PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Overexpression of AmCBF1 enhances drought and cold stress tolerance, and improves photosynthesis in transgenic cotton
items: Influence of hot air drying on capsaicinoids, phenolics, flavonoids and antioxidant activities of ‘Super Hot’ chilies
items: Heat stress response in Chinese cabbage (Brassica rapa L.) revealed by transcriptome and physiological analysis
items: Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing
items: Nutrient composition of Chenopodium formosanum Koidz. bran: Fractionation and bioactivity of its soluble active polysaccharides
items: Phytochemical content, especially spermidine derivatives, presenting antioxidant and antilipoxygenase activities in Thai bee pollens
items: Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue
items: Effect of a cover crop on the aphid incidence is not explained by increased top-down regulation
items: Down-regulated NEDD4L facilitates tumor progression through activating Notch signaling in lung adenocarcinoma
items: Fisetin glycosides synthesized by cyclodextrin glycosyltransferase from Paenibacillus sp. RB01: characterization, molecular docking, and antioxidant activity

Overexpression of AmCBF1 enhances drought and cold stress tolerance, and improves photosynthesis in transgenic cotton
type: item
type: AcademicArticle
description: China’s main cotton production area is located in the northwest where abiotic stresses, particularly cold and drought, have serious effects on cotton production. In this study, Ammopiptanthus mongolicus C-repeat-binding factor (AmCBF1) isolated from the shrub Ammopiptanthus mongolicus was inserted into upland cotton (Gossypium hirsutum L.) cultivar R15 to evaluate the potential benefits of this gene. Two transgenic lines were selected, and the transgene insertion site was identified using whole-genome sequencing. The results showed that AmCBF1 was incorporated into the cotton genome as a single copy. Transgenic plants had distinctly higher relative water content (RWC), chlorophyll content, soluble sugar content, and lower ion leakage than R15 after drought and cold stress. Some characteristics, such as the area of lower epidermal cells, stomatal density, and root to shoot ratio, varied significantly between transgenic cotton lines and R15. Although the photosynthetic ability of transgenic plants was inhibited after stress, the net photosynthetic rate, stomatal conductance, and transpiration rate in transgenic plants were significantly higher than in R15. This suggested that an enhanced stress tolerance and photosynthesis of transgenic cotton was achieved by overexpressing AmCBF1. All together, our results demonstrate that the new transgenic cotton germplasm has great application value against abiotic stresses, especially in the northwest inland area of China.
format: application/pdf
format: text/html
creator: Guoqing Lu
creator: Lihua Wang
creator: Lili Zhou
creator: Xiaofeng Su
creator: Huiming Guo
creator: Hongmei Cheng
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13422
publisher: PeerJ Inc.
rights: © 2022 Lu et al.
abstract: China’s main cotton production area is located in the northwest where abiotic stresses, particularly cold and drought, have serious effects on cotton production. In this study, Ammopiptanthus mongolicus C-repeat-binding factor (AmCBF1) isolated from the shrub Ammopiptanthus mongolicus was inserted into upland cotton (Gossypium hirsutum L.) cultivar R15 to evaluate the potential benefits of this gene. Two transgenic lines were selected, and the transgene insertion site was identified using whole-genome sequencing. The results showed that AmCBF1 was incorporated into the cotton genome as a single copy. Transgenic plants had distinctly higher relative water content (RWC), chlorophyll content, soluble sugar content, and lower ion leakage than R15 after drought and cold stress. Some characteristics, such as the area of lower epidermal cells, stomatal density, and root to shoot ratio, varied significantly between transgenic cotton lines and R15. Although the photosynthetic ability of transgenic plants was inhibited after stress, the net photosynthetic rate, stomatal conductance, and transpiration rate in transgenic plants were significantly higher than in R15. This suggested that an enhanced stress tolerance and photosynthesis of transgenic cotton was achieved by overexpressing AmCBF1. All together, our results demonstrate that the new transgenic cotton germplasm has great application value against abiotic stresses, especially in the northwest inland area of China.
bibliographic citation: Lu et al. (2022) Overexpression of AmCBF1 enhances drought and cold stress tolerance, and improves photosynthesis in transgenic cotton. PeerJ 10:e13422 https://doi.org/10.7717/peerj.13422
date submitted: 2021-11-30
date accepted: 2022-04-20
issued: 2022-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Guoqing
author list: Agent
  family name: Wang
  given name: Lihua
author list: Agent
  family name: Zhou
  given name: Lili
author list: Agent
  family name: Su
  given name: Xiaofeng
author list: Agent
  family name: Guo
  given name: Huiming
author list: Agent
  family name: Cheng
  given name: Hongmei
doi: 10.7717/peerj.13422
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-25
copyright: ©2022 Lu et al.
attribution name: Lu et al.

