PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form
items: Male-male competition and female choice are differentially affected by male call acoustics in the serrate-legged small treefrog, Kurixalus odontotarsus
items: Proteomics research and related functional classification of liquid sclerotial exudates of Sclerotinia ginseng
items: Record breaking achievements by spiders and the scientists who study them
items: A novel animal model for neuroinflammation and white matter degeneration
items: Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton

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
format: text/html
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.

Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form
type: item
type: AcademicArticle
description: Leptopoma is a species rich genus with approximately 100 species documented. Species-level identification in this group has been based on shell morphology and colouration, as well as some anatomical features based on small sample sizes. However, the implications of the inter- and intra-species variations in shell form to the taxonomy of Leptopoma species and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. There are four Leptopoma species found in Sabah, Borneo, and their taxonomy status remains uncertain due to substantial variation in shell forms. This study focuses on the phylogenetic relationships and geographical variation in shell form of three Leptopoma species from Sabah. The phylogenetic relationship of these species was first estimated by performing Maximum Likelihood and Bayesian analysis based on mitochondrial genes (16S rDNA and COI) and nuclear gene (ITS-1). Then, a total of six quantitative shell characters (i.e., shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height to width) and three qualitative shell characters (i.e., shell colour patterns, spiral ridges, and dark apertural band) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters of Leptopoma sericatum and Leptopoma pellucidum from two different locations (i.e., Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the three Leptopoma species was monophyletic and indicated congruence with only one of the shell characters (i.e., shell spiral ridges) in the current morphological-based classification. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the two Leptopoma species, these also pointed to in…
format: application/pdf
format: text/html
creator: Chee-Chean Phung
creator: Pooi-San Heng
creator: Thor-Seng Liew
subject: Biodiversity
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.3981
publisher: PeerJ Inc.
rights: © 2017 Phung et al.
abstract: Leptopoma is a species rich genus with approximately 100 species documented. Species-level identification in this group has been based on shell morphology and colouration, as well as some anatomical features based on small sample sizes. However, the implications of the inter- and intra-species variations in shell form to the taxonomy of Leptopoma species and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. There are four Leptopoma species found in Sabah, Borneo, and their taxonomy status remains uncertain due to substantial variation in shell forms. This study focuses on the phylogenetic relationships and geographical variation in shell form of three Leptopoma species from Sabah. The phylogenetic relationship of these species was first estimated by performing Maximum Likelihood and Bayesian analysis based on mitochondrial genes (16S rDNA and COI) and nuclear gene (ITS-1). Then, a total of six quantitative shell characters (i.e., shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height to width) and three qualitative shell characters (i.e., shell colour patterns, spiral ridges, and dark apertural band) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters of Leptopoma sericatum and Leptopoma pellucidum from two different locations (i.e., Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the three Leptopoma species was monophyletic and indicated congruence with only one of the shell characters (i.e., shell spiral ridges) in the current morphological-based classification. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the two Leptopoma species, these also pointed to in…
bibliographic citation: Phung et al. (2017) Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form. PeerJ 5:e3981 https://doi.org/10.7717/peerj.3981
date submitted: 2017-07-06
date accepted: 2017-10-11
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Phung
  given name: Chee-Chean
author list: Agent
  family name: Heng
  given name: Pooi-San
author list: Agent
  family name: Liew
  given name: Thor-Seng
doi: 10.7717/peerj.3981
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: ©2017 Phung et al.
attribution name: Phung et al.

