PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia
items: Repression of ZCT1, ZCT2 and ZCT3 affects expression of terpenoid indole alkaloid biosynthetic and regulatory genes
items: First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti
items: Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case
items: Confidence intervals for the difference between the coefficients of variation of Weibull distributions for analyzing wind speed dispersion
items: CGRP overexpression does not alter depression-like behavior in mice
items: Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels
items: https://peerj.com/articles/11465
items: Dumpster diving for diatom plastid 16S rRNA genes
items: Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia
type: item
type: AcademicArticle
description: Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.
format: application/pdf
format: text/html
creator: Siroj Bakoev
creator: Lyubov Getmantseva
creator: Olga Kostyunina
creator: Nekruz Bakoev
creator: Yuri Prytkov
creator: Alexander Usatov
creator: Tatiana V. Tatarinova
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Veterinary Medicine
description: doi:10.7717/peerj.11595
publisher: PeerJ Inc.
rights: © 2021 Bakoev et al.
abstract: Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.
bibliographic citation: Bakoev et al. (2021) Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia. PeerJ 9:e11595 https://doi.org/10.7717/peerj.11595
date submitted: 2021-02-15
date accepted: 2021-05-21
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bakoev
  given name: Siroj
author list: Agent
  family name: Getmantseva
  given name: Lyubov
author list: Agent
  family name: Kostyunina
  given name: Olga
author list: Agent
  family name: Bakoev
  given name: Nekruz
author list: Agent
  family name: Prytkov
  given name: Yuri
author list: Agent
  family name: Usatov
  given name: Alexander
author list: Agent
  family name: Tatarinova
  given name: Tatiana V.
doi: 10.7717/peerj.11595
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: ©2021 Bakoev et al.
attribution name: Bakoev et al.

Repression of ZCT1, ZCT2 and ZCT3 affects expression of terpenoid indole alkaloid biosynthetic and regulatory genes
type: item
type: AcademicArticle
description: Terpenoid indole alkaloids (TIAs) include several valuable pharmaceuticals. As Catharanthus roseus remains the primary source of these TIA pharmaceuticals, several research groups have devoted substantial efforts to increase production of these compounds by C. roseus. Efforts to increase TIA production by overexpressing positive regulators of TIA biosynthetic genes have met with limited success. This limited success might be due to the fact that overexpression of several positive TIA regulators turns on expression of negative regulators of TIA biosynthetic genes. Consequently, a more effective approach for increasing expression of TIA biosynthetic genes might be to decrease expression of negative regulators of TIA biosynthetic genes. Towards this end, an RNAi construct was generated that expresses a hairpin RNA carrying nucleotide fragments from three negative transcriptional regulators of TIA genes, ZCT1, ZCT2 and ZCT3, under the control of a beta-estradiol inducible promoter. Transgenic C. roseus hairy root lines carrying this ZCT RNAi construct exhibit significant reductions in transcript levels of all three ZCT genes. Surprisingly, out of eight TIA biosynthetic genes analyzed, seven (CPR, LAMT, TDC, STR, 16OMT, D4H and DAT) exhibited decreased rather than increased transcript levels in response to reductions in ZCT transcript levels. The lone exception was T19H, which exhibited the expected negative correlation in transcript levels with transcript levels of all three ZCT genes. A possible explanation for the T19H expression pattern being the opposite of the expression patterns of the other TIA biosynthetic genes tested is that T19H shunts metabolites away from vindoline production whereas the products of the other genes tested shunt metabolites towards vindoline metabolism. Consequently, both increased expression of T19H and decreased expression of one or more of the other seven genes tested would be expected to have similar effects on flux through the TIA pathw…
format: application/pdf
format: text/html
creator: Chun Yao Li
creator: Susan I. Gibson
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11624
publisher: PeerJ Inc.