Influence of hot air drying on capsaicinoids, phenolics, flavonoids and antioxidant activities of ‘Super Hot’ chilies
type: item
type: AcademicArticle
description: Hot air drying is an alternative technique to either maintain or increase bioactive compounds in agricultural products because temperatures can be controlled. The effects of different hot air oven drying temperatures and times on the physicochemical changes, bioactive compounds (capsaicinoids, phenolic and flavonoid profiles and contents) and antioxidant activities in dried ‘Super Hot’ chili fruits were evaluated. The chilies were dried in a hot air oven at low (60–100 °C) or high (120–160 °C) temperatures for 30, 60, 120 min and at 12–13% moisture content (MC). The main compounds presented in chili fruits were capsaicinoids, limonene, pinene, tocopherol and oleic acid, regardless of drying temperature and time. Although the total flavonoid contents decreased during the drying process, the total phenolic contents increased (38–51%), and capsaicinoids, the primary pungent compounds, increased six-times at 120–160 °C compared to the fresh chilies. The phenolic profiles showed that chlorogenic acid was the most stable and abundant amongst the nine quantified phenolic compounds. In the flavonoid profile, both rutin and quercetin can be detected at a high temperature of 160 °C, with a decreasing trend. The main pungent compounds, capsaicin and dihydrocapsaicin, were found to increase compared to the fresh chilies, especially at 12–13% wet basis (w.b.). Although the antioxidant activities (ABTS• + and DPPH•) of dried chilies at all temperatures decreased with increasing drying time, these activities were still detected. Therefore, drying chilies at 160 °C (120 min) can not only maintain the capsaicinoids, phenolics and flavonoids that can be utilized by the pharmaceutical and food industry, but can also reduce the production time.
format: application/pdf
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creator: Esther Shiau Ping Yap
creator: Apiradee Uthairatanakij
creator: Natta Laohakunjit
creator: Pongphen Jitareerat
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.13423
publisher: PeerJ Inc.
rights: © 2022 Yap et al.
abstract: Hot air drying is an alternative technique to either maintain or increase bioactive compounds in agricultural products because temperatures can be controlled. The effects of different hot air oven drying temperatures and times on the physicochemical changes, bioactive compounds (capsaicinoids, phenolic and flavonoid profiles and contents) and antioxidant activities in dried ‘Super Hot’ chili fruits were evaluated. The chilies were dried in a hot air oven at low (60–100 °C) or high (120–160 °C) temperatures for 30, 60, 120 min and at 12–13% moisture content (MC). The main compounds presented in chili fruits were capsaicinoids, limonene, pinene, tocopherol and oleic acid, regardless of drying temperature and time. Although the total flavonoid contents decreased during the drying process, the total phenolic contents increased (38–51%), and capsaicinoids, the primary pungent compounds, increased six-times at 120–160 °C compared to the fresh chilies. The phenolic profiles showed that chlorogenic acid was the most stable and abundant amongst the nine quantified phenolic compounds. In the flavonoid profile, both rutin and quercetin can be detected at a high temperature of 160 °C, with a decreasing trend. The main pungent compounds, capsaicin and dihydrocapsaicin, were found to increase compared to the fresh chilies, especially at 12–13% wet basis (w.b.). Although the antioxidant activities (ABTS• + and DPPH•) of dried chilies at all temperatures decreased with increasing drying time, these activities were still detected. Therefore, drying chilies at 160 °C (120 min) can not only maintain the capsaicinoids, phenolics and flavonoids that can be utilized by the pharmaceutical and food industry, but can also reduce the production time.
bibliographic citation: Yap et al. (2022) Influence of hot air drying on capsaicinoids, phenolics, flavonoids and antioxidant activities of ‘Super Hot’ chilies. PeerJ 10:e13423 https://doi.org/10.7717/peerj.13423
date submitted: 2021-11-04
date accepted: 2022-04-20
issued: 2022-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yap
  given name: Esther Shiau Ping
author list: Agent
  family name: Uthairatanakij
  given name: Apiradee
author list: Agent
  family name: Laohakunjit
  given name: Natta
author list: Agent
  family name: Jitareerat
  given name: Pongphen
doi: 10.7717/peerj.13423
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-25
copyright: ©2022 Yap et al.
attribution name: Yap et al.

Heat stress response in Chinese cabbage (Brassica rapa L.) revealed by transcriptome and physiological analysis
type: item
type: AcademicArticle
description: High temperatures have a serious impact on the quality and yield of cold-loving Chinese cabbage, which has evolved to have a unique set of stress mechanisms. To explore the relationship between these mechanisms and the heat-tolerance of Chinese cabbage, the physiological indicators of the heat-tolerant ‘268’ line and heat-sensitive ‘334’ line were measured. Under heat stress, the proline (Pro), soluble sugar (SS), and superoxide dismutase (SOD) indexes of the ‘268’ line increased significantly. When additionally using transcriptome analysis, we found that the identified 3,360 DEGs were abundantly enriched in many metabolic pathways including ‘plant hormone signal transduction’, ‘carbon metabolism’, and ‘glycolysis/gluconeogenesis’. Dynamic gene expression patterns showed that HKL1 in Cluster 15 may be a key factor in the regulation of sugar homeostasis. The interaction network screened four ABA-related genes in Cluster 15, suggesting that high temperatures lead to changes in hormonal signaling, especially an increase in ABA signaling. Compared with the ‘334’ line, the expressions of Prx50, Prx52, Prx54, SOD1, and SOD2 in the ‘268’ line were significantly upregulated, and these genes were actively involved in the reactive oxygen species (ROS) scavenging process. In summary, our results revealed the relationship between plant heat tolerance, physiology, and biochemistry and may also provide ideas for the future development of high-quality and heat-tolerant Chinese cabbage germplasm resources.
