PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Psychometric properties of the Perceived Stress Scale (PSS): measurement invariance between athletes and non-athletes and construct validity
items: Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri
items: Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking
items: In vitro gastrointestinal digestion study of a novel bio-tofu with special emphasis on the impact of microbial transglutaminase
items: In situ earthworm breeding in orchards significantly improves the growth, quality and yield of papaya (Carica papaya L.)
items: A retrospective study: cardiac MRI of fulminant myocarditis in children—can we evaluate the short-term outcomes?
items: Harvest year effects on Apulian EVOOs evaluated by 1H NMR based metabolomics
items: RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum)
items: Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
items: Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach

Psychometric properties of the Perceived Stress Scale (PSS): measurement invariance between athletes and non-athletes and construct validity
type: item
type: AcademicArticle
description: Background Although Perceived Stress Scale (PSS, Cohen, Kamarack & Mermelstein, 1983) has been validated and widely used in many domains, there is still no validation in sports by comparing athletes and non-athletes and examining related psychometric indices. Purpose The purpose of this study was to examine the measurement invariance of PSS between athletes and non-athletes, and examine construct validity and reliability in the sports contexts. Methods Study 1 sampled 359 college student-athletes (males = 233; females = 126) and 242 non-athletes (males = 124; females = 118) and examined factorial structure, measurement invariance and internal consistency. Study 2 sampled 196 student-athletes (males = 139, females = 57, Mage = 19.88 yrs, SD = 1.35) and examined discriminant validity and convergent validity of PSS. Study 3 sampled 37 student-athletes to assess test-retest reliability of PSS. Results Results found that 2-factor PSS-10 fitted the model the best and had appropriate reliability. Also, there was a measurement invariance between athletes and non-athletes; and PSS positively correlated with athletic burnout and life stress but negatively correlated with coping efficacy provided evidence of discriminant validity and convergent validity. Further, the test-retest reliability for PSS subscales was significant (r = .66 and r = .50). Discussion It is suggested that 2-factor PSS-10 can be a useful tool in assessing perceived stress either in sports or non-sports settings. We suggest future study may use 2-factor PSS-10 in examining the effects of stress on the athletic injury, burnout, and psychiatry disorders.
format: application/pdf
format: text/html
creator: Yi-Hsiang Chiu
creator: Frank Jing-Horng Lu
creator: Ju-Han Lin
creator: Chiao-Lin Nien
creator: Ya-Wen Hsu
creator: Hong-Yu Liu
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2790
publisher: PeerJ Inc.
rights: © 2016 Chiu et al.
abstract: Background Although Perceived Stress Scale (PSS, Cohen, Kamarack & Mermelstein, 1983) has been validated and widely used in many domains, there is still no validation in sports by comparing athletes and non-athletes and examining related psychometric indices. Purpose The purpose of this study was to examine the measurement invariance of PSS between athletes and non-athletes, and examine construct validity and reliability in the sports contexts. Methods Study 1 sampled 359 college student-athletes (males = 233; females = 126) and 242 non-athletes (males = 124; females = 118) and examined factorial structure, measurement invariance and internal consistency. Study 2 sampled 196 student-athletes (males = 139, females = 57, Mage = 19.88 yrs, SD = 1.35) and examined discriminant validity and convergent validity of PSS. Study 3 sampled 37 student-athletes to assess test-retest reliability of PSS. Results Results found that 2-factor PSS-10 fitted the model the best and had appropriate reliability. Also, there was a measurement invariance between athletes and non-athletes; and PSS positively correlated with athletic burnout and life stress but negatively correlated with coping efficacy provided evidence of discriminant validity and convergent validity. Further, the test-retest reliability for PSS subscales was significant (r = .66 and r = .50). Discussion It is suggested that 2-factor PSS-10 can be a useful tool in assessing perceived stress either in sports or non-sports settings. We suggest future study may use 2-factor PSS-10 in examining the effects of stress on the athletic injury, burnout, and psychiatry disorders.
bibliographic citation: Chiu et al. (2016) Psychometric properties of the Perceived Stress Scale (PSS): measurement invariance between athletes and non-athletes and construct validity. PeerJ 4:e2790 https://doi.org/10.7717/peerj.2790
date submitted: 2016-07-07
date accepted: 2016-11-13
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chiu
  given name: Yi-Hsiang
author list: Agent
  family name: Lu
  given name: Frank Jing-Horng
author list: Agent
  family name: Lin
  given name: Ju-Han
author list: Agent
  family name: Nien
  given name: Chiao-Lin
author list: Agent
  family name: Hsu
  given name: Ya-Wen
author list: Agent
  family name: Liu
  given name: Hong-Yu
doi: 10.7717/peerj.2790
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Chiu et al.
attribution name: Chiu et al.

