidence of association (p-values < 10−5). One of these markers, rs2373391, which is located in an intron of the ZNF804B gene on chromosome 7, was replicated in one of the Chinese samples (p = 0.003). For iris color, we observed genome-wide signals in the OCA2 region on chromosome 15. This signal is driven by the non-synonymous rs1800414 variant, which explains 11.9%, 10.4% and 6% of the variation observed in the b*, a* and L* coordinates in our sample, respectively. However, the OCA2 region was not associated with iris heterochromia. Discussion Additional genome-wide association studies in East Asian samples will be necessary to further disentangle the genetic architecture of pigmentary traits in East Asian populations.
bibliographic citation: Rawofi et al. (2017) Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. PeerJ 5:e3951 https://doi.org/10.7717/peerj.3951
date submitted: 2017-08-23
date accepted: 2017-10-01
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rawofi
  given name: Lida
author list: Agent
  family name: Edwards
  given name: Melissa
author list: Agent
  family name: Krithika
  given name: S
author list: Agent
  family name: Le
  given name: Phuong
author list: Agent
  family name: Cha
  given name: David
author list: Agent
  family name: Yang
  given name: Zhaohui
author list: Agent
  family name: Ma
  given name: Yanyun
author list: Agent
  family name: Wang
  given name: Jiucun
author list: Agent
  family name: Su
  given name: Bing
author list: Agent
  family name: Jin
  given name: Li
author list: Agent
  family name: Norton
  given name: Heather L.
author list: Agent
  family name: Parra
  given name: Esteban J.
doi: 10.7717/peerj.3951
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Rawofi et al.
attribution name: Rawofi et al.

Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar)
type: item
type: AcademicArticle
description: In female Atlantic salmon (Salmo salar), exposure to warm summer temperatures causes a reduction in plasma 17β-estradiol (E2), which impairs downstream vitellogenesis and zonagenesis, and reduces egg fertility and embryo survival. The aim of the present study was to determine whether E2-treatment could offset thermal impairment of endocrine function and maintain egg quality in maiden (first-time-spawning) S. salar reared at 22 °C. Treatment with E2 at 22 °C stimulated vitellogenin (vtg) gene expression and subsequent protein synthesis which promoted oocyte growth and increased egg size relative to untreated fish at 14 and 22 °C. However, E2-treatment at 22 °C was not associated with an increase in egg fertility and embryo survival relative to untreated fish at 22 °C, despite the positive effects of E2-treatment on vitellogenesis and oocyte growth. As there was no evidence to suggest that the estrogen receptor alpha expression was suppressed by high temperature, this could be due to the lack of stimulation on zonagenesis by E2-treatment observed at high temperature during oocyte development. Our results demonstrate that treatment with E2 is not able to maintain zonagenesis or egg quality in maiden S. salar at high temperature, even when vtg gene expression, protein synthesis and subsequent oocyte growth is promoted. This implies that the mechanisms regulating zonagenesis, but not vitellogenesis are impaired at elevated temperature in female S. salar broodstock, and highlights the remarkable complexity of thermally induced endocrine disruption in fish.
format: application/pdf
format: text/html
creator: Kelli Anderson
creator: Ned Pankhurst
creator: Harry King
creator: Abigail Elizur
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3897
publisher: PeerJ Inc.
rights: © 2017 Anderson et al.
abstract: In female Atlantic salmon (Salmo salar), exposure to warm summer temperatures causes a reduction in plasma 17β-estradiol (E2), which impairs downstream vitellogenesis and zonagenesis, and reduces egg fertility and embryo survival. The aim of the present study was to determine whether E2-treatment could offset thermal impairment of endocrine function and maintain egg quality in maiden (first-time-spawning) S. salar reared at 22 °C. Treatment with E2 at 22 °C stimulated vitellogenin (vtg) gene expression and subsequent protein synthesis which promoted oocyte growth and increased egg size relative to untreated fish at 14 and 22 °C. However, E2-treatment at 22 °C was not associated with an increase in egg fertility and embryo survival relative to untreated fish at 22 °C, despite the positive effects of E2-treatment on vitellogenesis and oocyte growth. As there was no evidence to suggest that the estrogen receptor alpha expression was suppressed by high temperature, this could be due to the lack of stimulation on zonagenesis by E2-treatment observed at high temperature during oocyte development. Our results demonstrate that treatment with E2 is not able to maintain zonagenesis or egg quality in maiden S. salar at high temperature, even when vtg gene expression, protein synthesis and subsequent oocyte growth is promoted. This implies that the mechanisms regulating zonagenesis, but not vitellogenesis are impaired at elevated temperature in female S. salar broodstock, and highlights the remarkable complexity of thermally induced endocrine disruption in fish.