rights: © 2021 Li and Gibson
abstract: Terpenoid indole alkaloids (TIAs) include several valuable pharmaceuticals. As Catharanthus roseus remains the primary source of these TIA pharmaceuticals, several research groups have devoted substantial efforts to increase production of these compounds by C. roseus. Efforts to increase TIA production by overexpressing positive regulators of TIA biosynthetic genes have met with limited success. This limited success might be due to the fact that overexpression of several positive TIA regulators turns on expression of negative regulators of TIA biosynthetic genes. Consequently, a more effective approach for increasing expression of TIA biosynthetic genes might be to decrease expression of negative regulators of TIA biosynthetic genes. Towards this end, an RNAi construct was generated that expresses a hairpin RNA carrying nucleotide fragments from three negative transcriptional regulators of TIA genes, ZCT1, ZCT2 and ZCT3, under the control of a beta-estradiol inducible promoter. Transgenic C. roseus hairy root lines carrying this ZCT RNAi construct exhibit significant reductions in transcript levels of all three ZCT genes. Surprisingly, out of eight TIA biosynthetic genes analyzed, seven (CPR, LAMT, TDC, STR, 16OMT, D4H and DAT) exhibited decreased rather than increased transcript levels in response to reductions in ZCT transcript levels. The lone exception was T19H, which exhibited the expected negative correlation in transcript levels with transcript levels of all three ZCT genes. A possible explanation for the T19H expression pattern being the opposite of the expression patterns of the other TIA biosynthetic genes tested is that T19H shunts metabolites away from vindoline production whereas the products of the other genes tested shunt metabolites towards vindoline metabolism. Consequently, both increased expression of T19H and decreased expression of one or more of the other seven genes tested would be expected to have similar effects on flux through the TIA pathw…
bibliographic citation: Li et al. (2021) Repression of ZCT1, ZCT2 and ZCT3 affects expression of terpenoid indole alkaloid biosynthetic and regulatory genes. PeerJ 9:e11624 https://doi.org/10.7717/peerj.11624
date submitted: 2021-01-25
date accepted: 2021-05-26
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Chun Yao
author list: Agent
  family name: Gibson
  given name: Susan I.
doi: 10.7717/peerj.11624
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: © 2021 Li and Gibson
attribution name: Li and Gibson

First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti
type: item
type: AcademicArticle
description: Background Biological control using entomopathogenic nematodes (EPN) has demonstrated good potential to contribute to the integral control of mosquito larvae, which as adults are vectors of diseases such as Dengue fever, Zika and Chikungunya. However, until now there are no records of the presence of EPN or their killing capacity in Yucatán state, southern México. The objectives of the current study were: (1) to report the entomopathogenic nematodes present in Yucatán soils and (2) to determine the killing capacity of the most frequent and abundant EPN against Aedes aegypti mosquito larvae and the microbial community developed by Ae. Aegypti exposed to this EPN. Methods The nematodes were collected by the insect trap technique using the great wax moth Galleria mellonella. Internal transcribed spacer (ITS), 28S gene of ribosomal DNA and phylogenetic analyses were performed to identify the EPN. For the bioassay, four concentrations of the most frequent and abundant EPN were tested: 1,260:1 infective juveniles (IJs) per mosquito larvae, 2,520 IJs:1, 3,780 IJs:1 and 5,040 IJs:1. High-throughput sequencing of the 16S rRNA gene was used to identify bacterial amplicon sequences in the mosquito larvae infected with EPN. Results Six isolates of Heterorhabditis were recovered from 144 soil samples. Heterorhabditis indica (four isolates) was the most frequent and abundant EPN, followed by Heterorhabditis n. sp. (two isolates). Both nematodes are reported for the first time for Yucatán state, Mexico. The concentration of 2,520 IJs:1 produced 80% of mosquito larvae mortality in 48 h. Representative members of Photorhabdus genus were numerically dominant (74%) in mosquito larvae infected by H. indica. It is most likely that these bacteria produce secondary toxic metabolites that enhance the mortality of these mosquito larvae.