Male-male competition and female choice are differentially affected by male call acoustics in the serrate-legged small treefrog, Kurixalus odontotarsus
type: item
type: AcademicArticle
description: Background The evolution of exaggerated vocal signals in anuran species is an important topic. Males and females have both evolved the ability to discriminate communication sounds. However, the nature of sexual dimorphism in cognition and sensory discrimination and in the evolution and limitation of sexual signal exaggeration remain relatively unexplored. Methods In the present study, we used male calls of varied complexity in the serrate-legged small treefrog, Kurixalus odontotarsus, as probes to investigate how both sexes respond to variations in call complexity and how sex differences in signal discrimination play a role in the evolution of sexual signal exaggeration. The compound calls of male K. odontotarsus consist of a series of one or more harmonic notes (A notes) which may be followed by one or more short broadband notes (B notes). Results Male playback experiments and female phonotaxis tests showed that increasing the number of A notes in stimulus calls elicits increased numbers of response calls by males and increases the attractiveness of the stimulus calls to females. The addition of B notes, however, reduces male calling responses. Moreover, call stimuli which contain only B notes suppress spontaneous male calling responses. Phonotaxis experiments show that females prefer calls with greater numbers of A notes and calls containing both A notes and B notes, but do not prefer calls with only B notes. Discussion Male-male competition and female choice appear to have played different roles in the evolution and limitation of signal complexity in K. odontotarsus. These results provide new insights into how exaggerated compound signals evolve and how signal complexity may be limited in anurans.
format: application/pdf
format: text/html
creator: Bicheng Zhu
creator: Jichao Wang
creator: Longhui Zhao
creator: Qinghua Chen
creator: Zhixin Sun
creator: Yue Yang
creator: Steven E. Brauth
creator: Yezhong Tang
creator: Jianguo Cui
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3980
publisher: PeerJ Inc.
rights: © 2017 Zhu et al.
abstract: Background The evolution of exaggerated vocal signals in anuran species is an important topic. Males and females have both evolved the ability to discriminate communication sounds. However, the nature of sexual dimorphism in cognition and sensory discrimination and in the evolution and limitation of sexual signal exaggeration remain relatively unexplored. Methods In the present study, we used male calls of varied complexity in the serrate-legged small treefrog, Kurixalus odontotarsus, as probes to investigate how both sexes respond to variations in call complexity and how sex differences in signal discrimination play a role in the evolution of sexual signal exaggeration. The compound calls of male K. odontotarsus consist of a series of one or more harmonic notes (A notes) which may be followed by one or more short broadband notes (B notes). Results Male playback experiments and female phonotaxis tests showed that increasing the number of A notes in stimulus calls elicits increased numbers of response calls by males and increases the attractiveness of the stimulus calls to females. The addition of B notes, however, reduces male calling responses. Moreover, call stimuli which contain only B notes suppress spontaneous male calling responses. Phonotaxis experiments show that females prefer calls with greater numbers of A notes and calls containing both A notes and B notes, but do not prefer calls with only B notes. Discussion Male-male competition and female choice appear to have played different roles in the evolution and limitation of signal complexity in K. odontotarsus. These results provide new insights into how exaggerated compound signals evolve and how signal complexity may be limited in anurans.
bibliographic citation: Zhu et al. (2017) Male-male competition and female choice are differentially affected by male call acoustics in the serrate-legged small treefrog, Kurixalus odontotarsus. PeerJ 5:e3980 https://doi.org/10.7717/peerj.3980
date submitted: 2017-08-02
date accepted: 2017-10-11
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Bicheng
author list: Agent
  family name: Wang
  given name: Jichao
author list: Agent
  family name: Zhao
  given name: Longhui
author list: Agent
  family name: Chen
  given name: Qinghua
author list: Agent
  family name: Sun
  given name: Zhixin
author list: Agent
  family name: Yang
  given name: Yue
author list: Agent
  family name: Brauth
  given name: Steven E.
author list: Agent
  family name: Tang
  given name: Yezhong
author list: Agent
  family name: Cui
  given name: Jianguo
doi: 10.7717/peerj.3980
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: ©2017 Zhu et al.
attribution name: Zhu et al.