bibliographic citation: Anderson et al. (2017) Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar). PeerJ 5:e3897 https://doi.org/10.7717/peerj.3897
date submitted: 2017-06-19
date accepted: 2017-09-16
issued: 2017-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Kelli
author list: Agent
  family name: Pankhurst
  given name: Ned
author list: Agent
  family name: King
  given name: Harry
author list: Agent
  family name: Elizur
  given name: Abigail
doi: 10.7717/peerj.3897
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-02
copyright: ©2017 Anderson et al.
attribution name: Anderson et al.

Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands)
type: item
type: AcademicArticle
description: Background The family Pontoporiidae (Cetacea, Odontoceti, Inioidea) is currently represented in our oceans by just one species of diminutive dolphin (Pontoporia blainvillei, franciscana). Although P. blainvillei is limited to coastal waters of the South Atlantic along Brazil, Uruguay and Argentina, multiple Miocene and Pliocene fossils indicate the past presence of members of the family in the South Atlantic, South Paciifc and North Atlantic oceans. Our comprehension of the origin and diversity of this clade and of the relationships of its members with other inioids is hampered by the fact that part of the described fossil specimens, especially from the North Atlantic realm, are cranial fragments often associated to limited stratigraphic information. Methods Based on an almost complete fossil cranium of pontoporiid from the Westerschelde estuary, The Netherlands, whose preservation allows for detailed morphological observations, we describe a new genus and species. The latter is compared to other pontoporiids, as well as a few non-pontoporiid inioids. A phylogenetic analysis is performed to investigate the relationship of S. vandokkumi with the best-known extinct and extant inioids. Palynological analysis of the sediment associated to the holotype is used to assess its geological age. Results and discussion The new genus and species Scaldiporia vandokkumi is characterized among others by greatly thickened premaxillary eminences reaching the level of the antorbital notch. Palynologically dated from the late Tortonian—earliest Zanclean (7.6–5 Ma, Late Miocene—earliest Pliocene), this new pontoporiid confirms the surprising past diversity of marine inioids in the North Atlantic area. Finally the content of the pontoporiid subfamily Brachydelphininae is briefly discussed.
format: application/pdf
format: text/html
creator: Klaas Post
creator: Stephen Louwye
creator: Olivier Lambert
subject: Paleontology
description: doi:10.7717/peerj.3991
publisher: PeerJ Inc.
rights: © 2017 Post et al.
abstract: Background The family Pontoporiidae (Cetacea, Odontoceti, Inioidea) is currently represented in our oceans by just one species of diminutive dolphin (Pontoporia blainvillei, franciscana). Although P. blainvillei is limited to coastal waters of the South Atlantic along Brazil, Uruguay and Argentina, multiple Miocene and Pliocene fossils indicate the past presence of members of the family in the South Atlantic, South Paciifc and North Atlantic oceans. Our comprehension of the origin and diversity of this clade and of the relationships of its members with other inioids is hampered by the fact that part of the described fossil specimens, especially from the North Atlantic realm, are cranial fragments often associated to limited stratigraphic information. Methods Based on an almost complete fossil cranium of pontoporiid from the Westerschelde estuary, The Netherlands, whose preservation allows for detailed morphological observations, we describe a new genus and species. The latter is compared to other pontoporiids, as well as a few non-pontoporiid inioids. A phylogenetic analysis is performed to investigate the relationship of S. vandokkumi with the best-known extinct and extant inioids. Palynological analysis of the sediment associated to the holotype is used to assess its geological age. Results and discussion The new genus and species Scaldiporia vandokkumi is characterized among others by greatly thickened premaxillary eminences reaching the level of the antorbital notch. Palynologically dated from the late Tortonian—earliest Zanclean (7.6–5 Ma, Late Miocene—earliest Pliocene), this new pontoporiid confirms the surprising past diversity of marine inioids in the North Atlantic area. Finally the content of the pontoporiid subfamily Brachydelphininae is briefly discussed.
bibliographic citation: Post et al. (2017) Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands). PeerJ 5:e3991 https://doi.org/10.7717/peerj.3991
date submitted: 2017-07-17
date accepted: 2017-10-14
issued: 2017-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Post
  given name: Klaas
author list: Agent
  family name: Louwye
  given name: Stephen
author list: Agent
  family name: Lambert
  given name: Olivier
doi: 10.7717/peerj.3991
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-01
copyright: ©2017 Post et al.
attribution name: Post et al.

