PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China
items: BLAST-based validation of metagenomic sequence assignments
items: Predicting New Zealand riverine fish reference assemblages
items: Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta)
items: Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia
items: Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles
items: Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells
items: Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV
items: Estimation of different data compositions for early-season crop type classification
items: Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress

Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China
type: item
type: AcademicArticle
description: Objectives The prognosis of people with pancreatic cancer is extremely unfavorable. However, the prognostic factors remain largely undefined. We aimed to perform comprehensive analyses of clinicopathologic characteristics, laboratory parameters, and treatment protocols for exploring their role as prognostic factors of pancreatic cancer. Methods Patients diagnosed with pancreatic cancer and hospitalized at the China National Cancer Center between April 2006 and May 2016 were enrolled in this retrospective cohort study. Clinicopathologic characteristics, laboratory parameters, and treatment protocols were compared among patients at different stages of the disease. The association between these factors and overall survival (OS) was analyzed using the Kaplan–Meier method and Cox proportional hazards model. Results The present study included 1,433 consecutive patients with pancreatic cancer. Median OS was 10.6 months (95% confidence interval [CI] 9.8–11.3 months), with 1-, 3-, and 5-year survival rates of 43.7%, 14.8%, and 8.8%, respectively. Cox multivariate analysis findings identified the following factors as independent predictors of OS: gender (female vs male, hazard ratio 0.72, 95% CI [0.54–0.95]); elevated total bilirubin (TBil; 1.82, 1.34–2.47); elevated carbohydrate antigen 19-9 (CA19-9; 1.72, 1.17–2.54); tumor being located in pancreatic body and tail (1.52, 1.10–2.10); advanced T stage (T3-4 vs T1-2, 1.62, 1.15–2.27); lymph node metastasis (1.57, 1.20–2.07); distant metastasis (1.59, 1.12–2.27); the presence of surgical resection (0.53, 0.34–0.81); and the presence of systemic chemotherapy (0.62, 0.45–0.82). Conclusions Being male, elevated TBil and carcinoembryonic antigen, tumor being located in pancreatic body and tail, advanced T stage, lymph node and distant metastasis, the absence of surgical resection, and the absence of systematic chemotherapy were associated with worse OS in patients with pancreatic cancer.
format: application/pdf
format: text/html
creator: Shuisheng Zhang
creator: Xiaozhun Huang
creator: Yuan Tian
creator: Saderbieke Aimaiti
creator: Jianwei Zhang
creator: Jiuda Zhao
creator: Yingtai Chen
creator: Chengfeng Wang
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.4893
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Objectives The prognosis of people with pancreatic cancer is extremely unfavorable. However, the prognostic factors remain largely undefined. We aimed to perform comprehensive analyses of clinicopathologic characteristics, laboratory parameters, and treatment protocols for exploring their role as prognostic factors of pancreatic cancer. Methods Patients diagnosed with pancreatic cancer and hospitalized at the China National Cancer Center between April 2006 and May 2016 were enrolled in this retrospective cohort study. Clinicopathologic characteristics, laboratory parameters, and treatment protocols were compared among patients at different stages of the disease. The association between these factors and overall survival (OS) was analyzed using the Kaplan–Meier method and Cox proportional hazards model. Results The present study included 1,433 consecutive patients with pancreatic cancer. Median OS was 10.6 months (95% confidence interval [CI] 9.8–11.3 months), with 1-, 3-, and 5-year survival rates of 43.7%, 14.8%, and 8.8%, respectively. Cox multivariate analysis findings identified the following factors as independent predictors of OS: gender (female vs male, hazard ratio 0.72, 95% CI [0.54–0.95]); elevated total bilirubin (TBil; 1.82, 1.34–2.47); elevated carbohydrate antigen 19-9 (CA19-9; 1.72, 1.17–2.54); tumor being located in pancreatic body and tail (1.52, 1.10–2.10); advanced T stage (T3-4 vs T1-2, 1.62, 1.15–2.27); lymph node metastasis (1.57, 1.20–2.07); distant metastasis (1.59, 1.12–2.27); the presence of surgical resection (0.53, 0.34–0.81); and the presence of systemic chemotherapy (0.62, 0.45–0.82). Conclusions Being male, elevated TBil and carcinoembryonic antigen, tumor being located in pancreatic body and tail, advanced T stage, lymph node and distant metastasis, the absence of surgical resection, and the absence of systematic chemotherapy were associated with worse OS in patients with pancreatic cancer.