Proteomics research and related functional classification of liquid sclerotial exudates of Sclerotinia ginseng
type: item
type: AcademicArticle
description: Sclerotinia ginseng is a necrotrophic soil pathogen that mainly infects the root and basal stem of ginseng, causing serious commercial losses. Sclerotia, which are important in the fungal life cycle, are hard, asexual, resting structures that can survive in soil for several years. Generally, sclerotium development is accompanied by the exudation of droplets. Here, the yellowish droplets of S. ginseng were first examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the proteome was identified by a combination of different analytical platforms. A total of 59 proteins were identified and classified into six categories: carbohydrate metabolism (39%), oxidation-reduction process (12%), transport and catabolism (5%), amino acid metabolism (3%), other functions (18%), and unknown protein (23%), which exhibited considerable differences in protein composition compared with droplets of S. sclerotium. In the carbohydrate metabolism group, several proteins were associated with sclerotium development, particularly fungal cell wall formation. The pathogenicity and virulence of the identified proteins are also discussed in this report. The findings of this study may improve our understanding of the function of exudate droplets as well as the life cycle and pathogenesis of S. ginseng.
format: application/pdf
format: text/html
creator: Dan Wang
creator: Jun Fan Fu
creator: Ru Jun Zhou
creator: Zi Bo Li
creator: Yu Jiao Xie
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.3979
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Sclerotinia ginseng is a necrotrophic soil pathogen that mainly infects the root and basal stem of ginseng, causing serious commercial losses. Sclerotia, which are important in the fungal life cycle, are hard, asexual, resting structures that can survive in soil for several years. Generally, sclerotium development is accompanied by the exudation of droplets. Here, the yellowish droplets of S. ginseng were first examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the proteome was identified by a combination of different analytical platforms. A total of 59 proteins were identified and classified into six categories: carbohydrate metabolism (39%), oxidation-reduction process (12%), transport and catabolism (5%), amino acid metabolism (3%), other functions (18%), and unknown protein (23%), which exhibited considerable differences in protein composition compared with droplets of S. sclerotium. In the carbohydrate metabolism group, several proteins were associated with sclerotium development, particularly fungal cell wall formation. The pathogenicity and virulence of the identified proteins are also discussed in this report. The findings of this study may improve our understanding of the function of exudate droplets as well as the life cycle and pathogenesis of S. ginseng.
bibliographic citation: Wang et al. (2017) Proteomics research and related functional classification of liquid sclerotial exudates of Sclerotinia ginseng. PeerJ 5:e3979 https://doi.org/10.7717/peerj.3979
date submitted: 2017-07-03
date accepted: 2017-10-11
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Fu
  given name: Jun Fan
author list: Agent
  family name: Zhou
  given name: Ru Jun
author list: Agent
  family name: Li
  given name: Zi Bo
author list: Agent
  family name: Xie
  given name: Yu Jiao
doi: 10.7717/peerj.3979
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: ©2017 Wang et al.
attribution name: Wang et al.

Record breaking achievements by spiders and the scientists who study them
type: item
type: AcademicArticle
description: Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students—as well as scientists themselves—into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the “Spider World Records”). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements.
format: application/pdf
format: text/html
creator: Stefano Mammola
creator: Peter Michalik
creator: Eileen A. Hebets
creator: Marco Isaia
subject: Biodiversity
subject: Entomology
subject: Zoology
subject: Science and Medical Education
description: doi:10.7717/peerj.3972
publisher: PeerJ Inc.
rights: © 2017 Mammola et al.
abstract: Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students—as well as scientists themselves—into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the “Spider World Records”). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements.
bibliographic citation: Mammola et al. (2017) Record breaking achievements by spiders and the scientists who study them. PeerJ 5:e3972 https://doi.org/10.7717/peerj.3972
date submitted: 2017-06-14
date accepted: 2017-10-09
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mammola
  given name: Stefano
author list: Agent
  family name: Michalik
  given name: Peter
author list: Agent
  family name: Hebets
  given name: Eileen A.
author list: Agent
  family name: Isaia
  given name: Marco
doi: 10.7717/peerj.3972
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: © 2017 Mammola et al.
attribution name: Mammola et al.