Self-medication practices and rational drug use habits among university students: a cross-sectional study from Kahramanmaraş, Turkey
type: item
type: AcademicArticle
description: Background Self-medication refers to the use of medicines to treat self-diagnosed diseases without consulting any healthcare professionals. Irrational drug use and self-medication have serious negative consequences both on health and economy. Therefore, the aim of this study is to assess the habits related to rational use of drugs (RUD) and to estimate the prevalence of self-medication practices among university students. Methods This cross-sectional study was conducted on university students in Kahramanmaraş. From May 2017 to June 2017 a total of 960 students filled a “Rational Use of Drugs Questionnaire”. Results The prevalence of practicing self-medication in students was 63.4%. The most common medicines that the students had consumed without prescription were analgesics by 39.5%, antibiotics by 36.9% and cold remedies by 24.0%. The rate of students who declared that they were familiar with RUD and “rational use of antibiotics” (RUA) was 45.9%. Reading/checking the instructions in the prospectus (OR = 1.529, 95% CI [1.176–1.990]), understanding the context of the prospectus (OR = 1.893, 95% CI [1.387–2.584]), compliance with the duration of antibiotic treatment (OR = 1.597, 95% CI [1.231–2.071]) and consulting a physician in case of a side effect (OR = 1.350, 95% CI [1.037–1.757]) were significantly higher among students who were familiar with RUD as compared to who were not. Discussion Since the awareness of RUD among university students was found to be inadequate, it has critical importance to hold educational activities with the cooperation of physicians, health organizations, universities, non-governmental organizations and media to avoid negative consequences of irrational drug use and self-medication.
format: application/pdf
format: text/html
creator: Ramazan Azim Okyay
creator: Ayşegül Erdoğan
subject: Epidemiology
subject: Pharmacology
subject: Public Health
description: doi:10.7717/peerj.3990
publisher: PeerJ Inc.
rights: © 2017 Okyay and Erdoğan
abstract: Background Self-medication refers to the use of medicines to treat self-diagnosed diseases without consulting any healthcare professionals. Irrational drug use and self-medication have serious negative consequences both on health and economy. Therefore, the aim of this study is to assess the habits related to rational use of drugs (RUD) and to estimate the prevalence of self-medication practices among university students. Methods This cross-sectional study was conducted on university students in Kahramanmaraş. From May 2017 to June 2017 a total of 960 students filled a “Rational Use of Drugs Questionnaire”. Results The prevalence of practicing self-medication in students was 63.4%. The most common medicines that the students had consumed without prescription were analgesics by 39.5%, antibiotics by 36.9% and cold remedies by 24.0%. The rate of students who declared that they were familiar with RUD and “rational use of antibiotics” (RUA) was 45.9%. Reading/checking the instructions in the prospectus (OR = 1.529, 95% CI [1.176–1.990]), understanding the context of the prospectus (OR = 1.893, 95% CI [1.387–2.584]), compliance with the duration of antibiotic treatment (OR = 1.597, 95% CI [1.231–2.071]) and consulting a physician in case of a side effect (OR = 1.350, 95% CI [1.037–1.757]) were significantly higher among students who were familiar with RUD as compared to who were not. Discussion Since the awareness of RUD among university students was found to be inadequate, it has critical importance to hold educational activities with the cooperation of physicians, health organizations, universities, non-governmental organizations and media to avoid negative consequences of irrational drug use and self-medication.