bibliographic citation: Zhang et al. (2018) Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China. PeerJ 6:e4893 https://doi.org/10.7717/peerj.4893
date submitted: 2018-02-23
date accepted: 2018-05-14
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shuisheng
author list: Agent
  family name: Huang
  given name: Xiaozhun
author list: Agent
  family name: Tian
  given name: Yuan
author list: Agent
  family name: Aimaiti
  given name: Saderbieke
author list: Agent
  family name: Zhang
  given name: Jianwei
author list: Agent
  family name: Zhao
  given name: Jiuda
author list: Agent
  family name: Chen
  given name: Yingtai
author list: Agent
  family name: Wang
  given name: Chengfeng
doi: 10.7717/peerj.4893
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Zhang et al.
attribution name: Zhang et al.

BLAST-based validation of metagenomic sequence assignments
type: item
type: AcademicArticle
description: When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by “first-pass” classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.
format: application/pdf
format: text/html
creator: Adam L. Bazinet
creator: Brian D. Ondov
creator: Daniel D. Sommer
creator: Shashikala Ratnayake
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.4892
publisher: PeerJ Inc.
rights: © 2018 Bazinet et al.
abstract: When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by “first-pass” classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.
bibliographic citation: Bazinet et al. (2018) BLAST-based validation of metagenomic sequence assignments. PeerJ 6:e4892 https://doi.org/10.7717/peerj.4892
date submitted: 2018-01-22
date accepted: 2018-05-13
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bazinet
  given name: Adam L.
author list: Agent
  family name: Ondov
  given name: Brian D.
author list: Agent
  family name: Sommer
  given name: Daniel D.
author list: Agent
  family name: Ratnayake
  given name: Shashikala
doi: 10.7717/peerj.4892
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Bazinet et al.
attribution name: Bazinet et al.

Predicting New Zealand riverine fish reference assemblages
type: item
type: AcademicArticle
description: Biomonitoring is a common method to monitor environmental change in river ecosystems, a key advantage of biomonitoring over snap-shot physicochemical monitoring is that it provides a more stable, long-term insight into change that is also effects-based. In New Zealand, the main biomonitoring method is a macroinvertebrate sensitivity scoring index, with little established methods available for biomonitoring of fish. This study models the contemporary distribution of common freshwater fish and then uses those models to predict freshwater fish assemblages for each river reach under reference conditions. Comparison of current fish assemblages with those predicted in reference conditions (as observed/expected (O/E) ratios) may provide a suitable option for freshwater fish biomonitoring. Most of the fish communities throughout the central North Island and lower reaches show substantial deviation from the modelled reference community. Most of this deviation is explained by nutrient enrichment, followed by downstream barriers (i.e. dams) and loss of riparian vegetation. The presence of modelled introduced species had relatively little impact on the presence of the modelled native fish. The maps of O/E fish assemblage may provide a rapid way to identify potential restoration sites.
format: application/pdf
format: text/html
creator: Adam D. Canning
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
subject: Freshwater Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.4890
publisher: PeerJ Inc.
rights: © 2018 Canning
abstract: Biomonitoring is a common method to monitor environmental change in river ecosystems, a key advantage of biomonitoring over snap-shot physicochemical monitoring is that it provides a more stable, long-term insight into change that is also effects-based. In New Zealand, the main biomonitoring method is a macroinvertebrate sensitivity scoring index, with little established methods available for biomonitoring of fish. This study models the contemporary distribution of common freshwater fish and then uses those models to predict freshwater fish assemblages for each river reach under reference conditions. Comparison of current fish assemblages with those predicted in reference conditions (as observed/expected (O/E) ratios) may provide a suitable option for freshwater fish biomonitoring. Most of the fish communities throughout the central North Island and lower reaches show substantial deviation from the modelled reference community. Most of this deviation is explained by nutrient enrichment, followed by downstream barriers (i.e. dams) and loss of riparian vegetation. The presence of modelled introduced species had relatively little impact on the presence of the modelled native fish. The maps of O/E fish assemblage may provide a rapid way to identify potential restoration sites.
