PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Inhibiting SLC26A4 reverses cardiac hypertrophy in H9C2 cells and in rats
items: Variability of soil carbon and nitrogen stocks after conversion of natural forest to plantations in Eastern China
items: Soil temperatures and active carbon components as key drivers of C stock dynamics between two different stand ages of Larix principis-rupprechtii plantation
items: Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses
items: Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights
items: Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves
items: Toward a clinical real time tissue ablation technology: combining electroporation and electrolysis (E2)
items: Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano
items: TRANSPARENT TESTA GLABRA 1 participates in flowering time regulation in Arabidopsis thaliana
items: A revised Holocene coral sea-level database from the Florida reef tract, USA

Inhibiting SLC26A4 reverses cardiac hypertrophy in H9C2 cells and in rats
type: item
type: AcademicArticle
description: Background It has been confirmed that mutations in solute carrier family 26 member 4 (SLC26A4) contribute to pendred syndrome. However, the role of SLC26A4 in cardiac hypertrophy and the signaling pathways remain unclear. Methods Cardiomyocytes were treated by 200 µM phenylephrine (PE) to induce cardiac hypertrophy. Also, the expression of SLC26A4, GSK3, cardiac hypertrophy markers including atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) was detected through real-time quantitative polymerase chain reaction (RT-qPCR). Flow cytometry assay was used to test the apoptosis of PE-induced cardiomyocytes transfected by small interfere RNA (siRNA)-SLC26A4. Furthermore, we detected the expression of autophagy-related markers including light chain 3 (LC3) and P62. Finally, we established a rat model of abdominal aortic constriction (AAC)-induced cardiac hypertrophy in vivo. Results RT-qPCR results showed that the mRNA expression of SLC26A4 was significantly up-regulated in PE-induced cardiac hypertrophy. After inhibiting SLC26A4, the release of ANP and BNP was significantly decreased and GSK3β was elevated in vivo and in vitro. Furthermore, inhibiting SLC26A4 promoted apoptosis of cardiac hypertrophy cells. In addition, LC3 was down-regulated and P62 was enhanced after transfection of siRNA-SLC26A4. Conclusion Our findings revealed that SLC26A4 increases cardiac hypertrophy, and inhibiting SLC26A4 could decrease the release of ANP/BNP and promote the expression of GSK-3β in vitro and in vivo. Moreover, SLC26A4 silencing inhibits autophagy of cardiomyocytes and induces apoptosis of cardiomyocytes. Therefore, SLC26A4 possesses potential value to be a therapeutic target of cardiac hypertrophy, and our study provides new insights into the mechanisms of cardiac hypertrophy.
format: application/pdf
format: text/html
creator: Liqun Tang
creator: Xiaoqin Yu
creator: Yangyang Zheng
creator: Ning Zhou
subject: Molecular Biology
subject: Cardiology
description: doi:10.7717/peerj.8253
publisher: PeerJ Inc.
rights: © 2020 Tang et al.
abstract: Background It has been confirmed that mutations in solute carrier family 26 member 4 (SLC26A4) contribute to pendred syndrome. However, the role of SLC26A4 in cardiac hypertrophy and the signaling pathways remain unclear. Methods Cardiomyocytes were treated by 200 µM phenylephrine (PE) to induce cardiac hypertrophy. Also, the expression of SLC26A4, GSK3, cardiac hypertrophy markers including atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) was detected through real-time quantitative polymerase chain reaction (RT-qPCR). Flow cytometry assay was used to test the apoptosis of PE-induced cardiomyocytes transfected by small interfere RNA (siRNA)-SLC26A4. Furthermore, we detected the expression of autophagy-related markers including light chain 3 (LC3) and P62. Finally, we established a rat model of abdominal aortic constriction (AAC)-induced cardiac hypertrophy in vivo. Results RT-qPCR results showed that the mRNA expression of SLC26A4 was significantly up-regulated in PE-induced cardiac hypertrophy. After inhibiting SLC26A4, the release of ANP and BNP was significantly decreased and GSK3β was elevated in vivo and in vitro. Furthermore, inhibiting SLC26A4 promoted apoptosis of cardiac hypertrophy cells. In addition, LC3 was down-regulated and P62 was enhanced after transfection of siRNA-SLC26A4. Conclusion Our findings revealed that SLC26A4 increases cardiac hypertrophy, and inhibiting SLC26A4 could decrease the release of ANP/BNP and promote the expression of GSK-3β in vitro and in vivo. Moreover, SLC26A4 silencing inhibits autophagy of cardiomyocytes and induces apoptosis of cardiomyocytes. Therefore, SLC26A4 possesses potential value to be a therapeutic target of cardiac hypertrophy, and our study provides new insights into the mechanisms of cardiac hypertrophy.