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creator: Mariana B. Ávila-López
creator: José Q. García-Maldonado
creator: Héctor Estrada-Medina
creator: David I. Hernández-Mena
creator: Daniel Cerqueda-García
creator: Víctor M. Vidal-Martínez
subject: Entomology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.11633
publisher: PeerJ Inc.
rights: © 2021 Ávila-López et al.
abstract: Background Biological control using entomopathogenic nematodes (EPN) has demonstrated good potential to contribute to the integral control of mosquito larvae, which as adults are vectors of diseases such as Dengue fever, Zika and Chikungunya. However, until now there are no records of the presence of EPN or their killing capacity in Yucatán state, southern México. The objectives of the current study were: (1) to report the entomopathogenic nematodes present in Yucatán soils and (2) to determine the killing capacity of the most frequent and abundant EPN against Aedes aegypti mosquito larvae and the microbial community developed by Ae. Aegypti exposed to this EPN. Methods The nematodes were collected by the insect trap technique using the great wax moth Galleria mellonella. Internal transcribed spacer (ITS), 28S gene of ribosomal DNA and phylogenetic analyses were performed to identify the EPN. For the bioassay, four concentrations of the most frequent and abundant EPN were tested: 1,260:1 infective juveniles (IJs) per mosquito larvae, 2,520 IJs:1, 3,780 IJs:1 and 5,040 IJs:1. High-throughput sequencing of the 16S rRNA gene was used to identify bacterial amplicon sequences in the mosquito larvae infected with EPN. Results Six isolates of Heterorhabditis were recovered from 144 soil samples. Heterorhabditis indica (four isolates) was the most frequent and abundant EPN, followed by Heterorhabditis n. sp. (two isolates). Both nematodes are reported for the first time for Yucatán state, Mexico. The concentration of 2,520 IJs:1 produced 80% of mosquito larvae mortality in 48 h. Representative members of Photorhabdus genus were numerically dominant (74%) in mosquito larvae infected by H. indica. It is most likely that these bacteria produce secondary toxic metabolites that enhance the mortality of these mosquito larvae.
bibliographic citation: Ávila-López et al. (2021) First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti. PeerJ 9:e11633 https://doi.org/10.7717/peerj.11633
date submitted: 2021-03-19
date accepted: 2021-05-27
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ávila-López
  given name: Mariana B.
author list: Agent
  family name: García-Maldonado
  given name: José Q.
author list: Agent
  family name: Estrada-Medina
  given name: Héctor
author list: Agent
  family name: Hernández-Mena
  given name: David I.
author list: Agent
  family name: Cerqueda-García
  given name: Daniel
author list: Agent
  family name: Vidal-Martínez
  given name: Víctor M.
doi: 10.7717/peerj.11633
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: © 2021 Ávila-López et al.
attribution name: Ávila-López et al.

Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case
type: item
type: AcademicArticle
description: This paper presents the impact of the choice of building representation techniques and hydrodynamic models on urban flood simulations using HEC-RAS 2-D for the Toce River physical model. To this end, eight numerical models based on previous laboratory experiments were prepared to simulate unsteady urban flooding on each side of building units. Two simplified building layouts (aligned and staggered) were examined, where models were prepared for two different building representation techniques: Building Block (BB) and Building Resistance (BR). Water depth variation computations using the BR and BB techniques were compared to the laboratory measurements and previous studies in the literature. A statistical analysis was performed using both the Root Mean Square Error (RMSE) and the Pearson Product-Moment Correlation Coefficient (PPMCC) in order to evaluate the performance of the models. A sensitivity analysis showed that the proper mesh resolution and model parameter values were obtained. As far as the BR technique is concerned, it is well-suited for representing building units in numerical simulations using high Manning coefficients. Furthermore, this study confirms the importance of the BR technique, which should help researchers in using low-resolution Digital Elevation Models (DEMs) along with open-source programs. Moreover, the study aims to produce a deeper comprehension of numerical modeling and urban flooding.
