PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multiple comparisons of precipitation variations in different areas using simultaneous confidence intervals for all possible ratios of variances of several zero-inflated lognormal models
items: miR-15a-5p regulates myocardial fibrosis in atrial fibrillation by targeting Smad7
items: Light intensity drives different growth strategies in two duckweed species: Lemna minor L. and Spirodela polyrhiza (L.) Schleiden
items: Palatal mucosa thickness and palatal neurovascular bundle position evaluation by cone-beam computed tomography—retrospective study on relationships with palatal vault anatomy
items: Methodological recommendations for assessing scleractinian and octocoral recruitment to settlement tiles
items: Inhibition of LINK-A lncRNA overcomes ibrutinib resistance in mantle cell lymphoma by regulating Akt/Bcl2 pathway
items: Characterizing the Type 6 Secretion System (T6SS) and its role in the virulence of avian pathogenic Escherichia coli strain APECO18
items: Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets
items: Novel visual analytics approach for chromosome territory analysis
items: Quantifying the association of natal household wealth with women’s early marriage in Nepal

Multiple comparisons of precipitation variations in different areas using simultaneous confidence intervals for all possible ratios of variances of several zero-inflated lognormal models
type: item
type: AcademicArticle
description: Flash flooding and landslides regularly cause injury, death, and homelessness in Thailand. An advancedwarning system is necessary for predicting natural disasters, and analyzing the variability of daily precipitation might be usable in this regard. Moreover, analyzing the differences in precipitation data among multiple weather stations could be used to predict variations in meteorological conditions throughout the country. Since precipitation data in Thailand follow a zero-inflated lognormal (ZILN) distribution, multiple comparisons of precipitation variation in different areas can be addressed by using simultaneous confidence intervals (SCIs) for all possible pairwise ratios of variances of several ZILN models. Herein, we formulate SCIs using Bayesian, generalized pivotal quantity (GPQ), and parametric bootstrap (PB) approaches. The results of a simulation study provide insight into the performances of the SCIs. Those based on PB and the Bayesian approach via probability matching with the beta prior performed well in situations with a large amount of zero-inflated data with a large variance. Besides, the Bayesian based on the reference-beta prior and GPQ SCIs can be considered as alternative approaches for small-to-large and medium-to-large sample sizes from large population, respectively. These approaches were applied to estimate the precipitation variability among weather stations in lower southern Thailand to illustrate their efficacies.
format: application/pdf
format: text/html
creator: Patcharee Maneerat
creator: Sa-Aat Niwitpong
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.12659
publisher: PeerJ Inc.
rights: © 2021 Maneerat and Niwitpong
abstract: Flash flooding and landslides regularly cause injury, death, and homelessness in Thailand. An advancedwarning system is necessary for predicting natural disasters, and analyzing the variability of daily precipitation might be usable in this regard. Moreover, analyzing the differences in precipitation data among multiple weather stations could be used to predict variations in meteorological conditions throughout the country. Since precipitation data in Thailand follow a zero-inflated lognormal (ZILN) distribution, multiple comparisons of precipitation variation in different areas can be addressed by using simultaneous confidence intervals (SCIs) for all possible pairwise ratios of variances of several ZILN models. Herein, we formulate SCIs using Bayesian, generalized pivotal quantity (GPQ), and parametric bootstrap (PB) approaches. The results of a simulation study provide insight into the performances of the SCIs. Those based on PB and the Bayesian approach via probability matching with the beta prior performed well in situations with a large amount of zero-inflated data with a large variance. Besides, the Bayesian based on the reference-beta prior and GPQ SCIs can be considered as alternative approaches for small-to-large and medium-to-large sample sizes from large population, respectively. These approaches were applied to estimate the precipitation variability among weather stations in lower southern Thailand to illustrate their efficacies.
bibliographic citation: Maneerat et al. (2021) Multiple comparisons of precipitation variations in different areas using simultaneous confidence intervals for all possible ratios of variances of several zero-inflated lognormal models. PeerJ 9:e12659 https://doi.org/10.7717/peerj.12659
date submitted: 2021-10-07
date accepted: 2021-11-30
issued: 2021-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maneerat
  given name: Patcharee
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
doi: 10.7717/peerj.12659
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-20
copyright: ©2021 Maneerat and Niwitpong
attribution name: Maneerat and Niwitpong

miR-15a-5p regulates myocardial fibrosis in atrial fibrillation by targeting Smad7
type: item
type: AcademicArticle
description: Background At present, there is no effective treatment for myocardial fibrosis in atrial fibrillation (AF). It is reported that miR-15a-5p is abnormally expressed in AF patients but its specific role remains unclear. This study aims to investigate the effect of miR-15a-5p in myocardial fibrosis. Methods Left atrial appendage (LAA) tissues were collected from AF and non-AF patients. In lipopolysaccharide (LPS) stimulated H9C2 cells, miR-15a-5p mimic, inhibitor, pcDNA3.1-Smad7 and small interfering RNA-Smad7 (siRNA-Smad7) were respectively transfected to up-regulate or down-regulate the intracellular expression levels of miR-15a-5p and Smad7. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) were used to determine the expression levels of miR-15a-5p, Smad7, transforming growth factor β1 (TGF-β1) and collagen I. Cell counting kit-8 (CCK-8) and ethylene deoxyuridine (EdU) were used to determine cell viability and proliferation capacity, respectively. Dual-luciferase was used to detect whether miR-15a-5p interacted with Smad7, hydroxyproline (HYP) and Hematoxylin-Eosin (HE) staining were used to detect tissue fibrosis. Results The expression levels of miR-15a-5p, TGF-β1 and collagen I were up-regulated, while Smad7 was down-regulated in AF tissues and LPS-stimulated cells. MiR-15a-5p mimic can inhibit the expression of Smad7, and the dual-luciferase experiment confirmed their interaction. MiR-15a-5p inhibitor or pcDNA3.1-Smad7 can inhibit LPS-induced fibrosis and cell proliferation, while siRNA-Smad7 can reverse the changes caused by miR-15a-5p inhibitor. Conclusion We combined clinical studies with LPS-stimulated H9C2 cell model to validate the role of miR-15a-5p in the regulation of Smad7 and fibrosis. Taken together, the miR-15a-5p/Smad7 pathway might be a potential target for AF therapy.