bibliographic citation: Tang et al. (2020) Inhibiting SLC26A4 reverses cardiac hypertrophy in H9C2 cells and in rats. PeerJ 8:e8253 https://doi.org/10.7717/peerj.8253
date submitted: 2019-07-04
date accepted: 2019-11-20
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Liqun
author list: Agent
  family name: Yu
  given name: Xiaoqin
author list: Agent
  family name: Zheng
  given name: Yangyang
author list: Agent
  family name: Zhou
  given name: Ning
doi: 10.7717/peerj.8253
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: ©2020 Tang et al.
attribution name: Tang et al.

Variability of soil carbon and nitrogen stocks after conversion of natural forest to plantations in Eastern China
type: item
type: AcademicArticle
description: Forest plantation, either through afforestation or reforestation, has been suggested to reverse and mitigate the process of deforestation. However, uncertainties remain in the potential of plantation forest (PF) to sequestrate carbon (C) and nitrogen (N) compared to natural forest (NF). Soil C and N stocks require a critical and updated look at what is happening especially in the context of increasing rate of land use change and climate change. The current study was conducted in China’s Eastern forest to estimate soil C and N stocks in six depth layers (0–10, 10–20, 20–40, 40–60, 60–80 and 80–100 cm) and two forest types (NF and PF) at four sites along climate factors gradient. The results showed that the overall mean soil C and N amounts to a depth of 20 cm ranged from 2.6 ± 1.1 Mg ha−1 to 38.6 ± 23.1 Mg ha−1, and soil nitrogen stock ranged from 0.2 ± 0.1 Mg ha−1 to 3.3 ± 1.5 Mg ha−1. Moreover, a loss of C stock was observed at Qingyuan (QY) by −7%, Dinghushan (DH) by −26%, Jianfengling (JF) by −13% while that of N stock was observed at QY (−8%), DH (−19%) and JF (−12%) at both depth layers. These results indicate that NFs have a better capacity to accumulate soil C and N. The soil C and N decreased from the southeast to the northeast and increased from tropical to temperate mixed forests zone in the eastern part of the study area. The C and N stock mainly occurred in the topsoil and decreased significantly with depth. Moreover, soil C and N stocks increased with age of plantation. This study provides an overview of the current spatial distribution and soil stocks of C and N, as well as the effects of environmental factors on soil C and N stocks. It also indicated that, although mean annual temperature and mean annual precipitation are the key factors affecting the variations in soil C and N, their vertical and horizontal distribution differed in various aspects.
format: application/pdf
format: text/html
creator: Mbezele Junior Yannick Ngaba
creator: Xiang-Qing Ma
creator: Ya-Lin Hu
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.8377
publisher: PeerJ Inc.
rights: © 2020 Ngaba et al.
abstract: Forest plantation, either through afforestation or reforestation, has been suggested to reverse and mitigate the process of deforestation. However, uncertainties remain in the potential of plantation forest (PF) to sequestrate carbon (C) and nitrogen (N) compared to natural forest (NF). Soil C and N stocks require a critical and updated look at what is happening especially in the context of increasing rate of land use change and climate change. The current study was conducted in China’s Eastern forest to estimate soil C and N stocks in six depth layers (0–10, 10–20, 20–40, 40–60, 60–80 and 80–100 cm) and two forest types (NF and PF) at four sites along climate factors gradient. The results showed that the overall mean soil C and N amounts to a depth of 20 cm ranged from 2.6 ± 1.1 Mg ha−1 to 38.6 ± 23.1 Mg ha−1, and soil nitrogen stock ranged from 0.2 ± 0.1 Mg ha−1 to 3.3 ± 1.5 Mg ha−1. Moreover, a loss of C stock was observed at Qingyuan (QY) by −7%, Dinghushan (DH) by −26%, Jianfengling (JF) by −13% while that of N stock was observed at QY (−8%), DH (−19%) and JF (−12%) at both depth layers. These results indicate that NFs have a better capacity to accumulate soil C and N. The soil C and N decreased from the southeast to the northeast and increased from tropical to temperate mixed forests zone in the eastern part of the study area. The C and N stock mainly occurred in the topsoil and decreased significantly with depth. Moreover, soil C and N stocks increased with age of plantation. This study provides an overview of the current spatial distribution and soil stocks of C and N, as well as the effects of environmental factors on soil C and N stocks. It also indicated that, although mean annual temperature and mean annual precipitation are the key factors affecting the variations in soil C and N, their vertical and horizontal distribution differed in various aspects.