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creator: Andam Mustafa
creator: Michał Szydłowski
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.11667
publisher: PeerJ Inc.
rights: © 2021 Mustafa and Szydłowski
abstract: This paper presents the impact of the choice of building representation techniques and hydrodynamic models on urban flood simulations using HEC-RAS 2-D for the Toce River physical model. To this end, eight numerical models based on previous laboratory experiments were prepared to simulate unsteady urban flooding on each side of building units. Two simplified building layouts (aligned and staggered) were examined, where models were prepared for two different building representation techniques: Building Block (BB) and Building Resistance (BR). Water depth variation computations using the BR and BB techniques were compared to the laboratory measurements and previous studies in the literature. A statistical analysis was performed using both the Root Mean Square Error (RMSE) and the Pearson Product-Moment Correlation Coefficient (PPMCC) in order to evaluate the performance of the models. A sensitivity analysis showed that the proper mesh resolution and model parameter values were obtained. As far as the BR technique is concerned, it is well-suited for representing building units in numerical simulations using high Manning coefficients. Furthermore, this study confirms the importance of the BR technique, which should help researchers in using low-resolution Digital Elevation Models (DEMs) along with open-source programs. Moreover, the study aims to produce a deeper comprehension of numerical modeling and urban flooding.
bibliographic citation: Mustafa et al. (2021) Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case. PeerJ 9:e11667 https://doi.org/10.7717/peerj.11667
date submitted: 2020-10-15
date accepted: 2021-06-02
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mustafa
  given name: Andam
author list: Agent
  family name: Szydłowski
  given name: Michał
doi: 10.7717/peerj.11667
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: © 2021 Mustafa and Szydłowski
attribution name: Mustafa and Szydłowski

Confidence intervals for the difference between the coefficients of variation of Weibull distributions for analyzing wind speed dispersion
type: item
type: AcademicArticle
description: Wind energy is an important renewable energy source for generating electricity that has the potential to replace fossil fuels. Herein, we propose confidence intervals for the difference between the coefficients of variation of Weibull distributions constructed using the concepts of the generalized confidence interval (GCI), Bayesian methods, the method of variance estimates recovery (MOVER) based on Hendricks and Robey’s confidence interval, a percentile bootstrap method, and a bootstrap method with standard errors. To analyze their performances, their coverage probabilities and expected lengths were evaluated via Monte Carlo simulation. The simulation results indicate that the coverage probabilities of GCI were greater than or sometimes close to the nominal confidence level. However, when the Weibull shape parameter was small, the Bayesian- highest posterior density interval was preferable. All of the proposed confidence intervals were applied to wind speed data measured at 90-meter wind energy potential stations at various regions in Thailand.
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creator: Manussaya La-ongkaew
creator: Sa-Aat Niwitpong
creator: Suparat Niwitpong
subject: Statistics
subject: Natural Resource Management
subject: Atmospheric Chemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.11676
publisher: PeerJ Inc.
rights: © 2021 La-ongkaew et al.
abstract: Wind energy is an important renewable energy source for generating electricity that has the potential to replace fossil fuels. Herein, we propose confidence intervals for the difference between the coefficients of variation of Weibull distributions constructed using the concepts of the generalized confidence interval (GCI), Bayesian methods, the method of variance estimates recovery (MOVER) based on Hendricks and Robey’s confidence interval, a percentile bootstrap method, and a bootstrap method with standard errors. To analyze their performances, their coverage probabilities and expected lengths were evaluated via Monte Carlo simulation. The simulation results indicate that the coverage probabilities of GCI were greater than or sometimes close to the nominal confidence level. However, when the Weibull shape parameter was small, the Bayesian- highest posterior density interval was preferable. All of the proposed confidence intervals were applied to wind speed data measured at 90-meter wind energy potential stations at various regions in Thailand.
bibliographic citation: La-ongkaew et al. (2021) Confidence intervals for the difference between the coefficients of variation of Weibull distributions for analyzing wind speed dispersion. PeerJ 9:e11676 https://doi.org/10.7717/peerj.11676
date submitted: 2021-03-03
date accepted: 2021-06-04
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: La-ongkaew
  given name: Manussaya
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
author list: Agent
  family name: Niwitpong
  given name: Suparat
doi: 10.7717/peerj.11676
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: ©2021 La-ongkaew et al.
attribution name: La-ongkaew et al.