format: application/pdf
format: text/html
creator: Dan He
creator: Zhong-bao Ruan
creator: Gui-xian Song
creator: Ge-cai Chen
creator: Fei Wang
creator: Mei-xiang Wang
creator: Mao-kun Yuan
creator: Li Zhu
subject: Biochemistry
subject: Cell Biology
subject: Genomics
description: doi:10.7717/peerj.12686
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: Background At present, there is no effective treatment for myocardial fibrosis in atrial fibrillation (AF). It is reported that miR-15a-5p is abnormally expressed in AF patients but its specific role remains unclear. This study aims to investigate the effect of miR-15a-5p in myocardial fibrosis. Methods Left atrial appendage (LAA) tissues were collected from AF and non-AF patients. In lipopolysaccharide (LPS) stimulated H9C2 cells, miR-15a-5p mimic, inhibitor, pcDNA3.1-Smad7 and small interfering RNA-Smad7 (siRNA-Smad7) were respectively transfected to up-regulate or down-regulate the intracellular expression levels of miR-15a-5p and Smad7. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) were used to determine the expression levels of miR-15a-5p, Smad7, transforming growth factor β1 (TGF-β1) and collagen I. Cell counting kit-8 (CCK-8) and ethylene deoxyuridine (EdU) were used to determine cell viability and proliferation capacity, respectively. Dual-luciferase was used to detect whether miR-15a-5p interacted with Smad7, hydroxyproline (HYP) and Hematoxylin-Eosin (HE) staining were used to detect tissue fibrosis. Results The expression levels of miR-15a-5p, TGF-β1 and collagen I were up-regulated, while Smad7 was down-regulated in AF tissues and LPS-stimulated cells. MiR-15a-5p mimic can inhibit the expression of Smad7, and the dual-luciferase experiment confirmed their interaction. MiR-15a-5p inhibitor or pcDNA3.1-Smad7 can inhibit LPS-induced fibrosis and cell proliferation, while siRNA-Smad7 can reverse the changes caused by miR-15a-5p inhibitor. Conclusion We combined clinical studies with LPS-stimulated H9C2 cell model to validate the role of miR-15a-5p in the regulation of Smad7 and fibrosis. Taken together, the miR-15a-5p/Smad7 pathway might be a potential target for AF therapy.
bibliographic citation: He et al. (2021) miR-15a-5p regulates myocardial fibrosis in atrial fibrillation by targeting Smad7. PeerJ 9:e12686 https://doi.org/10.7717/peerj.12686
date submitted: 2021-08-23
date accepted: 2021-12-03
issued: 2021-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Dan
author list: Agent
  family name: Ruan
  given name: Zhong-bao
author list: Agent
  family name: Song
  given name: Gui-xian
author list: Agent
  family name: Chen
  given name: Ge-cai
author list: Agent
  family name: Wang
  given name: Fei
author list: Agent
  family name: Wang
  given name: Mei-xiang
author list: Agent
  family name: Yuan
  given name: Mao-kun
author list: Agent
  family name: Zhu
  given name: Li
doi: 10.7717/peerj.12686
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-20
copyright: ©2021 He et al.
attribution name: He et al.

Light intensity drives different growth strategies in two duckweed species: Lemna minor L. and Spirodela polyrhiza (L.) Schleiden
type: item
type: AcademicArticle
description: Duckweed species Lemna minor and Spirodela polyrhiza are clonal plants with vegetative organs reduced to a frond and a root in L. minor or a frond and several roots in S. polyrhiza. They reproduce vegetatively by relatively rapid multiplication of their fronds. The habit of S. polyrhiza (large fronds with up to 21 roots) makes it a strong competitor among representatives of the family Lemnaceae, probably due to different resource-use strategies compared to small duckweed. In our study, light was the resource that affected the plants before and during the laboratory experiment. We sampled the plants from natural habitats differing in light conditions (open and shady) and grew them for 16 days in a thermostatic growth room at 22 °C under a 16:8 photoperiod and three light intensities (125, 236, 459 µmol photons m–2 s–1) to investigate the trade-off between frond enlargement and multiplication. Both species from the open habitat had higher growth rates based on the frond numbers and on surface area of fronds compared to plants from the shady habitat. They adopted different species-specific strategies in response to the experimental light conditions. The species size affected the growth rates in L. minor and S. polyrhiza. Spirodela polyrhiza grew slower than L. minor, but both species grew fastest at medium light intensity (236 µmol m–2 s–1). Lemna minor maintained the growth rates at high light intensity, while S. polyrhiza slowed down. Spirodela polyrhiza responded to deteriorating light conditions by increasing its frond surface area, thus optimising light capture. Lemna minor from the shady habitat enhanced light harvest by increasing chlorophyll a concentration, but did not invest more in frond enlargement than L. minor from the open habitat. Under shady conditions, S. polyrhiza is likely to achieve an advantage over L. minor due to the larger frond size of the former. Our findings suggest the existence of a trade-off between size and number in duckweed.