bibliographic citation: Canning (2018) Predicting New Zealand riverine fish reference assemblages. PeerJ 6:e4890 https://doi.org/10.7717/peerj.4890
date submitted: 2018-02-01
date accepted: 2018-05-14
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Canning
  given name: Adam D.
doi: 10.7717/peerj.4890
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Canning
attribution name: Canning

Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta)
type: item
type: AcademicArticle
description: Vitellogenin has been proposed to regulate division of labor and social organization in social insects. The red imported fire ant (Solenopsis invicta) harbors four distinct, adjacent vitellogenin genes (Vg1, Vg2, Vg3, and Vg4). Contrary to honey bees that have a single Vg ortholog as well as potentially fertile nurses, and to other ant species that lay trophic eggs, S. invicta workers completely lack ovaries or the ability to lay eggs. This provides a unique model to investigate whether Vg duplication in S. invicta was followed by subfunctionalization to acquire non-reproductive functions and whether Vg was co-opted to regulate behavior within the worker caste. To investigate these questions, we compared the expression patterns of S. invicta Vg genes among workers from different morphological subcastes or performing different tasks. RT-qPCRs revealed higher relative expression of Vg1 in major workers compared to both medium and minor workers, and of Vg2 in major workers when compared to minor workers. Relative expression of Vg1 was also higher in carbohydrate foragers when compared to nurses and protein foragers. By contrast, the level of expression of Vg2, Vg3, and Vg4 were not significantly different among the workers performing the specific tasks. Additionally, we analyzed the relationship between the expression of the Vg genes and S-hydroprene, a juvenile hormone analog. No changes in Vg expression were recorded in workers 12 h after application of the analog. Our results suggest that in S. invicta the Vg gene underwent subfunctionalization after duplication to new functions based on the expression bias observed in these data. This may suggest an alternative and still unknown function for Vg in the workers that needs to be investigated further.
format: application/pdf
format: text/html
creator: Chloe Hawkings
creator: Cecilia Tamborindeguy
subject: Entomology
subject: Evolutionary Studies
subject: Molecular Biology
description: doi:10.7717/peerj.4875
publisher: PeerJ Inc.
rights: © 2018 Hawkings and Tamborindeguy
abstract: Vitellogenin has been proposed to regulate division of labor and social organization in social insects. The red imported fire ant (Solenopsis invicta) harbors four distinct, adjacent vitellogenin genes (Vg1, Vg2, Vg3, and Vg4). Contrary to honey bees that have a single Vg ortholog as well as potentially fertile nurses, and to other ant species that lay trophic eggs, S. invicta workers completely lack ovaries or the ability to lay eggs. This provides a unique model to investigate whether Vg duplication in S. invicta was followed by subfunctionalization to acquire non-reproductive functions and whether Vg was co-opted to regulate behavior within the worker caste. To investigate these questions, we compared the expression patterns of S. invicta Vg genes among workers from different morphological subcastes or performing different tasks. RT-qPCRs revealed higher relative expression of Vg1 in major workers compared to both medium and minor workers, and of Vg2 in major workers when compared to minor workers. Relative expression of Vg1 was also higher in carbohydrate foragers when compared to nurses and protein foragers. By contrast, the level of expression of Vg2, Vg3, and Vg4 were not significantly different among the workers performing the specific tasks. Additionally, we analyzed the relationship between the expression of the Vg genes and S-hydroprene, a juvenile hormone analog. No changes in Vg expression were recorded in workers 12 h after application of the analog. Our results suggest that in S. invicta the Vg gene underwent subfunctionalization after duplication to new functions based on the expression bias observed in these data. This may suggest an alternative and still unknown function for Vg in the workers that needs to be investigated further.