bibliographic citation: Ngaba et al. (2020) Variability of soil carbon and nitrogen stocks after conversion of natural forest to plantations in Eastern China. PeerJ 8:e8377 https://doi.org/10.7717/peerj.8377
date submitted: 2019-10-11
date accepted: 2019-12-09
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ngaba
  given name: Mbezele Junior Yannick
author list: Agent
  family name: Ma
  given name: Xiang-Qing
author list: Agent
  family name: Hu
  given name: Ya-Lin
doi: 10.7717/peerj.8377
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: © 2020 Ngaba et al.
attribution name: Ngaba et al.

Soil temperatures and active carbon components as key drivers of C stock dynamics between two different stand ages of Larix principis-rupprechtii plantation
type: item
type: AcademicArticle
description: Forest soils sequester a large amount of carbon (C) and have a significant effect on the global C balance. Forests are commonly managed to maintain certain age structures but the effects of this management on soil C pools (kg C m−2) is still uncertain. We compared 40-year-old (1GF) and 24-year-old (2GF) plantations of Larix principis-rupprechtii in North China. Specifically, we measured environmental factors (e.g., soil temperature, moisture, and pH), the active C and nitrogen (N) pools (e.g., soil organic C, soil total N, dissolved organic C and N, microbial biomass C and N), and soil processes (e.g., C mineralization and microbial activity in different seasons) in five soil layers (0–50 cm, 10 cm for each soil layer) across the growing seasons in three 25 m × 25 m plots in each age class (1GF and 2GF). Findings indicated that the soil organic C pool in the older 1GF forest (12.43 kg C m−2) was significantly higher than 2GF forests (9.56 kg C m−2), and that soil temperature in 1GF forests was 9.8 °C, on average, 2.9% warmer than temperature in 2GF forests. The C lost as carbon dioxide (CO2) as a result of mineralization in the 2GF plots may partly explain the lower soil organic C pool in these younger forests; microorganisms likely drive this process.
format: application/pdf
format: text/html
creator: Junyong Ma
creator: Hairong Han
creator: Xiaoqin Cheng
subject: Ecosystem Science
subject: Soil Science
subject: Climate Change Biology
subject: Forestry
description: doi:10.7717/peerj.8384
publisher: PeerJ Inc.
rights: © 2020 Ma et al.
abstract: Forest soils sequester a large amount of carbon (C) and have a significant effect on the global C balance. Forests are commonly managed to maintain certain age structures but the effects of this management on soil C pools (kg C m−2) is still uncertain. We compared 40-year-old (1GF) and 24-year-old (2GF) plantations of Larix principis-rupprechtii in North China. Specifically, we measured environmental factors (e.g., soil temperature, moisture, and pH), the active C and nitrogen (N) pools (e.g., soil organic C, soil total N, dissolved organic C and N, microbial biomass C and N), and soil processes (e.g., C mineralization and microbial activity in different seasons) in five soil layers (0–50 cm, 10 cm for each soil layer) across the growing seasons in three 25 m × 25 m plots in each age class (1GF and 2GF). Findings indicated that the soil organic C pool in the older 1GF forest (12.43 kg C m−2) was significantly higher than 2GF forests (9.56 kg C m−2), and that soil temperature in 1GF forests was 9.8 °C, on average, 2.9% warmer than temperature in 2GF forests. The C lost as carbon dioxide (CO2) as a result of mineralization in the 2GF plots may partly explain the lower soil organic C pool in these younger forests; microorganisms likely drive this process.
bibliographic citation: Ma et al. (2020) Soil temperatures and active carbon components as key drivers of C stock dynamics between two different stand ages of Larix principis-rupprechtii plantation. PeerJ 8:e8384 https://doi.org/10.7717/peerj.8384
date submitted: 2019-04-18
date accepted: 2019-12-11
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Junyong
author list: Agent
  family name: Han
  given name: Hairong
author list: Agent
  family name: Cheng
  given name: Xiaoqin
doi: 10.7717/peerj.8384
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: © 2020 Ma et al.
attribution name: Ma et al.

Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses
type: item
type: AcademicArticle
description: Background BRCA1 and BRCA2 genes are currently proven to be closely related to high lifetime risks of breast cancer. To date, the closely related genes to BRCA1/2 mutations in breast cancer remains to be fully elucidated. This study aims to identify the gene expression profiles and interaction networks influenced by BRCA1/2 mutations, so as to reflect underlying disease mechanisms and provide new biomarkers for breast cancer diagnosis or prognosis. Methods Gene expression profiles from The Cancer Genome Atlas (TCGA) database were downloaded and combined with cBioPortal website to identify exact breast cancer patients with BRCA1/2 mutations. Gene set enrichment analysis (GSEA) was used to analyze some enriched pathways and biological processes associated BRCA mutations. For BRCA1/2-mutant breast cancer, wild-type breast cancer and corresponding normal tissues, three independent differentially expressed genes (DEGs) analysis were performed to validate potential hub genes with each other. Protein–protein interaction (PPI) networks, survival analysis and diagnostic value assessment helped identify key genes associated with BRCA1/2 mutations. Results The regulation process of cell cycle was significantly enriched in mutant group compared with wild-type group. A total of 294 genes were identified after analysis of DEGs between mutant patients and wild-type patients. Interestingly, by the other two comparisons, we identified 43 overlapping genes that not only significantly expressed in wild-type breast cancer patients relative to normal tissues, but more significantly expressed in BRCA1/2-mutant breast patients. Based on the STRING database and cytoscape software, we constructed a PPI network using 294 DEGs. Through topological analysis scores of the PPI network and 43 overlapping genes, we sought to select some genes, thereby using survival analysis and diagnostic value assessment to identify key genes pertaining to BRCA1/2-mutant breast cancer. CCNE1, NPBWR1, A2ML1, EXO1…
format: application/pdf
format: text/html
creator: Yue Li
creator: Xiaoyan Zhou
creator: Jiali Liu
creator: Yang Yin
creator: Xiaohong Yuan
creator: Ruihua Yang
creator: Qi Wang
creator: Jing Ji
creator: Qian He
subject: Bioinformatics
subject: Oncology
subject: Computational Science
description: doi:10.7717/peerj.8403
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background BRCA1 and BRCA2 genes are currently proven to be closely related to high lifetime risks of breast cancer. To date, the closely related genes to BRCA1/2 mutations in breast cancer remains to be fully elucidated. This study aims to identify the gene expression profiles and interaction networks influenced by BRCA1/2 mutations, so as to reflect underlying disease mechanisms and provide new biomarkers for breast cancer diagnosis or prognosis. Methods Gene expression profiles from The Cancer Genome Atlas (TCGA) database were downloaded and combined with cBioPortal website to identify exact breast cancer patients with BRCA1/2 mutations. Gene set enrichment analysis (GSEA) was used to analyze some enriched pathways and biological processes associated BRCA mutations. For BRCA1/2-mutant breast cancer, wild-type breast cancer and corresponding normal tissues, three independent differentially expressed genes (DEGs) analysis were performed to validate potential hub genes with each other. Protein–protein interaction (PPI) networks, survival analysis and diagnostic value assessment helped identify key genes associated with BRCA1/2 mutations. Results The regulation process of cell cycle was significantly enriched in mutant group compared with wild-type group. A total of 294 genes were identified after analysis of DEGs between mutant patients and wild-type patients. Interestingly, by the other two comparisons, we identified 43 overlapping genes that not only significantly expressed in wild-type breast cancer patients relative to normal tissues, but more significantly expressed in BRCA1/2-mutant breast patients. Based on the STRING database and cytoscape software, we constructed a PPI network using 294 DEGs. Through topological analysis scores of the PPI network and 43 overlapping genes, we sought to select some genes, thereby using survival analysis and diagnostic value assessment to identify key genes pertaining to BRCA1/2-mutant breast cancer. CCNE1, NPBWR1, A2ML1, EXO1…
bibliographic citation: Li et al. (2020) Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses. PeerJ 8:e8403 https://doi.org/10.7717/peerj.8403
date submitted: 2019-10-01
date accepted: 2019-12-16
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yue
author list: Agent
  family name: Zhou
  given name: Xiaoyan
author list: Agent
  family name: Liu
  given name: Jiali
author list: Agent
  family name: Yin
  given name: Yang
author list: Agent
  family name: Yuan
  given name: Xiaohong
author list: Agent
  family name: Yang
  given name: Ruihua
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Ji
  given name: Jing
author list: Agent
  family name: He
  given name: Qian
doi: 10.7717/peerj.8403
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: ©2020 Li et al.