format: application/pdf
format: text/html
creator: Małgorzata Strzałek
creator: Lech Kufel
subject: Ecology
subject: Plant Science
subject: Freshwater Biology
description: doi:10.7717/peerj.12698
publisher: PeerJ Inc.
rights: © 2021 Strzałek et al.
abstract: Duckweed species Lemna minor and Spirodela polyrhiza are clonal plants with vegetative organs reduced to a frond and a root in L. minor or a frond and several roots in S. polyrhiza. They reproduce vegetatively by relatively rapid multiplication of their fronds. The habit of S. polyrhiza (large fronds with up to 21 roots) makes it a strong competitor among representatives of the family Lemnaceae, probably due to different resource-use strategies compared to small duckweed. In our study, light was the resource that affected the plants before and during the laboratory experiment. We sampled the plants from natural habitats differing in light conditions (open and shady) and grew them for 16 days in a thermostatic growth room at 22 °C under a 16:8 photoperiod and three light intensities (125, 236, 459 µmol photons m–2 s–1) to investigate the trade-off between frond enlargement and multiplication. Both species from the open habitat had higher growth rates based on the frond numbers and on surface area of fronds compared to plants from the shady habitat. They adopted different species-specific strategies in response to the experimental light conditions. The species size affected the growth rates in L. minor and S. polyrhiza. Spirodela polyrhiza grew slower than L. minor, but both species grew fastest at medium light intensity (236 µmol m–2 s–1). Lemna minor maintained the growth rates at high light intensity, while S. polyrhiza slowed down. Spirodela polyrhiza responded to deteriorating light conditions by increasing its frond surface area, thus optimising light capture. Lemna minor from the shady habitat enhanced light harvest by increasing chlorophyll a concentration, but did not invest more in frond enlargement than L. minor from the open habitat. Under shady conditions, S. polyrhiza is likely to achieve an advantage over L. minor due to the larger frond size of the former. Our findings suggest the existence of a trade-off between size and number in duckweed.
bibliographic citation: Strzałek et al. (2021) Light intensity drives different growth strategies in two duckweed species: Lemna minor L. and Spirodela polyrhiza (L.) Schleiden. PeerJ 9:e12698 https://doi.org/10.7717/peerj.12698
date submitted: 2021-08-31
date accepted: 2021-12-06
issued: 2021-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strzałek
  given name: Małgorzata
author list: Agent
  family name: Kufel
  given name: Lech
doi: 10.7717/peerj.12698
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-20
copyright: ©2021 Strzałek et al.
attribution name: Strzałek et al.

Palatal mucosa thickness and palatal neurovascular bundle position evaluation by cone-beam computed tomography—retrospective study on relationships with palatal vault anatomy
type: item
type: AcademicArticle
description: Background Measuring the thickness of the palatal mucosa at the planning of the surgical procedure is an important step in order to obtain the maximum width and thickness of the graft from the appropriate area. The aim of this study is to determine whether there is a relationship between palatal angle (PA) or palatal depth (PD) and palatal mucosa thickness (PMT) or palatal neurovascular bundle distance (PNBD). Methods PMT, PNBD, PD and PA were measured on cone-beam computed tomography (CBCT) images of maxillary posterior region of 200 male and 200 female patients. The mean of all parameters according to gender was compared and the significance of the difference detected between groups was evaluated. Potential relationship between PMT or PNBD and PA or PD was also evaluated. Results In females, the palatal mucosa was significantly thinner at all tooth regions (p < 0.005), and PNBD was lower only at the level of the second molar (p < 0.001). In addition, it was found that there was a significant inverse correlation between the palatal depth value and the palatal mucosal thickness, and palatal depth was correlated with the palatal neurovascular bundle distance (p ≤ 0.001). Discussion Consistent with previous studies, it was observed that the thickest mucosa in the palatal region was located in the region of the premolar teeth, and women had thinner palatal mucosa. In addition, in patients with a deeper palate vault, the palatal mucosa was thinner, but the palatal neurovascular bundle was more distant from the cemento-enamel junction.
format: application/pdf
format: text/html
creator: Ilkim Karadag
creator: Hasan Guney Yilmaz
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.12699
publisher: PeerJ Inc.