bibliographic citation: Okyay et al. (2017) Self-medication practices and rational drug use habits among university students: a cross-sectional study from Kahramanmaraş, Turkey. PeerJ 5:e3990 https://doi.org/10.7717/peerj.3990
date submitted: 2017-08-03
date accepted: 2017-10-13
issued: 2017-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Okyay
  given name: Ramazan Azim
author list: Agent
  family name: Erdoğan
  given name: Ayşegül
doi: 10.7717/peerj.3990
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-01
copyright: ©2017 Okyay and Erdoğan
attribution name: Okyay and Erdoğan

Mechanisms of oat (Avena sativa L.) acclimation to phosphate deficiency
type: item
type: AcademicArticle
description: Background Deficiency of available forms of phosphorus is common in most soils and causes reduction of crop plants growth and yield. Recently, model plants responses to phosphate (Pi) deficiency have been intensively studied. However, acclimation mechanisms of cereals like oat (Avena sativa L.), to low Pi stress remains not fully understood. Oat plants have been usually cultured on poor soils, with a low nutrient content, but their responses to such conditions are not well known, therefore the main goal of the study was to investigate the mechanisms that enable oat plants to grow under low Pi conditions. Methods Four oat cultivars (A. sativa, cv. Arab, Krezus, Rajtar and Szakal) were grown for three weeks in a nutrient media with various P sources: inorganic—KH2PO4 (control), organic—phytate (PA) and with no phosphate (−P). The effects of Pi deficiency on the level of P, oat growth parameters, intensity of photosynthesis, plant productivity, root exudation ability, localization, activity and isoforms of acid phosphatases, enzymes involved in Pi mobilization, were estimated. In addition, the effect of mycorrhization on plant growth was also observed. Results All studied oat cultivars grown on Pi-deficient media had significantly decreased Pi content in the tissues. Pi deficiency caused inhibition of shoot growth, but generally it did not affect root elongation; root diameter was decreased, root/shoot ratios increased, whereas PA plants showed a similar growth to control. Photosynthesis rate and productivity parameters decreased under low Pi nutrition, however, sugar content generally increased. Studied oat cultivars did not respond to low Pi via increased exudation of carboxylates from the roots, as pH changes in the growth media were not observed. Pi starvation significantly increased the activity of extracellular and intracellular acid phosphatases (APases) in comparison to the control plants. Three major APase isoforms were detected in oat tissues and the isoform …
format: application/pdf
format: text/html
creator: Ewa Żebrowska
creator: Marta Milewska
creator: Iwona Ciereszko
subject: Agricultural Science
subject: Biochemistry
subject: Environmental Sciences
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.3989
publisher: PeerJ Inc.
rights: © 2017 Żebrowska et al.
abstract: Background Deficiency of available forms of phosphorus is common in most soils and causes reduction of crop plants growth and yield. Recently, model plants responses to phosphate (Pi) deficiency have been intensively studied. However, acclimation mechanisms of cereals like oat (Avena sativa L.), to low Pi stress remains not fully understood. Oat plants have been usually cultured on poor soils, with a low nutrient content, but their responses to such conditions are not well known, therefore the main goal of the study was to investigate the mechanisms that enable oat plants to grow under low Pi conditions. Methods Four oat cultivars (A. sativa, cv. Arab, Krezus, Rajtar and Szakal) were grown for three weeks in a nutrient media with various P sources: inorganic—KH2PO4 (control), organic—phytate (PA) and with no phosphate (−P). The effects of Pi deficiency on the level of P, oat growth parameters, intensity of photosynthesis, plant productivity, root exudation ability, localization, activity and isoforms of acid phosphatases, enzymes involved in Pi mobilization, were estimated. In addition, the effect of mycorrhization on plant growth was also observed. Results All studied oat cultivars grown on Pi-deficient media had significantly decreased Pi content in the tissues. Pi deficiency caused inhibition of shoot growth, but generally it did not affect root elongation; root diameter was decreased, root/shoot ratios increased, whereas PA plants showed a similar growth to control. Photosynthesis rate and productivity parameters decreased under low Pi nutrition, however, sugar content generally increased. Studied oat cultivars did not respond to low Pi via increased exudation of carboxylates from the roots, as pH changes in the growth media were not observed. Pi starvation significantly increased the activity of extracellular and intracellular acid phosphatases (APases) in comparison to the control plants. Three major APase isoforms were detected in oat tissues and the isoform …
bibliographic citation: Żebrowska et al. (2017) Mechanisms of oat (Avena sativa L.) acclimation to phosphate deficiency. PeerJ 5:e3989 https://doi.org/10.7717/peerj.3989
date submitted: 2017-08-22
date accepted: 2017-10-13
issued: 2017-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Żebrowska
  given name: Ewa
author list: Agent
  family name: Milewska
  given name: Marta
author list: Agent
  family name: Ciereszko
  given name: Iwona
doi: 10.7717/peerj.3989
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-01
copyright: ©2017 Żebrowska et al.
attribution name: Żebrowska et al.