attribution name: Li et al.

Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights
type: item
type: AcademicArticle
description: The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish.
format: application/pdf
format: text/html
creator: Huaxing Zhou
creator: Yuting Hu
creator: He Jiang
creator: Guoqing Duan
creator: Jun Ling
creator: Tingshuang Pan
creator: Xiaolei Chen
creator: Huan Wang
creator: Ye Zhang
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Genetics
subject: Molecular Biology
subject: Population Biology
description: doi:10.7717/peerj.8415
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish.
bibliographic citation: Zhou et al. (2020) Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights. PeerJ 8:e8415 https://doi.org/10.7717/peerj.8415
date submitted: 2019-07-31
date accepted: 2019-12-16
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Huaxing
author list: Agent
  family name: Hu
  given name: Yuting
author list: Agent
  family name: Jiang
  given name: He
author list: Agent
  family name: Duan
  given name: Guoqing
author list: Agent
  family name: Ling
  given name: Jun
author list: Agent
  family name: Pan
  given name: Tingshuang
author list: Agent
  family name: Chen
  given name: Xiaolei
author list: Agent
  family name: Wang
  given name: Huan
author list: Agent
  family name: Zhang
  given name: Ye
doi: 10.7717/peerj.8415
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: ©2020 Zhou et al.
attribution name: Zhou et al.

Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves
type: item
type: AcademicArticle
description: Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa.
format: application/pdf
format: text/html
creator: Jianbo Yuan
creator: Xinbo Sun
creator: Tao Guo
creator: Yuehui Chao
creator: Liebao Han
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.8426
publisher: PeerJ Inc.
rights: © 2020 Yuan et al.
abstract: Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa.
bibliographic citation: Yuan et al. (2020) Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves. PeerJ 8:e8426 https://doi.org/10.7717/peerj.8426
date submitted: 2019-05-16
date accepted: 2019-12-18
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Jianbo
author list: Agent
  family name: Sun
  given name: Xinbo
author list: Agent
  family name: Guo
  given name: Tao
author list: Agent
  family name: Chao
  given name: Yuehui
author list: Agent
  family name: Han
  given name: Liebao
doi: 10.7717/peerj.8426
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: ©2020 Yuan et al.
attribution name: Yuan et al.

Toward a clinical real time tissue ablation technology: combining electroporation and electrolysis (E2)
type: item
type: AcademicArticle
description: Background Percutaneous image-guided tissue ablation (IGA) plays a growing role in the clinical management of solid malignancies. Electroporation is used for IGA in several modalities: irreversible electroporation (IRE), and reversible electroporation with chemotoxic drugs, called electrochemotherapy (ECT). It was shown that the combination of electrolysis and electroporation—E2—affords tissue ablation with greater efficiency, that is, lower voltages, lower energy and shorter procedure times than IRE and without the need for chemotoxic additives as in ECT. Methods A new E2 waveform was designed that delivers optimal doses of electroporation and electrolysis in a single waveform. A series of experiments were performed in the liver of pigs to evaluate E2 in the context of clinical applications. The goal was to find initial parameter boundaries in terms of electrical field, pulse duration and charge as well as tissue behavior to enable real time tissue ablation of clinically relevant volumes. Results Histological results show that a single several hundred millisecond long E2 waveform can ablate large volume of tissue at relatively low voltages while preserving the integrity of large blood vessels and lumen structures in the ablation zone without the use of chemotoxic drugs or paralyzing drugs during anesthesia. This could translate clinically into much shorter treatment times and ease of use compared to other techniques that are currently applied.