rights: © 2021 Karadag and Yilmaz
abstract: Background Measuring the thickness of the palatal mucosa at the planning of the surgical procedure is an important step in order to obtain the maximum width and thickness of the graft from the appropriate area. The aim of this study is to determine whether there is a relationship between palatal angle (PA) or palatal depth (PD) and palatal mucosa thickness (PMT) or palatal neurovascular bundle distance (PNBD). Methods PMT, PNBD, PD and PA were measured on cone-beam computed tomography (CBCT) images of maxillary posterior region of 200 male and 200 female patients. The mean of all parameters according to gender was compared and the significance of the difference detected between groups was evaluated. Potential relationship between PMT or PNBD and PA or PD was also evaluated. Results In females, the palatal mucosa was significantly thinner at all tooth regions (p < 0.005), and PNBD was lower only at the level of the second molar (p < 0.001). In addition, it was found that there was a significant inverse correlation between the palatal depth value and the palatal mucosal thickness, and palatal depth was correlated with the palatal neurovascular bundle distance (p ≤ 0.001). Discussion Consistent with previous studies, it was observed that the thickest mucosa in the palatal region was located in the region of the premolar teeth, and women had thinner palatal mucosa. In addition, in patients with a deeper palate vault, the palatal mucosa was thinner, but the palatal neurovascular bundle was more distant from the cemento-enamel junction.
bibliographic citation: Karadag et al. (2021) Palatal mucosa thickness and palatal neurovascular bundle position evaluation by cone-beam computed tomography—retrospective study on relationships with palatal vault anatomy. PeerJ 9:e12699 https://doi.org/10.7717/peerj.12699
date submitted: 2021-10-27
date accepted: 2021-12-06
issued: 2021-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karadag
  given name: Ilkim
author list: Agent
  family name: Yilmaz
  given name: Hasan Guney
doi: 10.7717/peerj.12699
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-20
copyright: ©2021 Karadag and Yilmaz
attribution name: Karadag and Yilmaz

Methodological recommendations for assessing scleractinian and octocoral recruitment to settlement tiles
type: item
type: AcademicArticle
description: Quantifying recruitment of corals is important for evaluating their capacity to recover after disturbances through natural processes, yet measuring recruitment rates in situ is challenging due to the minute size of the study organism and the complexity of benthic communities. Settlement tiles are widely used in studies of coral recruitment because they can be viewed under a microscope to enhance accuracy, but methodological choices such as the rugosity of tiles used and when and how to scan tiles for recruits post-collection may cause inconsistencies in measured recruitment rates. We deployed 2,880 tiles with matching rugosity on top and bottom surfaces to 30 sites along the Florida Reef Tract for year-long saturations during a three year study. We scanned the top and bottom surfaces of the same tiles for scleractinian recruits before (live scans) and after treating tiles with sodium hypochlorite (corallite scans). Recruit counts were higher in corallite than live scans, indicating that scleractinian recruitment rates should not be directly compared between studies using live scans and those scanning tiles which have been processed to remove fouling material. Recruit counts also were higher on tile tops in general, but the proportion of settlement to the top and bottom surfaces varied significantly by scleractinian family. Thus, biases may be introduced in recruitment datasets by differences in tile rugosity or by only scanning a subset of tile surfaces. Finally, we quantified octocoral recruitment during live scans and found they preferentially settled to tile tops. We recommend that recruitment tile studies include corallite scans for scleractinian skeletons, deploy tiles with matching rugosity on top and bottom surfaces, and scan all tile surfaces.
format: application/pdf
format: text/html
creator: Leah M. Harper
creator: Lindsay K. Huebner
creator: Elijah D. O’Cain
creator: Rob Ruzicka
creator: Daniel F. Gleason
creator: Nicole D. Fogarty
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12549
publisher: PeerJ Inc.
rights: © 2021 Harper et al.
abstract: Quantifying recruitment of corals is important for evaluating their capacity to recover after disturbances through natural processes, yet measuring recruitment rates in situ is challenging due to the minute size of the study organism and the complexity of benthic communities. Settlement tiles are widely used in studies of coral recruitment because they can be viewed under a microscope to enhance accuracy, but methodological choices such as the rugosity of tiles used and when and how to scan tiles for recruits post-collection may cause inconsistencies in measured recruitment rates. We deployed 2,880 tiles with matching rugosity on top and bottom surfaces to 30 sites along the Florida Reef Tract for year-long saturations during a three year study. We scanned the top and bottom surfaces of the same tiles for scleractinian recruits before (live scans) and after treating tiles with sodium hypochlorite (corallite scans). Recruit counts were higher in corallite than live scans, indicating that scleractinian recruitment rates should not be directly compared between studies using live scans and those scanning tiles which have been processed to remove fouling material. Recruit counts also were higher on tile tops in general, but the proportion of settlement to the top and bottom surfaces varied significantly by scleractinian family. Thus, biases may be introduced in recruitment datasets by differences in tile rugosity or by only scanning a subset of tile surfaces. Finally, we quantified octocoral recruitment during live scans and found they preferentially settled to tile tops. We recommend that recruitment tile studies include corallite scans for scleractinian skeletons, deploy tiles with matching rugosity on top and bottom surfaces, and scan all tile surfaces.
bibliographic citation: Harper et al. (2021) Methodological recommendations for assessing scleractinian and octocoral recruitment to settlement tiles. PeerJ 9:e12549 https://doi.org/10.7717/peerj.12549
date submitted: 2021-06-23
date accepted: 2021-11-04
issued: 2021-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harper
  given name: Leah M.
author list: Agent
  family name: Huebner
  given name: Lindsay K.
author list: Agent
  family name: O’Cain
  given name: Elijah D.
author list: Agent
  family name: Ruzicka
  given name: Rob
author list: Agent
  family name: Gleason
  given name: Daniel F.
author list: Agent
  family name: Fogarty
  given name: Nicole D.
doi: 10.7717/peerj.12549
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-17
copyright: ©2021 Harper et al.
attribution name: Harper et al.