bibliographic citation: Hawkings et al. (2018) Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta). PeerJ 6:e4875 https://doi.org/10.7717/peerj.4875
date submitted: 2018-01-09
date accepted: 2018-05-09
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hawkings
  given name: Chloe
author list: Agent
  family name: Tamborindeguy
  given name: Cecilia
doi: 10.7717/peerj.4875
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Hawkings and Tamborindeguy
attribution name: Hawkings and Tamborindeguy

Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia
type: item
type: AcademicArticle
description: Hulsanpes perlei is an enigmatic theropod dinosaur from the Baruungoyot Formation (?mid- to upper Campanian, Upper Cretaceous) of Mongolia. It was discovered in 1970, during the third Polish-Mongolian paleontological expedition to the Nemegt Basin. The taxon is known based on a partial braincase and an incomplete right hindlimb. However, the braincase fragment has never been described nor illustrated. We redescribe all elements that form the holotype of Hulsanpes and discuss the affinities of this taxon. The braincase fragment is interpreted as belonging to the inner ear region, and includes the floccular recess and part of the labyrinth. Hulsanpes perlei is confirmed as a valid taxon, diagnosed by a unique combination of metatarsal characters, including two autapomorphies. Historically, it represents the oldest record of the recently-established clade Halszkaraptorinae. Our findings identify subcursorial adaptations for Hulsanpes, shared with Mahakala, and differentiating them from Halszkaraptor. As such, appendicular disparity in the potentially sympatric halszkaraptorines suggest a reduced ecological overlap among these taxa, which may explain the co-occurrence of multiple species of this clade during the latest Cretaceous in what is now the Nemegt Basin.
format: application/pdf
format: text/html
creator: Andrea Cau
creator: Daniel Madzia
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4868
publisher: PeerJ Inc.
rights: © 2018 Cau and Madzia
abstract: Hulsanpes perlei is an enigmatic theropod dinosaur from the Baruungoyot Formation (?mid- to upper Campanian, Upper Cretaceous) of Mongolia. It was discovered in 1970, during the third Polish-Mongolian paleontological expedition to the Nemegt Basin. The taxon is known based on a partial braincase and an incomplete right hindlimb. However, the braincase fragment has never been described nor illustrated. We redescribe all elements that form the holotype of Hulsanpes and discuss the affinities of this taxon. The braincase fragment is interpreted as belonging to the inner ear region, and includes the floccular recess and part of the labyrinth. Hulsanpes perlei is confirmed as a valid taxon, diagnosed by a unique combination of metatarsal characters, including two autapomorphies. Historically, it represents the oldest record of the recently-established clade Halszkaraptorinae. Our findings identify subcursorial adaptations for Hulsanpes, shared with Mahakala, and differentiating them from Halszkaraptor. As such, appendicular disparity in the potentially sympatric halszkaraptorines suggest a reduced ecological overlap among these taxa, which may explain the co-occurrence of multiple species of this clade during the latest Cretaceous in what is now the Nemegt Basin.
bibliographic citation: Cau et al. (2018) Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia. PeerJ 6:e4868 https://doi.org/10.7717/peerj.4868
date submitted: 2018-04-02
date accepted: 2018-05-09
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cau
  given name: Andrea
author list: Agent
  family name: Madzia
  given name: Daniel
doi: 10.7717/peerj.4868
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: ©2018 Cau and Madzia
attribution name: Cau and Madzia

Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles
type: item
type: AcademicArticle
description: Background Selenium is an essential element; however, at higher doses, it can be toxic. Therefore, alternative nanotechnological solutions are required to overcome toxicological issues, rather than conventional alternatives. Nanoparticles show new and promising properties that may be able to suppress toxicity while maintaining the positive effects of selenium on an organism. The aim of the experiment was to determine the influence of sodium selenite and selenium nanoparticles (SeNPs) on the antioxidant status of rats. Methods The males of the outbreed rat strain Wistar albino were selected as a model organism. Animals were fed different forms of selenium. The control group was given a mixture without selenium addition, whereas other groups were fed a mixture containing sodium selenite, Se-49, and Se-100 SeNPs respectively. The duration of the trial was 30 days. Results Analysis of blood and liver was performed where the concentration of reduced (GSH) and oxidised (GSSG) glutathione, and total selenium content were measured. In the liver, a significant reduction in GSSG was found for all experiment groups. Blood samples showed a significant reduction in GSH and an increase in GSSG. Discussion These results show that SeNPs may be an alternative to dietary selenium for animal organisms.
format: application/pdf
format: text/html
creator: Lenka Urbankova
creator: Pavel Horky
creator: Jiri Skladanka
creator: Magdalena Pribilova
creator: Vendula Smolikova
creator: Pavel Nevrkla
creator: Natalia Cernei
creator: Zuzana Lackova
creator: Josef Hedbavny
creator: Andrea Ridoskova
creator: Vojtech Adam
creator: Pavel Kopel
subject: Agricultural Science
subject: Biochemistry
subject: Nutrition
description: doi:10.7717/peerj.4862
publisher: PeerJ Inc.