format: application/pdf
format: text/html
creator: Enric Guenther
creator: Nina Klein
creator: Paul Mikus
creator: Florin Botea
creator: Mihail Pautov
creator: Franco Lugnani
creator: Matteo Macchioro
creator: Irinel Popescu
creator: Michael K. Stehling
creator: Boris Rubinsky
subject: Biophysics
subject: Biotechnology
subject: Drugs and Devices
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.7985
publisher: PeerJ Inc.
rights: © 2020 Gunther et al.
abstract: Background Percutaneous image-guided tissue ablation (IGA) plays a growing role in the clinical management of solid malignancies. Electroporation is used for IGA in several modalities: irreversible electroporation (IRE), and reversible electroporation with chemotoxic drugs, called electrochemotherapy (ECT). It was shown that the combination of electrolysis and electroporation—E2—affords tissue ablation with greater efficiency, that is, lower voltages, lower energy and shorter procedure times than IRE and without the need for chemotoxic additives as in ECT. Methods A new E2 waveform was designed that delivers optimal doses of electroporation and electrolysis in a single waveform. A series of experiments were performed in the liver of pigs to evaluate E2 in the context of clinical applications. The goal was to find initial parameter boundaries in terms of electrical field, pulse duration and charge as well as tissue behavior to enable real time tissue ablation of clinically relevant volumes. Results Histological results show that a single several hundred millisecond long E2 waveform can ablate large volume of tissue at relatively low voltages while preserving the integrity of large blood vessels and lumen structures in the ablation zone without the use of chemotoxic drugs or paralyzing drugs during anesthesia. This could translate clinically into much shorter treatment times and ease of use compared to other techniques that are currently applied.
bibliographic citation: Guenther et al. (2020) Toward a clinical real time tissue ablation technology: combining electroporation and electrolysis (E2). PeerJ 8:e7985 https://doi.org/10.7717/peerj.7985
date submitted: 2019-05-09
date accepted: 2019-10-03
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guenther
  given name: Enric
author list: Agent
  family name: Klein
  given name: Nina
author list: Agent
  family name: Mikus
  given name: Paul
author list: Agent
  family name: Botea
  given name: Florin
author list: Agent
  family name: Pautov
  given name: Mihail
author list: Agent
  family name: Lugnani
  given name: Franco
author list: Agent
  family name: Macchioro
  given name: Matteo
author list: Agent
  family name: Popescu
  given name: Irinel
author list: Agent
  family name: Stehling
  given name: Michael K.
author list: Agent
  family name: Rubinsky
  given name: Boris
doi: 10.7717/peerj.7985
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: © 2020 Gunther et al.
attribution name: Gunther et al.

Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano
type: item
type: AcademicArticle
description: Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer…
format: application/pdf
format: text/html
creator: Jenny Urbina
creator: Tara Chestnut
creator: Donelle Schwalm
creator: Jenn Allen
creator: Taal Levi
subject: Conservation Biology
subject: Ecology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.8141
publisher: PeerJ Inc.
rights: © 2020 Urbina et al.
abstract: Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer…
bibliographic citation: Urbina et al. (2020) Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano. PeerJ 8:e8141 https://doi.org/10.7717/peerj.8141
date submitted: 2019-07-01
date accepted: 2019-11-01
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Urbina
  given name: Jenny
author list: Agent
  family name: Chestnut
  given name: Tara
author list: Agent
  family name: Schwalm
  given name: Donelle
author list: Agent
  family name: Allen
  given name: Jenn
author list: Agent
  family name: Levi
  given name: Taal
doi: 10.7717/peerj.8141
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: ©2020 Urbina et al.
attribution name: Urbina et al.