Inhibition of LINK-A lncRNA overcomes ibrutinib resistance in mantle cell lymphoma by regulating Akt/Bcl2 pathway
type: item
type: AcademicArticle
description: Ibrutinib, a bruton tyrosine kinase (BTK) inhibitor which suppresses B-cell receptor signaling, has remarkably improved the outcome of patients with mantle cell lymphoma (MCL). However, approximately 33% of MCL patients have primary Ibrutinib resistance, and acquired Ibrutinib resistance is nearly universal. Long intergenic non-coding RNA for kinase activation (LINK-A) exerts oncogenic role in different types of tumors, but the role of LINK-A in intrinsic ibrutinib resistance in MCL is still unclear. Here, LINK-A expression level was first assessed using quantitative Real-time PCR (qPCR) and immunofluorescence analysis in five MCL cell lines. The effect of LINK-A on regulating MCL cells viability and apoptosis was assayed using CCK-8 and TdT-mediated dUTP nick end labeling (TUNEL) assay, respectively. The association of LINK-A with AKT activation and B cell lymphoma 2 (Bcl2)expression was evaluated using qPCR and western blot analysis. We found that LINK-A level was elevated in Ibrutinib-resistant MCL cell lines (Mino, REC-1, MAVER-1, and Granta-519) compared to Ibrutinib-sensitive MCL cell lines (Jeko-1). Functionally, LINK-A overexpression in Jeko-1 cells enhanced cell viability and repressed Ibrutinib-induced cell apoptosis. LINK-A knockdown in MAVER-1 cells decreased cell viability and further accelerated Ibrutinib-induced cell apoptosis. LINK-A overexpression enhanced Bcl2 expression in Jeko-1 cells, and Bcl2 inhibition blocked the effect of LINK-A on increasing cell viability in the presence of Ibrutinib. On the contrary, LINK-A knockdown reduced Bcl2 expression in MAVER-1 cells, and Bcl2 overexpression damaged the role of LINK-A inhibition in regulating cell viability. Mechanistically, LINK-A positively regulated the activation of AKT signaling, and inhibition of AKT signaling destroyed LINK-A-induced increased of Bcl2 and resulted in a subsequent suppression of cell viability. Taken together, the current results demonstrate that LINK-A inhibition overcomes I…
format: application/pdf
format: text/html
creator: Ye Zhang
creator: Peng Lu
creator: Yan Zhou
creator: Lifei Zhang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12571
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Ibrutinib, a bruton tyrosine kinase (BTK) inhibitor which suppresses B-cell receptor signaling, has remarkably improved the outcome of patients with mantle cell lymphoma (MCL). However, approximately 33% of MCL patients have primary Ibrutinib resistance, and acquired Ibrutinib resistance is nearly universal. Long intergenic non-coding RNA for kinase activation (LINK-A) exerts oncogenic role in different types of tumors, but the role of LINK-A in intrinsic ibrutinib resistance in MCL is still unclear. Here, LINK-A expression level was first assessed using quantitative Real-time PCR (qPCR) and immunofluorescence analysis in five MCL cell lines. The effect of LINK-A on regulating MCL cells viability and apoptosis was assayed using CCK-8 and TdT-mediated dUTP nick end labeling (TUNEL) assay, respectively. The association of LINK-A with AKT activation and B cell lymphoma 2 (Bcl2)expression was evaluated using qPCR and western blot analysis. We found that LINK-A level was elevated in Ibrutinib-resistant MCL cell lines (Mino, REC-1, MAVER-1, and Granta-519) compared to Ibrutinib-sensitive MCL cell lines (Jeko-1). Functionally, LINK-A overexpression in Jeko-1 cells enhanced cell viability and repressed Ibrutinib-induced cell apoptosis. LINK-A knockdown in MAVER-1 cells decreased cell viability and further accelerated Ibrutinib-induced cell apoptosis. LINK-A overexpression enhanced Bcl2 expression in Jeko-1 cells, and Bcl2 inhibition blocked the effect of LINK-A on increasing cell viability in the presence of Ibrutinib. On the contrary, LINK-A knockdown reduced Bcl2 expression in MAVER-1 cells, and Bcl2 overexpression damaged the role of LINK-A inhibition in regulating cell viability. Mechanistically, LINK-A positively regulated the activation of AKT signaling, and inhibition of AKT signaling destroyed LINK-A-induced increased of Bcl2 and resulted in a subsequent suppression of cell viability. Taken together, the current results demonstrate that LINK-A inhibition overcomes I…
bibliographic citation: Zhang et al. (2021) Inhibition of LINK-A lncRNA overcomes ibrutinib resistance in mantle cell lymphoma by regulating Akt/Bcl2 pathway. PeerJ 9:e12571 https://doi.org/10.7717/peerj.12571
date submitted: 2021-06-29
date accepted: 2021-11-08
issued: 2021-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ye
author list: Agent
  family name: Lu
  given name: Peng
author list: Agent
  family name: Zhou
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Lifei
doi: 10.7717/peerj.12571
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-17
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Characterizing the Type 6 Secretion System (T6SS) and its role in the virulence of avian pathogenic Escherichia coli strain APECO18
type: item
type: AcademicArticle