Can 9q34.2 rs633862 polymorphism predict survival in epithelial ovarian cancer?
type: item
type: AcademicArticle
description: Objective Our previous genome-wide association study (GWAS) identified that the ABO rs633862 variant in chromosome 9q34.2 was associated with the risk of epithelial ovarian cancer (EOC) in Chinese Han women. The aim of the present study was to evaluate its prognostic effect on EOC. Methods A total of 669 EOC patients were enrolled for the genotyping of rs633862 variant in 9q34.2. We used Kaplan–Meier survival curves, univariate and multivariate Cox proportional hazard models to evaluate the association of rs633862 with overall survival (OS) in EOC patients. Results We found that rs633862 variant AG/GG genotypes were significantly associated with a longer OS by using univariate Cox proportional hazards regression analysis, compared with the rs633862 AA genotype (HR = 0.69, 95% CI [0.49–0.98], p = 0.035), albeit with a boardline significance in the multivariate analysis. Similar findings were observed in the subgroup of high-grade serous ovarian carcinoma. Further expression quantitative trait loci (eQTL) analysis indicated that the rs633862 AA genotype was associated with an increased level of ABO mRNA expression (p = 1.8 × 10−11). Conclusions Supplementary to the previous GWAS, our study provides additional evidence on the prognostic value of the 9q34.2 rs633862 variant in EOC patients, and this variant may function by regulating the ABO mRNA expression.
format: application/pdf
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creator: Rong Jiang
creator: Yuan Xu
creator: Pan Wang
creator: Xi Cheng
creator: Tingyan Shi
creator: Rongyu Zang
subject: Oncology
subject: Translational Medicine
subject: Women's Health
description: doi:10.7717/peerj.3946
publisher: PeerJ Inc.
rights: © 2017 Jiang et al.
abstract: Objective Our previous genome-wide association study (GWAS) identified that the ABO rs633862 variant in chromosome 9q34.2 was associated with the risk of epithelial ovarian cancer (EOC) in Chinese Han women. The aim of the present study was to evaluate its prognostic effect on EOC. Methods A total of 669 EOC patients were enrolled for the genotyping of rs633862 variant in 9q34.2. We used Kaplan–Meier survival curves, univariate and multivariate Cox proportional hazard models to evaluate the association of rs633862 with overall survival (OS) in EOC patients. Results We found that rs633862 variant AG/GG genotypes were significantly associated with a longer OS by using univariate Cox proportional hazards regression analysis, compared with the rs633862 AA genotype (HR = 0.69, 95% CI [0.49–0.98], p = 0.035), albeit with a boardline significance in the multivariate analysis. Similar findings were observed in the subgroup of high-grade serous ovarian carcinoma. Further expression quantitative trait loci (eQTL) analysis indicated that the rs633862 AA genotype was associated with an increased level of ABO mRNA expression (p = 1.8 × 10−11). Conclusions Supplementary to the previous GWAS, our study provides additional evidence on the prognostic value of the 9q34.2 rs633862 variant in EOC patients, and this variant may function by regulating the ABO mRNA expression.
bibliographic citation: Jiang et al. (2017) Can 9q34.2 rs633862 polymorphism predict survival in epithelial ovarian cancer?. PeerJ 5:e3946 https://doi.org/10.7717/peerj.3946
date submitted: 2017-06-08
date accepted: 2017-09-30
issued: 2017-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Rong
author list: Agent
  family name: Xu
  given name: Yuan
author list: Agent
  family name: Wang
  given name: Pan
author list: Agent
  family name: Cheng
  given name: Xi
author list: Agent
  family name: Shi
  given name: Tingyan
author list: Agent
  family name: Zang
  given name: Rongyu
doi: 10.7717/peerj.3946
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-01
copyright: ©2017 Jiang et al.
attribution name: Jiang et al.