rights: © 2018 Urbankova et al.
abstract: Background Selenium is an essential element; however, at higher doses, it can be toxic. Therefore, alternative nanotechnological solutions are required to overcome toxicological issues, rather than conventional alternatives. Nanoparticles show new and promising properties that may be able to suppress toxicity while maintaining the positive effects of selenium on an organism. The aim of the experiment was to determine the influence of sodium selenite and selenium nanoparticles (SeNPs) on the antioxidant status of rats. Methods The males of the outbreed rat strain Wistar albino were selected as a model organism. Animals were fed different forms of selenium. The control group was given a mixture without selenium addition, whereas other groups were fed a mixture containing sodium selenite, Se-49, and Se-100 SeNPs respectively. The duration of the trial was 30 days. Results Analysis of blood and liver was performed where the concentration of reduced (GSH) and oxidised (GSSG) glutathione, and total selenium content were measured. In the liver, a significant reduction in GSSG was found for all experiment groups. Blood samples showed a significant reduction in GSH and an increase in GSSG. Discussion These results show that SeNPs may be an alternative to dietary selenium for animal organisms.
bibliographic citation: Urbankova et al. (2018) Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles. PeerJ 6:e4862 https://doi.org/10.7717/peerj.4862
date submitted: 2018-02-19
date accepted: 2018-05-07
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Urbankova
  given name: Lenka
author list: Agent
  family name: Horky
  given name: Pavel
author list: Agent
  family name: Skladanka
  given name: Jiri
author list: Agent
  family name: Pribilova
  given name: Magdalena
author list: Agent
  family name: Smolikova
  given name: Vendula
author list: Agent
  family name: Nevrkla
  given name: Pavel
author list: Agent
  family name: Cernei
  given name: Natalia
author list: Agent
  family name: Lackova
  given name: Zuzana
author list: Agent
  family name: Hedbavny
  given name: Josef
author list: Agent
  family name: Ridoskova
  given name: Andrea
author list: Agent
  family name: Adam
  given name: Vojtech
author list: Agent
  family name: Kopel
  given name: Pavel
doi: 10.7717/peerj.4862
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Urbankova et al.
attribution name: Urbankova et al.

Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells
type: item
type: AcademicArticle
description: Background The Lepidopteran ambidensovirus 1 isolated from Junonia coenia (hereafter JcDV) is an invertebrate parvovirus considered as a viral transduction vector as well as a potential tool for the biological control of insect pests. Previous works showed that JcDV-based circular plasmids experimentally integrate into insect cells genomic DNA. Methods In order to approach the natural conditions of infection and possible integration, we generated linear JcDV-gfp based molecules which were transfected into non permissive Spodoptera frugiperda (Sf9) cultured cells. Cells were monitored for the expression of green fluorescent protein (GFP) and DNA was analyzed for integration of transduced viral sequences. Non-structural protein modulation of the VP-gene cassette promoter activity was additionally assayed. Results We show that linear JcDV-derived molecules are capable of long term genomic integration and sustained transgene expression in Sf9 cells. As expected, only the deletion of both inverted terminal repeats (ITR) or the polyadenylation signals of NS and VP genes dramatically impairs the global transduction/expression efficiency. However, all the integrated viral sequences we characterized appear “scrambled” whatever the viral content of the transfected vector. Despite a strong GFP expression, we were unable to recover any full sequence of the original constructs and found rearranged viral and non-viral sequences as well. Cellular flanking sequences were identified as non-coding ones. On the other hand, the kinetics of GFP expression over time led us to investigate the apparent down-regulation by non-structural proteins of the VP-gene cassette promoter. Conclusion Altogether, our results show that JcDV-derived sequences included in linear DNA molecules are able to drive efficiently the integration and expression of a foreign gene into the genome of insect cells, whatever their composition, provided that at least one ITR is present. However, the transfected sequence…
format: application/pdf
format: text/html
creator: Francine Rizk
creator: Sylvain Laverdure
creator: Emmanuelle d’Alençon
creator: Hervé Bossin
creator: Thierry Dupressoir
subject: Bioinformatics
subject: Biotechnology
subject: Cell Biology
subject: Virology
description: doi:10.7717/peerj.4860
publisher: PeerJ Inc.
rights: © 2018 Rizk et al.