description: Avian pathogenic E. coli is the causative agent of extra-intestinal infections in birds known as colibacillosis, which can manifest as localized or systemic infections. The disease affects all stages of poultry production, resulting in economic losses that occur due to morbidity, carcass condemnation and increased mortality of the birds. APEC strains have a diverse virulence trait repertoire, which includes virulence factors involved in adherence to and invasion of the host cells, serum resistance factors, and toxins. However, the pathogenesis of APEC infections remains to be fully elucidated. The Type 6 secretion (T6SS) system has recently gained attention due to its role in the infection process and protection of bacteria from host defenses in human and animal pathogens. Previous work has shown that T6SS components are involved in the adherence to and invasion of host cells, as well as in the formation of biofilm, and intramacrophage bacterial replication. Here, we analyzed the frequency of T6SS genes hcp, impK, evpB, vasK and icmF in a collection of APEC strains and their potential role in virulence-associated phenotypes of APECO18. The T6SS genes were found to be significantly more prevalent in APEC than in fecal E. coli isolates from healthy birds. Expression of T6SS genes was analyzed in culture media and upon contact with host cells. Mutants were generated for hcp, impK, evpB, and icmF and characterized for their impact on virulence-associated phenotypes, including adherence to and invasion of host model cells, and resistance to predation by Dictyostelium discoideum. Deletion of the aforementioned genes did not significantly affect adherence and invasion capabilities of APECO18. Deletion of hcp reduced resistance of APECO18 to predation by D. discoideum, suggesting that T6SS is involved in the virulence of APECO18.
format: application/pdf
format: text/html
creator: Aline L. de Oliveira
creator: Nicolle L. Barbieri
creator: Darby M. Newman
creator: Meaghan M. Young
creator: Lisa K. Nolan
creator: Catherine M. Logue
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12631
publisher: PeerJ Inc.
rights: © 2021 de Oliveira et al.
abstract: Avian pathogenic E. coli is the causative agent of extra-intestinal infections in birds known as colibacillosis, which can manifest as localized or systemic infections. The disease affects all stages of poultry production, resulting in economic losses that occur due to morbidity, carcass condemnation and increased mortality of the birds. APEC strains have a diverse virulence trait repertoire, which includes virulence factors involved in adherence to and invasion of the host cells, serum resistance factors, and toxins. However, the pathogenesis of APEC infections remains to be fully elucidated. The Type 6 secretion (T6SS) system has recently gained attention due to its role in the infection process and protection of bacteria from host defenses in human and animal pathogens. Previous work has shown that T6SS components are involved in the adherence to and invasion of host cells, as well as in the formation of biofilm, and intramacrophage bacterial replication. Here, we analyzed the frequency of T6SS genes hcp, impK, evpB, vasK and icmF in a collection of APEC strains and their potential role in virulence-associated phenotypes of APECO18. The T6SS genes were found to be significantly more prevalent in APEC than in fecal E. coli isolates from healthy birds. Expression of T6SS genes was analyzed in culture media and upon contact with host cells. Mutants were generated for hcp, impK, evpB, and icmF and characterized for their impact on virulence-associated phenotypes, including adherence to and invasion of host model cells, and resistance to predation by Dictyostelium discoideum. Deletion of the aforementioned genes did not significantly affect adherence and invasion capabilities of APECO18. Deletion of hcp reduced resistance of APECO18 to predation by D. discoideum, suggesting that T6SS is involved in the virulence of APECO18.
bibliographic citation: de Oliveira et al. (2021) Characterizing the Type 6 Secretion System (T6SS) and its role in the virulence of avian pathogenic Escherichia coli strain APECO18. PeerJ 9:e12631 https://doi.org/10.7717/peerj.12631
date submitted: 2021-09-27
date accepted: 2021-11-22
issued: 2021-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Oliveira
  given name: Aline L.
author list: Agent
  family name: Barbieri
  given name: Nicolle L.
author list: Agent
  family name: Newman
  given name: Darby M.
author list: Agent
  family name: Young
  given name: Meaghan M.
author list: Agent
  family name: Nolan
  given name: Lisa K.
author list: Agent
  family name: Logue
  given name: Catherine M.
doi: 10.7717/peerj.12631
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-17
copyright: ©2021 de Oliveira et al.
attribution name: de Oliveira et al.

Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets
type: item
type: AcademicArticle
description: Sexes often differ in foraging and diet, which is associated with sex differences in size, trophic morphology, use of habitats, and/or life history tactics. Herein, strikingly similar diets were found for adult sexes of a dragonfly (Leucorrhinia intacta), based on comparing 141 dietary taxa identified from the metabarcoding of mitochondrial DNA archived in feces. Arthropods in > 5% of samples included five species of dipterans, two hemipterans, two spider species and one parasitic mite. The mite was not traditional prey as its presence was likely due to DNA contamination of samples arising through parasitism or possibly via accidental consumption during grooming, and therefore the mite was excluded from diet characterizations. Common prey species were found with statistically indistinguishable frequencies in male and female diets, with one exception of an aphid more often found in male diets, although this pattern was not robust to corrections for multiple statistical tests. While rare prey species were often found in diets of only one sex, instances of this were more frequent in the more oft-sampled females, suggesting sampling artefact. Sexes did not differ in the mean prey species richness in their diets. Overall, sexes showed statistically indistinguishable diets both on a prey species-by-species basis and in terms of multivariate characterizations of diet composition, derived from presence-absence data of prey species analyzed via PERMANOVA and accumulation curves. Males and females may have similar diets by being both opportunistic and generalist predators of arthropods, using the same foraging habitats and having similar sizes and flight agilities. Notably, similarities in diet between sexes occur alongside large interindividual differences in diet, within sexes. Researchers intending on explaining adaptive sex differences in diet should consider characteristics of species whose sexes show similar diets.