Effects of graded concentrations of supplemental lead on lead concentrations in tissues of pigs and prediction equations for estimating dietary lead intake
type: item
type: AcademicArticle
description: The objectives of this experiment were to determine the effects of graded dietary lead (Pb) concentrations on body weight and Pb concentrations in blood, hair, soft tissues, and urine from pigs and to generate equations for estimating daily Pb intake. Sixteen barrows with initial body weight 36.3 kg (standard deviation = 2.3) were allotted to four dietary treatments that consisted of graded supplemental Pb concentrations (0, 10, 25, and 250 mg/kg of diet). Daily feed allowances for each pig were 1 kg for first two weeks and 2 kg for last two weeks. The hair and blood of pigs were collected on d 14 and 28. At the end of experiment, the pigs were euthanized, and the liver, kidneys, muscle, and urine samples were collected. The prediction equations for estimating daily Pb intake of pigs were generated using Pb concentration of blood, hair, tissues, or urine as an independent variable. The Pb concentrations in the blood, hair, liver, kidneys, muscle, and urine linearly increased (P < 0.01) with increasing dietary Pb concentrations. There were quadratic effects (P < 0.05) of increasing dietary Pb concentration on Pb concentrations in the blood, hair, and muscle. There were highly positive correlations between dietary Pb concentration and Pb concentrations in the blood, hair, liver, kidneys, muscle, and urine (r > 0.83; P < 0.01). The equations were significant (P < 0.01) and showed high r2 (>0.83), except the equation using Pb concentration in the muscle as an independent variable. In conclusion, the dietary Pb concentration was highly correlated with Pb concentrations in the blood, hair, soft tissues, and urine of pigs. The total dietary Pb intake can be estimated from the Pb concentrations in the blood, hair, soft tissues, or urine for pigs.
format: application/pdf
format: text/html
creator: Kondreddy Eswar Reddy
creator: Kyu Ree Park
creator: Sung Dae Lee
creator: Ji-Hyock Yoo
creator: Ah Reum Son
creator: Hyun-Jung Lee
subject: Agricultural Science
subject: Toxicology
subject: Nutrition
subject: Ecotoxicology
description: doi:10.7717/peerj.3936
publisher: PeerJ Inc.
rights: © 2017 Reddy et al.
abstract: The objectives of this experiment were to determine the effects of graded dietary lead (Pb) concentrations on body weight and Pb concentrations in blood, hair, soft tissues, and urine from pigs and to generate equations for estimating daily Pb intake. Sixteen barrows with initial body weight 36.3 kg (standard deviation = 2.3) were allotted to four dietary treatments that consisted of graded supplemental Pb concentrations (0, 10, 25, and 250 mg/kg of diet). Daily feed allowances for each pig were 1 kg for first two weeks and 2 kg for last two weeks. The hair and blood of pigs were collected on d 14 and 28. At the end of experiment, the pigs were euthanized, and the liver, kidneys, muscle, and urine samples were collected. The prediction equations for estimating daily Pb intake of pigs were generated using Pb concentration of blood, hair, tissues, or urine as an independent variable. The Pb concentrations in the blood, hair, liver, kidneys, muscle, and urine linearly increased (P < 0.01) with increasing dietary Pb concentrations. There were quadratic effects (P < 0.05) of increasing dietary Pb concentration on Pb concentrations in the blood, hair, and muscle. There were highly positive correlations between dietary Pb concentration and Pb concentrations in the blood, hair, liver, kidneys, muscle, and urine (r > 0.83; P < 0.01). The equations were significant (P < 0.01) and showed high r2 (>0.83), except the equation using Pb concentration in the muscle as an independent variable. In conclusion, the dietary Pb concentration was highly correlated with Pb concentrations in the blood, hair, soft tissues, and urine of pigs. The total dietary Pb intake can be estimated from the Pb concentrations in the blood, hair, soft tissues, or urine for pigs.
bibliographic citation: Reddy et al. (2017) Effects of graded concentrations of supplemental lead on lead concentrations in tissues of pigs and prediction equations for estimating dietary lead intake. PeerJ 5:e3936 https://doi.org/10.7717/peerj.3936
date submitted: 2017-05-09
date accepted: 2017-09-26
issued: 2017-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reddy
  given name: Kondreddy Eswar
author list: Agent
  family name: Park
  given name: Kyu Ree
author list: Agent
  family name: Lee
  given name: Sung Dae
author list: Agent
  family name: Yoo
  given name: Ji-Hyock
author list: Agent
  family name: Son
  given name: Ah Reum
author list: Agent
  family name: Lee
  given name: Hyun-Jung
doi: 10.7717/peerj.3936
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-01
copyright: ©2017 Reddy et al.
attribution name: Reddy et al.