abstract: Background The Lepidopteran ambidensovirus 1 isolated from Junonia coenia (hereafter JcDV) is an invertebrate parvovirus considered as a viral transduction vector as well as a potential tool for the biological control of insect pests. Previous works showed that JcDV-based circular plasmids experimentally integrate into insect cells genomic DNA. Methods In order to approach the natural conditions of infection and possible integration, we generated linear JcDV-gfp based molecules which were transfected into non permissive Spodoptera frugiperda (Sf9) cultured cells. Cells were monitored for the expression of green fluorescent protein (GFP) and DNA was analyzed for integration of transduced viral sequences. Non-structural protein modulation of the VP-gene cassette promoter activity was additionally assayed. Results We show that linear JcDV-derived molecules are capable of long term genomic integration and sustained transgene expression in Sf9 cells. As expected, only the deletion of both inverted terminal repeats (ITR) or the polyadenylation signals of NS and VP genes dramatically impairs the global transduction/expression efficiency. However, all the integrated viral sequences we characterized appear “scrambled” whatever the viral content of the transfected vector. Despite a strong GFP expression, we were unable to recover any full sequence of the original constructs and found rearranged viral and non-viral sequences as well. Cellular flanking sequences were identified as non-coding ones. On the other hand, the kinetics of GFP expression over time led us to investigate the apparent down-regulation by non-structural proteins of the VP-gene cassette promoter. Conclusion Altogether, our results show that JcDV-derived sequences included in linear DNA molecules are able to drive efficiently the integration and expression of a foreign gene into the genome of insect cells, whatever their composition, provided that at least one ITR is present. However, the transfected sequence…
bibliographic citation: Rizk et al. (2018) Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells. PeerJ 6:e4860 https://doi.org/10.7717/peerj.4860
date submitted: 2018-02-12
date accepted: 2018-05-04
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rizk
  given name: Francine
author list: Agent
  family name: Laverdure
  given name: Sylvain
author list: Agent
  family name: d’Alençon
  given name: Emmanuelle
author list: Agent
  family name: Bossin
  given name: Hervé
author list: Agent
  family name: Dupressoir
  given name: Thierry
doi: 10.7717/peerj.4860
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Rizk et al.
attribution name: Rizk et al.

Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV
type: item
type: AcademicArticle
description: It is generally feasible to classify different species of vegetation based on remotely sensed images, but identification of different sub-species or even cultivars is uncommon. Tea trees (Camellia sinensis L.) have been proven to show great differences in taste and quality between cultivars. We hypothesize that hyperspectral remote sensing would make it possibly to classify cultivars of plants and even to estimate their taste-related biochemical components. In this study, hyperspectral data of the canopies of tea trees were collected by hyperspectral camera mounted on an unmanned aerial vehicle (UAV). Tea cultivars were classified according to the spectral characteristics of the tea canopies. Furthermore, two major components influencing the taste of tea, tea polyphenols (TP) and amino acids (AA), were predicted. The results showed that the overall accuracy of tea cultivar classification achieved by support vector machine is higher than 95% with proper spectral pre-processing method. The best results to predict the TP and AA were achieved by partial least squares regression with standard normal variant normalized spectra, and the ratio of TP to AA—which is one proven index for tea taste—achieved the highest accuracy (RCV = 0.66, RMSECV = 13.27) followed by AA (RCV = 0.62, RMSECV = 1.16) and TP (RCV = 0.58, RMSECV = 10.01). The results indicated that classification of tea cultivars using the hyperspectral remote sensing from UAV was successful, and there is a potential to map the taste-related chemical components in tea plantations from UAV platform; however, further exploration is needed to increase the accuracy.
format: application/pdf
format: text/html
creator: Yexin Tu
creator: Meng Bian
creator: Yinkang Wan
creator: Teng Fei
subject: Biogeochemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.4858
publisher: PeerJ Inc.
rights: © 2018 Tu et al.