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri
type: item
type: AcademicArticle
description: Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
format: application/pdf
format: text/html
creator: Siqi Yuan
creator: Yun Xia
creator: Yuchi Zheng
creator: Xiaomao Zeng
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.2786
publisher: PeerJ Inc.
rights: © 2016 Yuan et al.
abstract: Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
bibliographic citation: Yuan et al. (2016) Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri. PeerJ 4:e2786 https://doi.org/10.7717/peerj.2786
date submitted: 2016-08-08
date accepted: 2016-11-11
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Siqi
author list: Agent
  family name: Xia
  given name: Yun
author list: Agent
  family name: Zheng
  given name: Yuchi
author list: Agent
  family name: Zeng
  given name: Xiaomao
doi: 10.7717/peerj.2786
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Yuan et al.
attribution name: Yuan et al.

Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking
type: item
type: AcademicArticle
description: Major research efforts have been devoted to the discovery and development of new chemical entities that could inhibit the protein–protein interaction between HIF-1α and the von Hippel–Lindau protein (pVHL), which serves as the substrate recognition subunit of an E3 ligase and is regarded as a crucial drug target in cancer, chronic anemia, and ischemia. Currently there is only one class of compounds available to interdict the HIF-1α/pVHL interaction, urging the need to discover chemical inhibitors with more diversified structures. We report here a strategy combining shape-based virtual screening and cascade docking to identify new chemical scaffolds for the designing of novel inhibitors. Based on this strategy, nine active hits have been identified and the most active hit, 9 (ZINC13466751), showed comparable activity to pVHL with an IC50 of 2.0 ± 0.14 µM, showing the great potential of utilizing these compounds for further optimization and serving as drug candidates for the inhibition of HIF-1α/von Hippel–Lindau interaction.
format: application/pdf
format: text/html
creator: Xin Xue
creator: Ning-Yi Zhao
creator: Hai-Tao Yu
creator: Yuan Sun
creator: Chen Kang
creator: Qiong-Bin Huang
creator: Hao-Peng Sun
creator: Xiao-Long Wang
creator: Nian-Guang Li
subject: Biochemistry
subject: Computational Biology
subject: Pharmacology
description: doi:10.7717/peerj.2757
publisher: PeerJ Inc.
rights: © 2016 Xue et al.
abstract: Major research efforts have been devoted to the discovery and development of new chemical entities that could inhibit the protein–protein interaction between HIF-1α and the von Hippel–Lindau protein (pVHL), which serves as the substrate recognition subunit of an E3 ligase and is regarded as a crucial drug target in cancer, chronic anemia, and ischemia. Currently there is only one class of compounds available to interdict the HIF-1α/pVHL interaction, urging the need to discover chemical inhibitors with more diversified structures. We report here a strategy combining shape-based virtual screening and cascade docking to identify new chemical scaffolds for the designing of novel inhibitors. Based on this strategy, nine active hits have been identified and the most active hit, 9 (ZINC13466751), showed comparable activity to pVHL with an IC50 of 2.0 ± 0.14 µM, showing the great potential of utilizing these compounds for further optimization and serving as drug candidates for the inhibition of HIF-1α/von Hippel–Lindau interaction.
bibliographic citation: Xue et al. (2016) Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking. PeerJ 4:e2757 https://doi.org/10.7717/peerj.2757
date submitted: 2016-06-09
date accepted: 2016-11-04
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xue
  given name: Xin
author list: Agent
  family name: Zhao
  given name: Ning-Yi
author list: Agent
  family name: Yu
  given name: Hai-Tao
author list: Agent
  family name: Sun
  given name: Yuan
author list: Agent
  family name: Kang
  given name: Chen
author list: Agent
  family name: Huang
  given name: Qiong-Bin
author list: Agent
  family name: Sun
  given name: Hao-Peng
author list: Agent
  family name: Wang
  given name: Xiao-Long
author list: Agent
  family name: Li
  given name: Nian-Guang
doi: 10.7717/peerj.2757
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Xue et al.
attribution name: Xue et al.