CGRP overexpression does not alter depression-like behavior in mice
type: item
type: AcademicArticle
description: Background The calcitonin gene-related peptide (CGRP) is a neuropeptide that is released from capsaicin-sensitive nerves as a potent vasodilator involved in nociceptive transmission. While CGRP has been rigorously studied for its role in migraines owing to its vasodilation and inflammation activities, the effects of CGRP overexpression on depressive-like behaviors remain insufficiently understood. Methods In the present study, we performed a battery of behavioral tests, including the social interaction test, open field test, and sucrose preference test, to evaluate social defeat stress using male C57BL6J or CGRP overexpression in transgenic (Tg) mice (CGRP Tg). We performed mRNA and protein analyses on the brain-derived neurotrophic factor (BDNF), phosphorylated Akt, mTOR, and p70S6K in the hippocampi. Results CGRP Tg mice showed increased levels of Bdnf mRNAs, low locomotor activity, and no deficits in social interaction, which indicate that CGRP Tg mice exhibit stress resistance and not depression. However, the open field test significantly decreased after 15-day social defeat stress exposure. We also evaluated depressive-like behavior using the sucrose preference and social interaction tests. Our data indicate that defeated CGRP Tg mice exhibited a depressive-like phenotype, which was inferred from increased social avoidance and reduced sucrose preference compared with non-defeated controls. Although stress exposure did not change the BDNF levels in CGRP Tg mice, it significantly decreased the expression levels of p-Akt, p-mTOR and p-p70S6K in the mice hippocampi. We conclude that CGRP-overexpressing Tg mice have normal sensitivity to stress and down-regulated hippocampal Akt/mTOR/p70S6K pathways.
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creator: Narumi Hashikawa-Hobara
creator: Ami Otsuka
creator: Chihiro Okujima
creator: Naoya Hashikawa
subject: Animal Behavior
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.11720
publisher: PeerJ Inc.
rights: © 2021 Hashikawa-Hobara et al.
abstract: Background The calcitonin gene-related peptide (CGRP) is a neuropeptide that is released from capsaicin-sensitive nerves as a potent vasodilator involved in nociceptive transmission. While CGRP has been rigorously studied for its role in migraines owing to its vasodilation and inflammation activities, the effects of CGRP overexpression on depressive-like behaviors remain insufficiently understood. Methods In the present study, we performed a battery of behavioral tests, including the social interaction test, open field test, and sucrose preference test, to evaluate social defeat stress using male C57BL6J or CGRP overexpression in transgenic (Tg) mice (CGRP Tg). We performed mRNA and protein analyses on the brain-derived neurotrophic factor (BDNF), phosphorylated Akt, mTOR, and p70S6K in the hippocampi. Results CGRP Tg mice showed increased levels of Bdnf mRNAs, low locomotor activity, and no deficits in social interaction, which indicate that CGRP Tg mice exhibit stress resistance and not depression. However, the open field test significantly decreased after 15-day social defeat stress exposure. We also evaluated depressive-like behavior using the sucrose preference and social interaction tests. Our data indicate that defeated CGRP Tg mice exhibited a depressive-like phenotype, which was inferred from increased social avoidance and reduced sucrose preference compared with non-defeated controls. Although stress exposure did not change the BDNF levels in CGRP Tg mice, it significantly decreased the expression levels of p-Akt, p-mTOR and p-p70S6K in the mice hippocampi. We conclude that CGRP-overexpressing Tg mice have normal sensitivity to stress and down-regulated hippocampal Akt/mTOR/p70S6K pathways.