abstract: It is generally feasible to classify different species of vegetation based on remotely sensed images, but identification of different sub-species or even cultivars is uncommon. Tea trees (Camellia sinensis L.) have been proven to show great differences in taste and quality between cultivars. We hypothesize that hyperspectral remote sensing would make it possibly to classify cultivars of plants and even to estimate their taste-related biochemical components. In this study, hyperspectral data of the canopies of tea trees were collected by hyperspectral camera mounted on an unmanned aerial vehicle (UAV). Tea cultivars were classified according to the spectral characteristics of the tea canopies. Furthermore, two major components influencing the taste of tea, tea polyphenols (TP) and amino acids (AA), were predicted. The results showed that the overall accuracy of tea cultivar classification achieved by support vector machine is higher than 95% with proper spectral pre-processing method. The best results to predict the TP and AA were achieved by partial least squares regression with standard normal variant normalized spectra, and the ratio of TP to AA—which is one proven index for tea taste—achieved the highest accuracy (RCV = 0.66, RMSECV = 13.27) followed by AA (RCV = 0.62, RMSECV = 1.16) and TP (RCV = 0.58, RMSECV = 10.01). The results indicated that classification of tea cultivars using the hyperspectral remote sensing from UAV was successful, and there is a potential to map the taste-related chemical components in tea plantations from UAV platform; however, further exploration is needed to increase the accuracy.
bibliographic citation: Tu et al. (2018) Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV. PeerJ 6:e4858 https://doi.org/10.7717/peerj.4858
date submitted: 2018-02-01
date accepted: 2018-05-08
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tu
  given name: Yexin
author list: Agent
  family name: Bian
  given name: Meng
author list: Agent
  family name: Wan
  given name: Yinkang
author list: Agent
  family name: Fei
  given name: Teng
doi: 10.7717/peerj.4858
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: © 2018 Tu et al.
attribution name: Tu et al.

Estimation of different data compositions for early-season crop type classification
type: item
type: AcademicArticle
description: Timely and accurate crop type distribution maps are an important inputs for crop yield estimation and production forecasting as multi-temporal images can observe phenological differences among crops. Therefore, time series remote sensing data are essential for crop type mapping, and image composition has commonly been used to improve the quality of the image time series. However, the optimal composition period is unclear as long composition periods (such as compositions lasting half a year) are less informative and short composition periods lead to information redundancy and missing pixels. In this study, we initially acquired daily 30 m Normalized Difference Vegetation Index (NDVI) time series by fusing MODIS, Landsat, Gaofen and Huanjing (HJ) NDVI, and then composited the NDVI time series using four strategies (daily, 8-day, 16-day, and 32-day). We used Random Forest to identify crop types and evaluated the classification performances of the NDVI time series generated from four composition strategies in two studies regions from Xinjiang, China. Results indicated that crop classification performance improved as crop separabilities and classification accuracies increased, and classification uncertainties dropped in the green-up stage of the crops. When using daily NDVI time series, overall accuracies saturated at 113-day and 116-day in Bole and Luntai, and the saturated overall accuracies (OAs) were 86.13% and 91.89%, respectively. Cotton could be identified 40∼60 days and 35∼45 days earlier than the harvest in Bole and Luntai when using daily, 8-day and 16-day composition NDVI time series since both producer’s accuracies (PAs) and user’s accuracies (UAs) were higher than 85%. Among the four compositions, the daily NDVI time series generated the highest classification accuracies. Although the 8-day, 16-day and 32-day compositions had similar saturated overall accuracies (around 85% in Bole and 83% in Luntai), the 8-day and 16-day compositions achieved these accuraci…
format: application/pdf
format: text/html
creator: Pengyu Hao
creator: Mingquan Wu
creator: Zheng Niu
creator: Li Wang
creator: Yulin Zhan
subject: Agricultural Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.4834
publisher: PeerJ Inc.
rights: © 2018 Hao et al.