In vitro gastrointestinal digestion study of a novel bio-tofu with special emphasis on the impact of microbial transglutaminase
type: item
type: AcademicArticle
description: We have developed a novel bio-tofu, made from mixed soy and cow milk (MSCM), using Lactobacillus helveticus MB2-1 and Lactobacillus plantarum B1-6 incorporated with microbial transglutaminase (MTGase) as coagulant. MTGase was added to improve the textural properties and suit for cooking. However, the effect of MTGase on the digestion of mixed-protein fermented by lactic acid bacteria was unclear. This study aimed at evaluating the effect of MTGase on protein digestion of bio-tofu under simulated gastrointestinal digestion condition. The results showed that addition of MTGase could affect the particle size distribution, degree of hydrolysis, the content of soluble proteins and free amino acids. Based on the electrophoresis data, MTGase addition enhanced protein polymerization. During gastric and intestinal digestion process, proteins from bio-tofu were degraded into low molecular mass peptides. Our results suggested that incorporation of MTGase could lead to enzymatic modification of proteins of bio-tofu which may help in controlling energy intake and decrease the chance of food allergy.
format: application/pdf
format: text/html
creator: Guangliang Xing
creator: Xin Rui
creator: Mei Jiang
creator: Yu Xiao
creator: Ying Guan
creator: Dan Wang
creator: Mingsheng Dong
subject: Food Science and Technology
subject: Microbiology
subject: Nutrition
description: doi:10.7717/peerj.2754
publisher: PeerJ Inc.
rights: © 2016 Xing et al.
abstract: We have developed a novel bio-tofu, made from mixed soy and cow milk (MSCM), using Lactobacillus helveticus MB2-1 and Lactobacillus plantarum B1-6 incorporated with microbial transglutaminase (MTGase) as coagulant. MTGase was added to improve the textural properties and suit for cooking. However, the effect of MTGase on the digestion of mixed-protein fermented by lactic acid bacteria was unclear. This study aimed at evaluating the effect of MTGase on protein digestion of bio-tofu under simulated gastrointestinal digestion condition. The results showed that addition of MTGase could affect the particle size distribution, degree of hydrolysis, the content of soluble proteins and free amino acids. Based on the electrophoresis data, MTGase addition enhanced protein polymerization. During gastric and intestinal digestion process, proteins from bio-tofu were degraded into low molecular mass peptides. Our results suggested that incorporation of MTGase could lead to enzymatic modification of proteins of bio-tofu which may help in controlling energy intake and decrease the chance of food allergy.
bibliographic citation: Xing et al. (2016) In vitro gastrointestinal digestion study of a novel bio-tofu with special emphasis on the impact of microbial transglutaminase. PeerJ 4:e2754 https://doi.org/10.7717/peerj.2754
date submitted: 2016-08-11
date accepted: 2016-11-04
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Guangliang
author list: Agent
  family name: Rui
  given name: Xin
author list: Agent
  family name: Jiang
  given name: Mei
author list: Agent
  family name: Xiao
  given name: Yu
author list: Agent
  family name: Guan
  given name: Ying
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Dong
  given name: Mingsheng
doi: 10.7717/peerj.2754
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Xing et al.
attribution name: Xing et al.