bibliographic citation: Hashikawa-Hobara et al. (2021) CGRP overexpression does not alter depression-like behavior in mice. PeerJ 9:e11720 https://doi.org/10.7717/peerj.11720
date submitted: 2021-04-14
date accepted: 2021-06-13
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hashikawa-Hobara
  given name: Narumi
author list: Agent
  family name: Otsuka
  given name: Ami
author list: Agent
  family name: Okujima
  given name: Chihiro
author list: Agent
  family name: Hashikawa
  given name: Naoya
doi: 10.7717/peerj.11720
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: © 2021 Hashikawa-Hobara et al.
attribution name: Hashikawa-Hobara et al.

Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels
type: item
type: AcademicArticle
description: Background Tracheal wash (TW) and bronchoalveolar lavage (BAL) have proven to be useful tools for the identification of disease-associated changes in the respiratory tract in human and different animal species. In the dromedary camel, little is known about cytological analysis of TW and BAL in health and disease. The aim of the present study was to evaluate the cytological composition of TW and BAL in health and respiratory disease in dromedary camels. Methods TW and BAL samples were collected from dromedary camels and cytological analysis was performed by microscopic examination of prepared smears. Camels with clinical respiratory disease (n = 18) were compared with apparently healthy (control) camels (n = 9). Results In the apparently healthy camels, differential cytological analysis of TW samples identified macrophages and neutrophils as the main cell populations with lesser proportions of lymphocytes and epithelial cells and very rare abundance of eosinophils and mast cells. In the TW of camels with respiratory disease, neutrophils were the most abundant cells followed by macrophages and lymphocytes. In the BAL of healthy camels, macrophages represented the main cell type followed by lymphocytes and neutrophils. In respiratory-diseased camels, BAL samples contained higher percentages of neutrophils with reduced percentages of macrophages and lymphocytes in comparison to camels from the control group. Collectively, the results of the current study revealed higher abundance of neutrophils in the TW and BAL from dromedary camels than many other veterinary species. The cytological patterns of TW and BAL from camels with respiratory diseases were characterized by increased proportion of neutrophils and decreased proportion of macrophages in comparison to healthy camels. The proportion of lymphocytes was also decreased in TW samples from diseased camels.
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creator: Turke Shawaf
creator: Abdullah Almubarak
creator: Naser Alhumam
creator: Faisal Almathen
creator: Jamal Hussen
subject: Veterinary Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.11723
publisher: PeerJ Inc.
rights: © 2021 Shawaf et al.
abstract: Background Tracheal wash (TW) and bronchoalveolar lavage (BAL) have proven to be useful tools for the identification of disease-associated changes in the respiratory tract in human and different animal species. In the dromedary camel, little is known about cytological analysis of TW and BAL in health and disease. The aim of the present study was to evaluate the cytological composition of TW and BAL in health and respiratory disease in dromedary camels. Methods TW and BAL samples were collected from dromedary camels and cytological analysis was performed by microscopic examination of prepared smears. Camels with clinical respiratory disease (n = 18) were compared with apparently healthy (control) camels (n = 9). Results In the apparently healthy camels, differential cytological analysis of TW samples identified macrophages and neutrophils as the main cell populations with lesser proportions of lymphocytes and epithelial cells and very rare abundance of eosinophils and mast cells. In the TW of camels with respiratory disease, neutrophils were the most abundant cells followed by macrophages and lymphocytes. In the BAL of healthy camels, macrophages represented the main cell type followed by lymphocytes and neutrophils. In respiratory-diseased camels, BAL samples contained higher percentages of neutrophils with reduced percentages of macrophages and lymphocytes in comparison to camels from the control group. Collectively, the results of the current study revealed higher abundance of neutrophils in the TW and BAL from dromedary camels than many other veterinary species. The cytological patterns of TW and BAL from camels with respiratory diseases were characterized by increased proportion of neutrophils and decreased proportion of macrophages in comparison to healthy camels. The proportion of lymphocytes was also decreased in TW samples from diseased camels.