format: application/pdf
format: text/html
creator: André Morrill
creator: Kari M. Kaunisto
creator: Julia J. Mlynarek
creator: Ella Sippola
creator: Eero J. Vesterinen
creator: Mark R. Forbes
subject: Animal Behavior
subject: Bioinformatics
subject: Ecology
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.12634
publisher: PeerJ Inc.
rights: © 2021 Morrill et al.
abstract: Sexes often differ in foraging and diet, which is associated with sex differences in size, trophic morphology, use of habitats, and/or life history tactics. Herein, strikingly similar diets were found for adult sexes of a dragonfly (Leucorrhinia intacta), based on comparing 141 dietary taxa identified from the metabarcoding of mitochondrial DNA archived in feces. Arthropods in > 5% of samples included five species of dipterans, two hemipterans, two spider species and one parasitic mite. The mite was not traditional prey as its presence was likely due to DNA contamination of samples arising through parasitism or possibly via accidental consumption during grooming, and therefore the mite was excluded from diet characterizations. Common prey species were found with statistically indistinguishable frequencies in male and female diets, with one exception of an aphid more often found in male diets, although this pattern was not robust to corrections for multiple statistical tests. While rare prey species were often found in diets of only one sex, instances of this were more frequent in the more oft-sampled females, suggesting sampling artefact. Sexes did not differ in the mean prey species richness in their diets. Overall, sexes showed statistically indistinguishable diets both on a prey species-by-species basis and in terms of multivariate characterizations of diet composition, derived from presence-absence data of prey species analyzed via PERMANOVA and accumulation curves. Males and females may have similar diets by being both opportunistic and generalist predators of arthropods, using the same foraging habitats and having similar sizes and flight agilities. Notably, similarities in diet between sexes occur alongside large interindividual differences in diet, within sexes. Researchers intending on explaining adaptive sex differences in diet should consider characteristics of species whose sexes show similar diets.
bibliographic citation: Morrill et al. (2021) Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets. PeerJ 9:e12634 https://doi.org/10.7717/peerj.12634
date submitted: 2021-07-23
date accepted: 2021-11-22
issued: 2021-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morrill
  given name: André
author list: Agent
  family name: Kaunisto
  given name: Kari M.
author list: Agent
  family name: Mlynarek
  given name: Julia J.
author list: Agent
  family name: Sippola
  given name: Ella
author list: Agent
  family name: Vesterinen
  given name: Eero J.
author list: Agent
  family name: Forbes
  given name: Mark R.
doi: 10.7717/peerj.12634
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-17
copyright: ©2021 Morrill et al.
attribution name: Morrill et al.

Novel visual analytics approach for chromosome territory analysis
type: item
type: AcademicArticle
description: This document presents a new and improved, more intuitive version of a novel method for visually representing the location of objects relative to each other in 3D. The motivation and inspiration for developing this new method came from the necessity for objective chromosome territory (CT) adjacency analysis. The earlier version, Distance Profile Chart (DPC), used octants for 3D orientation. This approach did not provide the best 3D space coverage since space was divided into just eight cones and was not intuitive with regard to orientation in 3D. However, the version presented in this article, called DPC12, allows users to achieve better space coverage during conification since space is now divided into twelve cones. DPC12 is faster than DPC and allows for a more precise determination of the location of objects in 3D. In this article a short introduction about the conification idea is presented. Then we explain how DPC12 is designed and created. After that, we show DPC12 on an instructional dataset to make it easier to understand and demonstrate how they appear and how to read them. Finally, using DPC12 we present an example of an adjacency analysis (AA) using the model of Chromosome Territories (CTs) distribution in the rice nucleus.
format: application/pdf
format: text/html
creator: Magdalena A. Tkacz
creator: Kornel Chromiński
creator: Dominika Idziak-Helmcke
creator: Ewa Robaszkiewicz
subject: Computational Biology
subject: Molecular Biology
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.12661
publisher: PeerJ Inc.
rights: © 2021 Tkacz et al.
abstract: This document presents a new and improved, more intuitive version of a novel method for visually representing the location of objects relative to each other in 3D. The motivation and inspiration for developing this new method came from the necessity for objective chromosome territory (CT) adjacency analysis. The earlier version, Distance Profile Chart (DPC), used octants for 3D orientation. This approach did not provide the best 3D space coverage since space was divided into just eight cones and was not intuitive with regard to orientation in 3D. However, the version presented in this article, called DPC12, allows users to achieve better space coverage during conification since space is now divided into twelve cones. DPC12 is faster than DPC and allows for a more precise determination of the location of objects in 3D. In this article a short introduction about the conification idea is presented. Then we explain how DPC12 is designed and created. After that, we show DPC12 on an instructional dataset to make it easier to understand and demonstrate how they appear and how to read them. Finally, using DPC12 we present an example of an adjacency analysis (AA) using the model of Chromosome Territories (CTs) distribution in the rice nucleus.