Water absorption through salivary gland type I acini in the blacklegged tick, Ixodes scapularis
type: item
type: AcademicArticle
description: Tick salivary glands play critical roles in maintaining water balance for survival, as they eliminate excess water and ions during blood feeding on hosts. In the long duration of fasting in the off-host period, ticks secrete hygroscopic saliva into the mouth cavity to uptake atmospheric water vapor. Type I acini of tick salivary glands are speculated to be involved in secretion of hygroscopic saliva based on ultrastructure studies. However, we recently proposed that type I acini play a role in resorption of water/ions from the primary saliva produced by other salivary acini (i.e., types II and III) during the tick blood feeding phase. In this study, we tested the function of type I acini in unfed female Ixodes scapularis. The route of ingested water was tracked after forced feeding of water with fluorescent dye rhodamine123. We found that type-I acini of the salivary glands, but not type II and III, are responsible for water uptake. In addition, the ingestion of water through the midgut was also observed. Injection or feeding of ouabain, a Na/K-ATPase inhibitor, suppressed water absorption in type I acini. When I. scapularis was offered a droplet of water, ticks rarely imbibed water directly (5%), while some approached the water droplet to use the high humidity formed in the vicinity of the droplet (23%). We conclude that during both on- and off-host stages, type I acini in salivary glands of female Ixodes scapularis absorb water and ions.
format: application/pdf
format: text/html
creator: Donghun Kim
creator: Paulina Maldonado-Ruiz
creator: Ludek Zurek
creator: Yoonseong Park
subject: Entomology
description: doi:10.7717/peerj.3984
publisher: PeerJ Inc.
rights: © 2017 Kim et al.
abstract: Tick salivary glands play critical roles in maintaining water balance for survival, as they eliminate excess water and ions during blood feeding on hosts. In the long duration of fasting in the off-host period, ticks secrete hygroscopic saliva into the mouth cavity to uptake atmospheric water vapor. Type I acini of tick salivary glands are speculated to be involved in secretion of hygroscopic saliva based on ultrastructure studies. However, we recently proposed that type I acini play a role in resorption of water/ions from the primary saliva produced by other salivary acini (i.e., types II and III) during the tick blood feeding phase. In this study, we tested the function of type I acini in unfed female Ixodes scapularis. The route of ingested water was tracked after forced feeding of water with fluorescent dye rhodamine123. We found that type-I acini of the salivary glands, but not type II and III, are responsible for water uptake. In addition, the ingestion of water through the midgut was also observed. Injection or feeding of ouabain, a Na/K-ATPase inhibitor, suppressed water absorption in type I acini. When I. scapularis was offered a droplet of water, ticks rarely imbibed water directly (5%), while some approached the water droplet to use the high humidity formed in the vicinity of the droplet (23%). We conclude that during both on- and off-host stages, type I acini in salivary glands of female Ixodes scapularis absorb water and ions.
bibliographic citation: Kim et al. (2017) Water absorption through salivary gland type I acini in the blacklegged tick, Ixodes scapularis. PeerJ 5:e3984 https://doi.org/10.7717/peerj.3984
date submitted: 2017-06-29
date accepted: 2017-10-12
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Donghun
author list: Agent
  family name: Maldonado-Ruiz
  given name: Paulina
author list: Agent
  family name: Zurek
  given name: Ludek
author list: Agent
  family name: Park
  given name: Yoonseong
doi: 10.7717/peerj.3984
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: ©2017 Kim et al.
attribution name: Kim et al.

Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa
type: item
type: AcademicArticle
description: Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.
format: application/pdf
format: text/html
creator: RuiJuan Feng
creator: Xin Wang
creator: Min Tao
creator: Guanchao Du
creator: Qishuo Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Genomics
subject: Freshwater Biology
description: doi:10.7717/peerj.3982
publisher: PeerJ Inc.
rights: © 2017 Feng et al.
abstract: Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.
bibliographic citation: Feng et al. (2017) Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa. PeerJ 5:e3982 https://doi.org/10.7717/peerj.3982
date submitted: 2017-09-12
date accepted: 2017-10-12
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: RuiJuan
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Tao
  given name: Min
author list: Agent
  family name: Du
  given name: Guanchao
author list: Agent
  family name: Wang
  given name: Qishuo
doi: 10.7717/peerj.3982
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: ©2017 Feng et al.
attribution name: Feng et al.

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