TRANSPARENT TESTA GLABRA 1 participates in flowering time regulation in Arabidopsis thaliana
type: item
type: AcademicArticle
description: Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is such a factor that has been predominantly described as a regulator of early developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 affect photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported. Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcript levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92. Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation.
format: application/pdf
format: text/html
creator: Barbara A.M. Paffendorf
creator: Rawan Qassrawi
creator: Andrea M. Meys
creator: Laura Trimborn
creator: Andrea Schrader
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.8303
publisher: PeerJ Inc.
rights: © 2020 Paffendorf et al.
abstract: Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is such a factor that has been predominantly described as a regulator of early developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 affect photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported. Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcript levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92. Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation.
bibliographic citation: Paffendorf et al. (2020) TRANSPARENT TESTA GLABRA 1 participates in flowering time regulation in Arabidopsis thaliana. PeerJ 8:e8303 https://doi.org/10.7717/peerj.8303
date submitted: 2019-09-18
date accepted: 2019-11-26
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paffendorf
  given name: Barbara A.M.
author list: Agent
  family name: Qassrawi
  given name: Rawan
author list: Agent
  family name: Meys
  given name: Andrea M.
author list: Agent
  family name: Trimborn
  given name: Laura
author list: Agent
  family name: Schrader
  given name: Andrea
doi: 10.7717/peerj.8303
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: ©2020 Paffendorf et al.
attribution name: Paffendorf et al.

A revised Holocene coral sea-level database from the Florida reef tract, USA
type: item
type: AcademicArticle
description: The coral reefs and mangrove habitats of the south Florida region have long been used in sea-level studies for the western Atlantic because of their broad geographic extent and composition of sea-level tracking biota. The data from this region have been used to support several very different Holocene sea-level reconstructions (SLRs) over the years. However, many of these SLRs did not incorporate all available coral-based data, in part because detailed characterizations necessary for inclusion into sea-level databases were lacking. Here, we present an updated database comprised of 303 coral samples from published sources that we extensively characterized for the first time. The data were carefully screened by evaluating and ranking the visual taphonomic characteristics of every dated sample within the database, which resulted in the identification of 134 high-quality coral samples for consideration as suitable sea-level indicators. We show that our database largely agrees with the most recent SLR for south Florida over the last ∼7,000 years; however, the early Holocene remains poorly characterized because there are few high-quality data spanning this period. Suggestions to refine future Holocene SLRs in the region are provided including filling spatial and temporal data gaps of coral samples, particularly from the early Holocene, as well as constructing a more robust peat database to better constrain sea-level variability during the middle to late Holocene. Our database and taphonomic-ranking protocol provide a framework for researchers to evaluate data-selection criteria depending on the robustness of their sea-level models.
format: application/pdf
format: text/html
creator: Anastasios Stathakopoulos
creator: Bernhard M. Riegl
creator: Lauren T. Toth
subject: Ecosystem Science
subject: Marine Biology
subject: Paleontology
description: doi:10.7717/peerj.8350
publisher: PeerJ Inc.
rights: © 2020 Stathakopoulos et al.
abstract: The coral reefs and mangrove habitats of the south Florida region have long been used in sea-level studies for the western Atlantic because of their broad geographic extent and composition of sea-level tracking biota. The data from this region have been used to support several very different Holocene sea-level reconstructions (SLRs) over the years. However, many of these SLRs did not incorporate all available coral-based data, in part because detailed characterizations necessary for inclusion into sea-level databases were lacking. Here, we present an updated database comprised of 303 coral samples from published sources that we extensively characterized for the first time. The data were carefully screened by evaluating and ranking the visual taphonomic characteristics of every dated sample within the database, which resulted in the identification of 134 high-quality coral samples for consideration as suitable sea-level indicators. We show that our database largely agrees with the most recent SLR for south Florida over the last ∼7,000 years; however, the early Holocene remains poorly characterized because there are few high-quality data spanning this period. Suggestions to refine future Holocene SLRs in the region are provided including filling spatial and temporal data gaps of coral samples, particularly from the early Holocene, as well as constructing a more robust peat database to better constrain sea-level variability during the middle to late Holocene. Our database and taphonomic-ranking protocol provide a framework for researchers to evaluate data-selection criteria depending on the robustness of their sea-level models.
bibliographic citation: Stathakopoulos et al. (2020) A revised Holocene coral sea-level database from the Florida reef tract, USA. PeerJ 8:e8350 https://doi.org/10.7717/peerj.8350
date submitted: 2018-09-13
date accepted: 2019-12-04
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Stathakopoulos
  given name: Anastasios
author list: Agent
  family name: Riegl
  given name: Bernhard M.
author list: Agent
  family name: Toth
  given name: Lauren T.
doi: 10.7717/peerj.8350
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: ©2020 Stathakopoulos et al.
attribution name: Stathakopoulos et al.

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