In situ earthworm breeding in orchards significantly improves the growth, quality and yield of papaya (Carica papaya L.)
type: item
type: AcademicArticle
description: The aim of this study was to compare the effects of four fertilizer applications—control (C), chemical fertilizer (F), compost (O), and in situ earthworm breeding (E)—on the growth, quality and yield of papaya (Carica papaya L.). In this study, 5 g plant−1 urea (CH4N2O, %N = 46.3%) and 100 g plant−1 microelement fertilizer was applied to each treatment. The fertilizer applications of these four treatments are different from each other. The results showed that the E treatment had the highest growth parameters over the whole growth period. At 127 days after transplantation, the order of plant heights from greatest to smallest was E > F > O > C, and the stem diameters were E > F > O > C, with significant differences between all treatments. Soluble-solid, sugar, vitamin C, and protein content significantly increased in the E treatment. In addition, the total acid and the electrical conductivity of the fruit significantly decreased in the E treatment. Fruit firmness clearly increased in the O treatment, and decreased in the F treatment. The fresh individual fruit weights, fruit numbers, and total yields were greatly improved in the F and E treatments, and the total yield of the E treatment was higher than that in the F treatment. In conclusion, the in situ earthworm breeding treatment performed better than conventional compost and chemical fertilizer treatments. Furthermore, in situ earthworm breeding may be a potential organic fertilizer application in orchards because it not only improves the fruit quality and yield but also reduces the amount of organic wastes from agriculture as a result of the activities of earthworms.
format: application/pdf
format: text/html
creator: Huimin Xiang
creator: Jia-en Zhang
creator: Lei Guo
creator: Benliang Zhao
subject: Agricultural Science
subject: Ecology
subject: Natural Resource Management
subject: Soil Science
description: doi:10.7717/peerj.2752
publisher: PeerJ Inc.
rights: © 2016 Xiang et al.
abstract: The aim of this study was to compare the effects of four fertilizer applications—control (C), chemical fertilizer (F), compost (O), and in situ earthworm breeding (E)—on the growth, quality and yield of papaya (Carica papaya L.). In this study, 5 g plant−1 urea (CH4N2O, %N = 46.3%) and 100 g plant−1 microelement fertilizer was applied to each treatment. The fertilizer applications of these four treatments are different from each other. The results showed that the E treatment had the highest growth parameters over the whole growth period. At 127 days after transplantation, the order of plant heights from greatest to smallest was E > F > O > C, and the stem diameters were E > F > O > C, with significant differences between all treatments. Soluble-solid, sugar, vitamin C, and protein content significantly increased in the E treatment. In addition, the total acid and the electrical conductivity of the fruit significantly decreased in the E treatment. Fruit firmness clearly increased in the O treatment, and decreased in the F treatment. The fresh individual fruit weights, fruit numbers, and total yields were greatly improved in the F and E treatments, and the total yield of the E treatment was higher than that in the F treatment. In conclusion, the in situ earthworm breeding treatment performed better than conventional compost and chemical fertilizer treatments. Furthermore, in situ earthworm breeding may be a potential organic fertilizer application in orchards because it not only improves the fruit quality and yield but also reduces the amount of organic wastes from agriculture as a result of the activities of earthworms.
bibliographic citation: Xiang et al. (2016) In situ earthworm breeding in orchards significantly improves the growth, quality and yield of papaya (Carica papaya L.). PeerJ 4:e2752 https://doi.org/10.7717/peerj.2752
date submitted: 2015-07-14
date accepted: 2016-11-04
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiang
  given name: Huimin
author list: Agent
  family name: Zhang
  given name: Jia-en
author list: Agent
  family name: Guo
  given name: Lei
author list: Agent
  family name: Zhao
  given name: Benliang
doi: 10.7717/peerj.2752
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Xiang et al.
attribution name: Xiang et al.

A retrospective study: cardiac MRI of fulminant myocarditis in children—can we evaluate the short-term outcomes?