A novel animal model for neuroinflammation and white matter degeneration
type: item
type: AcademicArticle
description: Small interference RNA has been widely used to suppress gene expression. Three different short hairpin RNAs (shRNAs) against dopamine D1 receptor (Drd1), driven by mouse U6 promoter in self-complementary AAV8 vector (scAAV8), were used to silence mouse striatal Drd1 expression. Transduction of mouse striatum with all three scAAV8-D1shRNA viruses, but not the control scAAV8 virus, causes extensive neuroinflammation, demyelination, and axon degeneration. RNA interference is known to be coupled to the innate immune system as a host cell defense against virus infection. Activation of the innate immune system may play a causal role in the development of neuroinflammation and white matter degeneration, providing a novel animal model for multiple sclerosis (MS) and other neuroinflammatory diseases.
format: application/pdf
format: text/html
creator: Baohu Ji
creator: Kerin Higa
creator: Virawudh Soontornniyomkij
creator: Atsushi Miyanohara
creator: Xianjin Zhou
subject: Neuroscience
subject: Neurology
subject: Pathology
description: doi:10.7717/peerj.3905
publisher: PeerJ Inc.
rights: © 2017 Ji et al.
abstract: Small interference RNA has been widely used to suppress gene expression. Three different short hairpin RNAs (shRNAs) against dopamine D1 receptor (Drd1), driven by mouse U6 promoter in self-complementary AAV8 vector (scAAV8), were used to silence mouse striatal Drd1 expression. Transduction of mouse striatum with all three scAAV8-D1shRNA viruses, but not the control scAAV8 virus, causes extensive neuroinflammation, demyelination, and axon degeneration. RNA interference is known to be coupled to the innate immune system as a host cell defense against virus infection. Activation of the innate immune system may play a causal role in the development of neuroinflammation and white matter degeneration, providing a novel animal model for multiple sclerosis (MS) and other neuroinflammatory diseases.
bibliographic citation: Ji et al. (2017) A novel animal model for neuroinflammation and white matter degeneration. PeerJ 5:e3905 https://doi.org/10.7717/peerj.3905
date submitted: 2017-07-31
date accepted: 2017-09-18
issued: 2017-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Baohu
author list: Agent
  family name: Higa
  given name: Kerin
author list: Agent
  family name: Soontornniyomkij
  given name: Virawudh
author list: Agent
  family name: Miyanohara
  given name: Atsushi
author list: Agent
  family name: Zhou
  given name: Xianjin
doi: 10.7717/peerj.3905
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-31
copyright: ©2017 Ji et al.
attribution name: Ji et al.

Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton
type: item
type: AcademicArticle
description: Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum) and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV). The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs) in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.
format: application/pdf
format: text/html
creator: Xueqiang Su
creator: Xu Sun
creator: Xi Cheng
creator: Yanan Wang
creator: Muhammad Abdullah
creator: Manli Li
creator: Dahui Li
creator: Junshan Gao
creator: Yongping Cai
creator: Yi Lin
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.3974
publisher: PeerJ Inc.
rights: © 2017 Su et al.
abstract: Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum) and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV). The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs) in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.
bibliographic citation: Su et al. (2017) Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton. PeerJ 5:e3974 https://doi.org/10.7717/peerj.3974
date submitted: 2017-05-29
date accepted: 2017-10-10
issued: 2017-10-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Xueqiang
author list: Agent
  family name: Sun
  given name: Xu
author list: Agent
  family name: Cheng
  given name: Xi
author list: Agent
  family name: Wang
  given name: Yanan
author list: Agent
  family name: Abdullah
  given name: Muhammad
author list: Agent
  family name: Li
  given name: Manli
author list: Agent
  family name: Li
  given name: Dahui
author list: Agent
  family name: Gao
  given name: Junshan
author list: Agent
  family name: Cai
  given name: Yongping
author list: Agent
  family name: Lin
  given name: Yi
doi: 10.7717/peerj.3974
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-30
copyright: ©2017 Su et al.
attribution name: Su et al.

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