bibliographic citation: Tkacz et al. (2021) Novel visual analytics approach for chromosome territory analysis. PeerJ 9:e12661 https://doi.org/10.7717/peerj.12661
date submitted: 2020-11-09
date accepted: 2021-11-30
issued: 2021-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tkacz
  given name: Magdalena A.
author list: Agent
  family name: Chromiński
  given name: Kornel
author list: Agent
  family name: Idziak-Helmcke
  given name: Dominika
author list: Agent
  family name: Robaszkiewicz
  given name: Ewa
doi: 10.7717/peerj.12661
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-17
copyright: ©2021 Tkacz et al.
attribution name: Tkacz et al.

Quantifying the association of natal household wealth with women’s early marriage in Nepal
type: item
type: AcademicArticle
description: Background Women’s early marriage (<18 years) is a critical global health issue affecting 650 million women worldwide. It is associated with a range of adverse maternal physical and mental health outcomes, including early childbearing, child undernutrition and morbidity. Poverty is widely asserted to be the key risk factor driving early marriage. However, most studies do not measure wealth in the natal household, but instead, use marital household wealth as a proxy for natal wealth. Further research is required to understand the key drivers of early marriage. Methods We investigated whether natal household poverty was associated with marrying early, independently of women’s lower educational attainment and broader markers of household disadvantage. Data on natal household wealth (material asset score) for 2,432 women aged 18–39 years was used from the cluster-randomized Low Birth Weight South Asia Trial in lowland rural Nepal. Different early marriage definitions (<15, <16, <17 and <18 years) were used because most of our population marries below the conventional 18-year cut-off. Logistic mixed-effects models were fitted to estimate the probabilities, derived from adjusted Odds Ratios, of (a) marrying at different early ages for the full sample and for the uneducated women, and (b) being uneducated in the first place. Results Women married at median age 15 years (interquartile range 3), and only 18% married ≥18 years. Two-thirds of the women were entirely uneducated. We found that, rather than poverty, women’s lower education was the primary factor associated with early marriage, regardless of how ‘early’ is defined. Neither poverty nor other markers of household disadvantage were associated with early marriage at any age in the uneducated women. However, poverty was associated with women being uneducated. Conclusion When assets are measured in the natal household in this population, there is no support for the conventional hypothesis that household poverty is assoc…
format: application/pdf
format: text/html
creator: Akanksha A. Marphatia
creator: Naomi M. Saville
creator: Dharma S. Manandhar
creator: Mario Cortina-Borja
creator: Jonathan C. K. Wells
creator: Alice M. Reid
subject: Epidemiology
subject: Global Health
subject: Health Policy
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.12324
publisher: PeerJ Inc.
rights: © 2021 Marphatia et al.
abstract: Background Women’s early marriage (<18 years) is a critical global health issue affecting 650 million women worldwide. It is associated with a range of adverse maternal physical and mental health outcomes, including early childbearing, child undernutrition and morbidity. Poverty is widely asserted to be the key risk factor driving early marriage. However, most studies do not measure wealth in the natal household, but instead, use marital household wealth as a proxy for natal wealth. Further research is required to understand the key drivers of early marriage. Methods We investigated whether natal household poverty was associated with marrying early, independently of women’s lower educational attainment and broader markers of household disadvantage. Data on natal household wealth (material asset score) for 2,432 women aged 18–39 years was used from the cluster-randomized Low Birth Weight South Asia Trial in lowland rural Nepal. Different early marriage definitions (<15, <16, <17 and <18 years) were used because most of our population marries below the conventional 18-year cut-off. Logistic mixed-effects models were fitted to estimate the probabilities, derived from adjusted Odds Ratios, of (a) marrying at different early ages for the full sample and for the uneducated women, and (b) being uneducated in the first place. Results Women married at median age 15 years (interquartile range 3), and only 18% married ≥18 years. Two-thirds of the women were entirely uneducated. We found that, rather than poverty, women’s lower education was the primary factor associated with early marriage, regardless of how ‘early’ is defined. Neither poverty nor other markers of household disadvantage were associated with early marriage at any age in the uneducated women. However, poverty was associated with women being uneducated. Conclusion When assets are measured in the natal household in this population, there is no support for the conventional hypothesis that household poverty is assoc…
bibliographic citation: Marphatia et al. (2021) Quantifying the association of natal household wealth with women’s early marriage in Nepal. PeerJ 9:e12324 https://doi.org/10.7717/peerj.12324
date submitted: 2021-07-14
date accepted: 2021-09-26
issued: 2021-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marphatia
  given name: Akanksha A.
author list: Agent
  family name: Saville
  given name: Naomi M.
author list: Agent
  family name: Manandhar
  given name: Dharma S.
author list: Agent
  family name: Cortina-Borja
  given name: Mario
author list: Agent
  family name: Wells
  given name: Jonathan C. K.
author list: Agent
  family name: Reid
  given name: Alice M.
doi: 10.7717/peerj.12324
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-16
copyright: © 2021 Marphatia et al.
attribution name: Marphatia et al.

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