bibliographic citation: Shawaf et al. (2021) Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels. PeerJ 9:e11723 https://doi.org/10.7717/peerj.11723
date submitted: 2020-11-11
date accepted: 2021-06-14
issued: 2021-07-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shawaf
  given name: Turke
author list: Agent
  family name: Almubarak
  given name: Abdullah
author list: Agent
  family name: Alhumam
  given name: Naser
author list: Agent
  family name: Almathen
  given name: Faisal
author list: Agent
  family name: Hussen
  given name: Jamal
doi: 10.7717/peerj.11723
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-02
copyright: ©2021 Shawaf et al.
attribution name: Shawaf et al.

https://peerj.com/articles/11465
type: item
type: AcademicArticle
title: Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage
description: Background The borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC. Results Gas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR. Conclusion This study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC.
format: application/pdf
format: text/html
creator: Zerui Yang
creator: Chunzhu Xie
creator: Yuying Huang
creator: Wenli An
creator: Shanshan Liu
creator: Song Huang
creator: Xiasheng Zheng
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11465
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background The borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC. Results Gas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR. Conclusion This study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC.
bibliographic citation: Yang et al. (2021) Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage. PeerJ 9:e11465 https://doi.org/10.7717/peerj.11465
date submitted: 2020-09-22
date accepted: 2021-04-26
issued: 2021-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zerui
author list: Agent
  family name: Xie
  given name: Chunzhu
author list: Agent
  family name: Huang
  given name: Yuying
author list: Agent
  family name: An
  given name: Wenli
author list: Agent
  family name: Liu
  given name: Shanshan
author list: Agent
  family name: Huang
  given name: Song
author list: Agent
  family name: Zheng
  given name: Xiasheng
doi: 10.7717/peerj.11465
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-01
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Dumpster diving for diatom plastid 16S rRNA genes
type: item
type: AcademicArticle
description: High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach an…
format: application/pdf
format: text/html
creator: Krista L. Bonfantine
creator: Stacey M. Trevathan-Tackett
creator: Ty G. Matthews
creator: Ana Neckovic
creator: Han Ming Gan
subject: Bioinformatics
subject: Ecology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.11576
publisher: PeerJ Inc.
rights: © 2021 Bonfantine et al.
abstract: High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach an…
bibliographic citation: Bonfantine et al. (2021) Dumpster diving for diatom plastid 16S rRNA genes. PeerJ 9:e11576 https://doi.org/10.7717/peerj.11576
date submitted: 2020-09-15
date accepted: 2021-05-18
issued: 2021-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bonfantine
  given name: Krista L.
author list: Agent
  family name: Trevathan-Tackett
  given name: Stacey M.
author list: Agent
  family name: Matthews
  given name: Ty G.
author list: Agent
  family name: Neckovic
  given name: Ana
author list: Agent
  family name: Gan
  given name: Han Ming
doi: 10.7717/peerj.11576
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-01
copyright: ©2021 Bonfantine et al.
attribution name: Bonfantine et al.

Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it
type: item
type: AcademicArticle
description: Background Hypopharyngeal cancer accounts for 2% in head and neck cancers and has a poor prognosis. Cisplatin is a widely used chemotherapeutic drug in kinds of carcinomas, concluding hypopharyngeal cancer. However, the resistance of cisplatin appeared in recent years. Cisplatin-resistance has been partly explored before, but rarely in hypopharyngeal cancer. Methods We cultured the hypopharyngeal cancer cell (FaDu) and induced its cisplatin-resistant cell (FaDu/DDP4). Then we tested the differentially expressed genes (DEGs) between FaDu and FaDu/DDP4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on the DEGs, and we drew the ceRNA networks of DEGs. Finally, we chose eight miRNAs and six mRNAs for qRT-PCR to verify our microarray. Results We induced cisplatin-resistant FaDu/DDP4 and proved its chemoresistance. The resistance index (RI) of FaDu/DDP4 was 2.828. DEGs contain 2,388 lncRNAs, 1,932 circRNAs, 745 mRNAs and 202 miRNAs. These 745 mRNAs were classified into three domains and 47 secondary GO terms. In KEGG pathway enrichment, the “TNF signaling pathway”, “IL-17 signaling pathway” and “JAK-STAT signaling pathway” were potentially significant signaling pathways. Then, 52 lncRNAs, 148 circRNAs, 155 mRNAs and 18 miRNAs were selected to draw the network. We noticed several potential targets (as miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1). At last, the eight miRNAs and six mRNAs that are critical RNAs in ceRNA network were verified by qRT-PCR. Conclusion The microarray helped to find DEGs in cisplatin-resistant hypopharyngeal cancer. TNF, IL-17 and JAK-STAT signaling pathways might be more significant for cisplatin-resistance. MiR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1 might be potential genes inducing resistance.
format: application/pdf
format: text/html
creator: Gehou Zhang
creator: Guolin Tan
creator: Tieqi Li
creator: Jingang Ai
creator: Yexun Song
creator: Zheng Zhou
creator: Jian Xiao
creator: Wei Li
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.11645
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background Hypopharyngeal cancer accounts for 2% in head and neck cancers and has a poor prognosis. Cisplatin is a widely used chemotherapeutic drug in kinds of carcinomas, concluding hypopharyngeal cancer. However, the resistance of cisplatin appeared in recent years. Cisplatin-resistance has been partly explored before, but rarely in hypopharyngeal cancer. Methods We cultured the hypopharyngeal cancer cell (FaDu) and induced its cisplatin-resistant cell (FaDu/DDP4). Then we tested the differentially expressed genes (DEGs) between FaDu and FaDu/DDP4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on the DEGs, and we drew the ceRNA networks of DEGs. Finally, we chose eight miRNAs and six mRNAs for qRT-PCR to verify our microarray. Results We induced cisplatin-resistant FaDu/DDP4 and proved its chemoresistance. The resistance index (RI) of FaDu/DDP4 was 2.828. DEGs contain 2,388 lncRNAs, 1,932 circRNAs, 745 mRNAs and 202 miRNAs. These 745 mRNAs were classified into three domains and 47 secondary GO terms. In KEGG pathway enrichment, the “TNF signaling pathway”, “IL-17 signaling pathway” and “JAK-STAT signaling pathway” were potentially significant signaling pathways. Then, 52 lncRNAs, 148 circRNAs, 155 mRNAs and 18 miRNAs were selected to draw the network. We noticed several potential targets (as miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1). At last, the eight miRNAs and six mRNAs that are critical RNAs in ceRNA network were verified by qRT-PCR. Conclusion The microarray helped to find DEGs in cisplatin-resistant hypopharyngeal cancer. TNF, IL-17 and JAK-STAT signaling pathways might be more significant for cisplatin-resistance. MiR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1 might be potential genes inducing resistance.
bibliographic citation: Zhang et al. (2021) Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it. PeerJ 9:e11645 https://doi.org/10.7717/peerj.11645
date submitted: 2021-02-24
date accepted: 2021-05-29
issued: 2021-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Gehou
author list: Agent
  family name: Tan
  given name: Guolin
author list: Agent
  family name: Li
  given name: Tieqi
author list: Agent
  family name: Ai
  given name: Jingang
author list: Agent
  family name: Song
  given name: Yexun
author list: Agent
  family name: Zhou
  given name: Zheng
author list: Agent
  family name: Xiao
  given name: Jian
author list: Agent
  family name: Li
  given name: Wei
doi: 10.7717/peerj.11645
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-01
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

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