type: item
type: AcademicArticle
description: Background Fulminant myocarditis (FM) is an inflammatory disease of the myocardium that results in ventricular systolic dysfunction and causes acute-onset heart failure. Cardiac magnetic resonance (CMR) has become the primary noninvasive tool for the diagnosis and evaluation of myocarditis. The aim of our study was to assess the CMR findings at different course of FM and the short-term outcomes of fulminant myocarditis (FM) in children. Methods Eight FM children with CMR examinations were included in our study. Initial baseline CMR was performed 10 days (range, 7–20 days) after onset of FM and follow-up CMR after 55 days (range, 33–75 days). Cardiac morphology and function and myocardial tissue characterization at baseline and follow-up CMR were compared using paired T-test and Mann–Whitney U test. The clinical data and initial CMR findings were also compared to predict short-term outcomes. Results The median age of eight FM children was 8.5 years old (range, 3–14). The initial CMR findings were most common with early gadolinium enhancement (EGE, 100%), followed by signal increasing on T2WI and late gadolinium enhancement (LGE, 87.5%), increased septal thickness (75.0%) and increased left ventricle ejection fraction (LVEF, 50.0%). Only three LGE (37.5%), one signal increasing on T2WI (12.5%) and one increased LVEF (12.5%) were found at follow-up. Statistically significant differences were found between initial and follow-up CMR abnormalities in the septal thickness, left ventricular end-diastolic diameter (LVEDD), end-systolic volume (ESV), LVEF, left ventricular mass, T2 ratio and LGE area (P = 0.011, P = 0.042, P = 0.016, P = 0.001, P = 0.003, P = 0.011, P = 0.020). The children with full recovery performed higher incidence of III° atrioventricular block (AVB, five cases VS 0 case) and smaller LGE area (104.0 ± 14.5 mm2 VS 138.0 ± 25.2 mm2) at baseline CMR. Discussion The CMR findings of FM in children were characteristic and useful for early diagnosis. Full recov…
format: application/pdf
format: text/html
creator: Haipeng Wang
creator: Bin Zhao
creator: Haipeng Jia
creator: Fei Gao
creator: Junyu Zhao
creator: Cuiyan Wang
subject: Cardiology
subject: Pediatrics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.2750
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Background Fulminant myocarditis (FM) is an inflammatory disease of the myocardium that results in ventricular systolic dysfunction and causes acute-onset heart failure. Cardiac magnetic resonance (CMR) has become the primary noninvasive tool for the diagnosis and evaluation of myocarditis. The aim of our study was to assess the CMR findings at different course of FM and the short-term outcomes of fulminant myocarditis (FM) in children. Methods Eight FM children with CMR examinations were included in our study. Initial baseline CMR was performed 10 days (range, 7–20 days) after onset of FM and follow-up CMR after 55 days (range, 33–75 days). Cardiac morphology and function and myocardial tissue characterization at baseline and follow-up CMR were compared using paired T-test and Mann–Whitney U test. The clinical data and initial CMR findings were also compared to predict short-term outcomes. Results The median age of eight FM children was 8.5 years old (range, 3–14). The initial CMR findings were most common with early gadolinium enhancement (EGE, 100%), followed by signal increasing on T2WI and late gadolinium enhancement (LGE, 87.5%), increased septal thickness (75.0%) and increased left ventricle ejection fraction (LVEF, 50.0%). Only three LGE (37.5%), one signal increasing on T2WI (12.5%) and one increased LVEF (12.5%) were found at follow-up. Statistically significant differences were found between initial and follow-up CMR abnormalities in the septal thickness, left ventricular end-diastolic diameter (LVEDD), end-systolic volume (ESV), LVEF, left ventricular mass, T2 ratio and LGE area (P = 0.011, P = 0.042, P = 0.016, P = 0.001, P = 0.003, P = 0.011, P = 0.020). The children with full recovery performed higher incidence of III° atrioventricular block (AVB, five cases VS 0 case) and smaller LGE area (104.0 ± 14.5 mm2 VS 138.0 ± 25.2 mm2) at baseline CMR. Discussion The CMR findings of FM in children were characteristic and useful for early diagnosis. Full recov…
bibliographic citation: Wang et al. (2016) A retrospective study: cardiac MRI of fulminant myocarditis in children—can we evaluate the short-term outcomes?. PeerJ 4:e2750 https://doi.org/10.7717/peerj.2750
date submitted: 2016-08-08
date accepted: 2016-11-03
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Haipeng
author list: Agent
  family name: Zhao
  given name: Bin
author list: Agent
  family name: Jia
  given name: Haipeng
author list: Agent
  family name: Gao
  given name: Fei
author list: Agent
  family name: Zhao
  given name: Junyu
author list: Agent
  family name: Wang
  given name: Cuiyan
doi: 10.7717/peerj.2750
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Wang et al.
attribution name: Wang et al.