abstract: Timely and accurate crop type distribution maps are an important inputs for crop yield estimation and production forecasting as multi-temporal images can observe phenological differences among crops. Therefore, time series remote sensing data are essential for crop type mapping, and image composition has commonly been used to improve the quality of the image time series. However, the optimal composition period is unclear as long composition periods (such as compositions lasting half a year) are less informative and short composition periods lead to information redundancy and missing pixels. In this study, we initially acquired daily 30 m Normalized Difference Vegetation Index (NDVI) time series by fusing MODIS, Landsat, Gaofen and Huanjing (HJ) NDVI, and then composited the NDVI time series using four strategies (daily, 8-day, 16-day, and 32-day). We used Random Forest to identify crop types and evaluated the classification performances of the NDVI time series generated from four composition strategies in two studies regions from Xinjiang, China. Results indicated that crop classification performance improved as crop separabilities and classification accuracies increased, and classification uncertainties dropped in the green-up stage of the crops. When using daily NDVI time series, overall accuracies saturated at 113-day and 116-day in Bole and Luntai, and the saturated overall accuracies (OAs) were 86.13% and 91.89%, respectively. Cotton could be identified 40∼60 days and 35∼45 days earlier than the harvest in Bole and Luntai when using daily, 8-day and 16-day composition NDVI time series since both producer’s accuracies (PAs) and user’s accuracies (UAs) were higher than 85%. Among the four compositions, the daily NDVI time series generated the highest classification accuracies. Although the 8-day, 16-day and 32-day compositions had similar saturated overall accuracies (around 85% in Bole and 83% in Luntai), the 8-day and 16-day compositions achieved these accuraci…
bibliographic citation: Hao et al. (2018) Estimation of different data compositions for early-season crop type classification. PeerJ 6:e4834 https://doi.org/10.7717/peerj.4834
date submitted: 2018-01-04
date accepted: 2018-05-03
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Pengyu
author list: Agent
  family name: Wu
  given name: Mingquan
author list: Agent
  family name: Niu
  given name: Zheng
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Zhan
  given name: Yulin
doi: 10.7717/peerj.4834
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: ©2018 Hao et al.
attribution name: Hao et al.

Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress
type: item
type: AcademicArticle
description: Barley yellow dwarf virus-PAV (BYDV-PAV) is one of the major viruses causing a widespread and serious viral disease affecting cereal crops. To gain a better understanding of plant defence mechanisms of BYDV resistance genes (Bdv2 and RYd2) against BYDV-PAV infection, the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars were investigated. We found that root growth and total dry matter of susceptible cultivars showed greater reduction than that of resistant ones after infection. BYDV infected leaves in susceptible wheat and barley cultivars showed a significant reduction in photosynthetic pigments, an increase in the concentration of reducing sugar. The protein levels were also low in infected leaves. There was a significant increase in total phenol contents in resistant cultivars, which might reflect a protective mechanism of plants against virus infection. In phloem tissue, sieve elements (SE) and companion cells (CC) were severely damaged in susceptible cultivars after infection. It is suggested that restriction of viral movement in the phloem tissue and increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and RYd2 against virus infection.
format: application/pdf
format: text/html
creator: Shormin Choudhury
creator: Hongliang Hu
creator: Philip Larkin
creator: Holger Meinke
creator: Sergey Shabala
creator: Ibrahim Ahmed
creator: Meixue Zhou
subject: Agricultural Science
subject: Virology
description: doi:10.7717/peerj.4833
publisher: PeerJ Inc.
rights: © 2018 Choudhury et al.
abstract: Barley yellow dwarf virus-PAV (BYDV-PAV) is one of the major viruses causing a widespread and serious viral disease affecting cereal crops. To gain a better understanding of plant defence mechanisms of BYDV resistance genes (Bdv2 and RYd2) against BYDV-PAV infection, the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars were investigated. We found that root growth and total dry matter of susceptible cultivars showed greater reduction than that of resistant ones after infection. BYDV infected leaves in susceptible wheat and barley cultivars showed a significant reduction in photosynthetic pigments, an increase in the concentration of reducing sugar. The protein levels were also low in infected leaves. There was a significant increase in total phenol contents in resistant cultivars, which might reflect a protective mechanism of plants against virus infection. In phloem tissue, sieve elements (SE) and companion cells (CC) were severely damaged in susceptible cultivars after infection. It is suggested that restriction of viral movement in the phloem tissue and increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and RYd2 against virus infection.
bibliographic citation: Choudhury et al. (2018) Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress. PeerJ 6:e4833 https://doi.org/10.7717/peerj.4833
date submitted: 2018-01-02
date accepted: 2018-05-03
issued: 2018-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choudhury
  given name: Shormin
author list: Agent
  family name: Hu
  given name: Hongliang
author list: Agent
  family name: Larkin
  given name: Philip
author list: Agent
  family name: Meinke
  given name: Holger
author list: Agent
  family name: Shabala
  given name: Sergey
author list: Agent
  family name: Ahmed
  given name: Ibrahim
author list: Agent
  family name: Zhou
  given name: Meixue
doi: 10.7717/peerj.4833
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-28
copyright: ©2018 Choudhury et al.
attribution name: Choudhury et al.

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