Harvest year effects on Apulian EVOOs evaluated by 1H NMR based metabolomics
type: item
type: AcademicArticle
description: Nine hundred extra virgin olive oils (EVOO) were extracted from individual olive trees of four olive cultivars (Coratina, Cima di Mola, Ogliarola, Peranzana), originating from the provinces of Bari and Foggia (Apulia region, Southern Italy) and collected during two consecutive harvesting seasons (2013/14 and 2014/15). Following genetic identification of individual olive trees, a detailed Apulian EVOO NMR database was built using 900 oils samples obtained from 900 cultivar certified single trees. A study on the olive oil lipid profile was carried out by statistical multivariate analysis (Principal Component Analysis, PCA, Partial Least-Squares Discriminant Analysis, PLS-DA, Orthogonal Partial Least-Squares Discriminant Analysis, OPLS-DA). Influence of cultivar and weather conditions, such as the summer rainfall, on the oil metabolic profile have been evaluated. Mahalanobis distances and J2 criterion have been measured to assess the quality of resulting scores clusters for each cultivar in the two harvesting campaigns. The four studied cultivars showed non homogeneous behavior. Notwithstanding the geographical spread and the wide number of samples, Coratina showed a consistent behavior of its metabolic profile in the two considered harvests. Among the other three Peranzana showed the second more consistent behavior, while Cima di Mola and Ogliarola having the biggest change over the two years.
format: application/pdf
format: text/html
creator: Chiara R. Girelli
creator: Laura Del Coco
creator: Paride Papadia
creator: Sandra A. De Pascali
creator: Francesco P. Fanizzi
subject: Agricultural Science
subject: Food Science and Technology
subject: Statistics
description: doi:10.7717/peerj.2740
publisher: PeerJ Inc.
rights: © 2016 Girelli et al.
abstract: Nine hundred extra virgin olive oils (EVOO) were extracted from individual olive trees of four olive cultivars (Coratina, Cima di Mola, Ogliarola, Peranzana), originating from the provinces of Bari and Foggia (Apulia region, Southern Italy) and collected during two consecutive harvesting seasons (2013/14 and 2014/15). Following genetic identification of individual olive trees, a detailed Apulian EVOO NMR database was built using 900 oils samples obtained from 900 cultivar certified single trees. A study on the olive oil lipid profile was carried out by statistical multivariate analysis (Principal Component Analysis, PCA, Partial Least-Squares Discriminant Analysis, PLS-DA, Orthogonal Partial Least-Squares Discriminant Analysis, OPLS-DA). Influence of cultivar and weather conditions, such as the summer rainfall, on the oil metabolic profile have been evaluated. Mahalanobis distances and J2 criterion have been measured to assess the quality of resulting scores clusters for each cultivar in the two harvesting campaigns. The four studied cultivars showed non homogeneous behavior. Notwithstanding the geographical spread and the wide number of samples, Coratina showed a consistent behavior of its metabolic profile in the two considered harvests. Among the other three Peranzana showed the second more consistent behavior, while Cima di Mola and Ogliarola having the biggest change over the two years.
bibliographic citation: Girelli et al. (2016) Harvest year effects on Apulian EVOOs evaluated by 1H NMR based metabolomics. PeerJ 4:e2740 https://doi.org/10.7717/peerj.2740
date submitted: 2016-08-19
date accepted: 2016-10-25
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Girelli
  given name: Chiara R.
author list: Agent
  family name: Del Coco
  given name: Laura
author list: Agent
  family name: Papadia
  given name: Paride
author list: Agent
  family name: De Pascali
  given name: Sandra A.
author list: Agent
  family name: Fanizzi
  given name: Francesco P.
doi: 10.7717/peerj.2740
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Girelli et al.
attribution name: Girelli et al.

RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum)
type: item
type: AcademicArticle
description: RNA interference (RNAi), a gene-silencing mechanism that involves providing double-stranded RNA molecules that match a specific target gene sequence, is now widely used in functional genetic studies. The potential application of RNAi-mediated control of agricultural insect pests has rapidly become evident. The production of transgenic plants expressing dsRNA molecules that target essential insect genes could provide a means of specific gene silencing in larvae that feed on these plants, resulting in larval phenotypes that range from loss of appetite to death. In this report, we show that the tomato leafminer (Tuta absoluta), a major threat to commercial tomato production, can be targeted by RNAi. We selected two target genes (Vacuolar ATPase-A and Arginine kinase) based on the RNAi response reported for these genes in other pest species. In view of the lack of an artificial diet for T. absoluta, we used two approaches to deliver dsRNA into tomato leaflets. The first approach was based on the uptake of dsRNA by leaflets and the second was based on “in planta-induced transient gene silencing” (PITGS), a well-established method for silencing plant genes, used here for the first time to deliver in planta-transcribed dsRNA to target insect genes. Tuta absoluta larvae that fed on leaves containing dsRNA of the target genes showed an ∼60% reduction in target gene transcript accumulation, an increase in larval mortality and less leaf damage. We then generated transgenic ‘Micro-Tom’ tomato plants that expressed hairpin sequences for both genes and observed a reduction in foliar damage by T. absoluta in these plants. Our results demonstrate the feasibility of RNAi as an alternative method for controlling this critical tomato pest.
format: application/pdf
format: text/html
creator: Roberto A. Camargo
creator: Guilherme O. Barbosa
creator: Isabella Presotto Possignolo
creator: Lazaro E. P. Peres
creator: Eric Lam
creator: Joni E. Lima
creator: Antonio Figueira
creator: Henrique Marques-Souza
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2673
publisher: PeerJ Inc.
rights: © 2016 Camargo et al.
abstract: RNA interference (RNAi), a gene-silencing mechanism that involves providing double-stranded RNA molecules that match a specific target gene sequence, is now widely used in functional genetic studies. The potential application of RNAi-mediated control of agricultural insect pests has rapidly become evident. The production of transgenic plants expressing dsRNA molecules that target essential insect genes could provide a means of specific gene silencing in larvae that feed on these plants, resulting in larval phenotypes that range from loss of appetite to death. In this report, we show that the tomato leafminer (Tuta absoluta), a major threat to commercial tomato production, can be targeted by RNAi. We selected two target genes (Vacuolar ATPase-A and Arginine kinase) based on the RNAi response reported for these genes in other pest species. In view of the lack of an artificial diet for T. absoluta, we used two approaches to deliver dsRNA into tomato leaflets. The first approach was based on the uptake of dsRNA by leaflets and the second was based on “in planta-induced transient gene silencing” (PITGS), a well-established method for silencing plant genes, used here for the first time to deliver in planta-transcribed dsRNA to target insect genes. Tuta absoluta larvae that fed on leaves containing dsRNA of the target genes showed an ∼60% reduction in target gene transcript accumulation, an increase in larval mortality and less leaf damage. We then generated transgenic ‘Micro-Tom’ tomato plants that expressed hairpin sequences for both genes and observed a reduction in foliar damage by T. absoluta in these plants. Our results demonstrate the feasibility of RNAi as an alternative method for controlling this critical tomato pest.
bibliographic citation: Camargo et al. (2016) RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum). PeerJ 4:e2673 https://doi.org/10.7717/peerj.2673
date submitted: 2016-08-08
date accepted: 2016-10-09
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Camargo
  given name: Roberto A.
author list: Agent
  family name: Barbosa
  given name: Guilherme O.
author list: Agent
  family name: Possignolo
  given name: Isabella Presotto
author list: Agent
  family name: Peres
  given name: Lazaro E. P.
author list: Agent
  family name: Lam
  given name: Eric
author list: Agent
  family name: Lima
  given name: Joni E.
author list: Agent
  family name: Figueira
  given name: Antonio
author list: Agent
  family name: Marques-Souza
  given name: Henrique
doi: 10.7717/peerj.2673
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Camargo et al.
attribution name: Camargo et al.

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
type: item
type: AcademicArticle
description: Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed th…
format: application/pdf
format: text/html
creator: Priyanka Mishra
creator: Amit Kumar
creator: Vereena Rodrigues
creator: Ashutosh K. Shukla
creator: Velusamy Sundaresan
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2638
publisher: PeerJ Inc.
rights: © 2016 Mishra et al.
abstract: Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed th…
bibliographic citation: Mishra et al. (2016) Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae). PeerJ 4:e2638 https://doi.org/10.7717/peerj.2638
date submitted: 2016-08-03
date accepted: 2016-09-30
issued: 2016-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mishra
  given name: Priyanka
author list: Agent
  family name: Kumar
  given name: Amit
author list: Agent
  family name: Rodrigues
  given name: Vereena
author list: Agent
  family name: Shukla
  given name: Ashutosh K.
author list: Agent
  family name: Sundaresan
  given name: Velusamy
doi: 10.7717/peerj.2638
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-15
copyright: ©2016 Mishra et al.
attribution name: Mishra et al.

Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach
type: item
type: AcademicArticle
description: Many pathogenic mycobacteria are known to cause severe disease in humans and animals. M. avium subspecies paratuberculosis (Map) is the causative agent of Johne’s disease—a chronic wasting disease affecting ruminants such as cattle and sheep, responsible for significant economic losses in the dairy and beef industries. Due to the lack of treatment options or effective vaccines, mitigating losses can be difficult. In addition, the early stages of Map infection may occur in asymptomatic hosts that continue to shed viable bacteria in their faeces, leading to the infection of other healthy animals. Using multi-locus short sequence repeat (ML-SSR) analysis we previously reported that individual Johne’s positive dairy cattle from farms across the island of Newfoundland were infected by Map with multiple SSR-types simultaneously. The occurrence of multiple mixed genotype infections has the potential to change pathogen and disease dynamics as well as reduce the efficacy of treatments and vaccines. Therefore, we conducted whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis on a subset of these isolates for a more in-depth examination. We also implemented a PCR assay using two discriminatory SNPs and demonstrated the incidence of a mixed infection by three genotypically diverse Map isolates in a single animal. In addition, results show that WGS and SNP analysis can provide a better understanding of the relationship between Map isolates from individual and different animals. In the future such studies on the occurrence of mixed genotype infections could potentially lead to the identification of variable pathogenicity of different genotypes and allow for better tracking of Map isolates for epidemiological studies.
format: application/pdf
format: text/html
creator: Fraser W. Davidson
creator: Christina Ahlstrom
creator: Jeroen De Buck
creator: Hugh G. Whitney
creator: Kapil Tahlan
subject: Genomics
subject: Microbiology
subject: Veterinary Medicine
subject: Infectious Diseases
description: doi:10.7717/peerj.2793
publisher: PeerJ Inc.
rights: © 2016 Davidson et al.
abstract: Many pathogenic mycobacteria are known to cause severe disease in humans and animals. M. avium subspecies paratuberculosis (Map) is the causative agent of Johne’s disease—a chronic wasting disease affecting ruminants such as cattle and sheep, responsible for significant economic losses in the dairy and beef industries. Due to the lack of treatment options or effective vaccines, mitigating losses can be difficult. In addition, the early stages of Map infection may occur in asymptomatic hosts that continue to shed viable bacteria in their faeces, leading to the infection of other healthy animals. Using multi-locus short sequence repeat (ML-SSR) analysis we previously reported that individual Johne’s positive dairy cattle from farms across the island of Newfoundland were infected by Map with multiple SSR-types simultaneously. The occurrence of multiple mixed genotype infections has the potential to change pathogen and disease dynamics as well as reduce the efficacy of treatments and vaccines. Therefore, we conducted whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis on a subset of these isolates for a more in-depth examination. We also implemented a PCR assay using two discriminatory SNPs and demonstrated the incidence of a mixed infection by three genotypically diverse Map isolates in a single animal. In addition, results show that WGS and SNP analysis can provide a better understanding of the relationship between Map isolates from individual and different animals. In the future such studies on the occurrence of mixed genotype infections could potentially lead to the identification of variable pathogenicity of different genotypes and allow for better tracking of Map isolates for epidemiological studies.
bibliographic citation: Davidson et al. (2016) Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach. PeerJ 4:e2793 https://doi.org/10.7717/peerj.2793
date submitted: 2016-08-04
date accepted: 2016-11-14
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davidson
  given name: Fraser W.
author list: Agent
  family name: Ahlstrom
  given name: Christina
author list: Agent
  family name: De Buck
  given name: Jeroen
author list: Agent
  family name: Whitney
  given name: Hugh G.
author list: Agent
  family name: Tahlan
  given name: Kapil
doi: 10.7717/peerj.2793
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Davidson et al.
attribution name: Davidson et al.

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