format: application/pdf
format: text/html
creator: Lei Zhang
creator: Yun Dai
creator: Lixin Yue
creator: Guohu Chen
creator: Lingyun Yuan
creator: Shifan Zhang
creator: Fei Li
creator: Hui Zhang
creator: Guoliang Li
creator: Shidong Zhu
creator: Jinfeng Hou
creator: Xiaoyan Tang
creator: Shujiang Zhang
creator: Chenggang Wang
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.13427
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: High temperatures have a serious impact on the quality and yield of cold-loving Chinese cabbage, which has evolved to have a unique set of stress mechanisms. To explore the relationship between these mechanisms and the heat-tolerance of Chinese cabbage, the physiological indicators of the heat-tolerant ‘268’ line and heat-sensitive ‘334’ line were measured. Under heat stress, the proline (Pro), soluble sugar (SS), and superoxide dismutase (SOD) indexes of the ‘268’ line increased significantly. When additionally using transcriptome analysis, we found that the identified 3,360 DEGs were abundantly enriched in many metabolic pathways including ‘plant hormone signal transduction’, ‘carbon metabolism’, and ‘glycolysis/gluconeogenesis’. Dynamic gene expression patterns showed that HKL1 in Cluster 15 may be a key factor in the regulation of sugar homeostasis. The interaction network screened four ABA-related genes in Cluster 15, suggesting that high temperatures lead to changes in hormonal signaling, especially an increase in ABA signaling. Compared with the ‘334’ line, the expressions of Prx50, Prx52, Prx54, SOD1, and SOD2 in the ‘268’ line were significantly upregulated, and these genes were actively involved in the reactive oxygen species (ROS) scavenging process. In summary, our results revealed the relationship between plant heat tolerance, physiology, and biochemistry and may also provide ideas for the future development of high-quality and heat-tolerant Chinese cabbage germplasm resources.
bibliographic citation: Zhang et al. (2022) Heat stress response in Chinese cabbage (Brassica rapa L.) revealed by transcriptome and physiological analysis. PeerJ 10:e13427 https://doi.org/10.7717/peerj.13427
date submitted: 2022-01-03
date accepted: 2022-04-21
issued: 2022-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: Dai
  given name: Yun
author list: Agent
  family name: Yue
  given name: Lixin
author list: Agent
  family name: Chen
  given name: Guohu
author list: Agent
  family name: Yuan
  given name: Lingyun
author list: Agent
  family name: Zhang
  given name: Shifan
author list: Agent
  family name: Li
  given name: Fei
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Li
  given name: Guoliang
author list: Agent
  family name: Zhu
  given name: Shidong
author list: Agent
  family name: Hou
  given name: Jinfeng
author list: Agent
  family name: Tang
  given name: Xiaoyan
author list: Agent
  family name: Zhang
  given name: Shujiang
author list: Agent
  family name: Wang
  given name: Chenggang
doi: 10.7717/peerj.13427
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-25
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing
type: item
type: AcademicArticle
description: Background In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells. Methods Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells’ transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR. Results The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.
format: application/pdf
format: text/html
creator: Shuxin Li
creator: Jiarui Wang
creator: Jiale Li
creator: Meihong Yue
creator: Chuncheng Liu
creator: Libing Ma
creator: Ying Liu
subject: Agricultural Science
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13446
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells. Methods Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells’ transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR. Results The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.
bibliographic citation: Li et al. (2022) Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing. PeerJ 10:e13446 https://doi.org/10.7717/peerj.13446
date submitted: 2022-02-03
date accepted: 2022-04-26
issued: 2022-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Shuxin
author list: Agent
  family name: Wang
  given name: Jiarui
author list: Agent
  family name: Li
  given name: Jiale
author list: Agent
  family name: Yue
  given name: Meihong
author list: Agent
  family name: Liu
  given name: Chuncheng
author list: Agent
  family name: Ma
  given name: Libing
author list: Agent
  family name: Liu
  given name: Ying
doi: 10.7717/peerj.13446
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-25
copyright: ©2022 Li et al.
attribution name: Li et al.

Nutrient composition of Chenopodium formosanum Koidz. bran: Fractionation and bioactivity of its soluble active polysaccharides
type: item
type: AcademicArticle
description: Background Chenopodium formosanum Koidz. Amaranthaceae—also known as Djulis or red quinoa (RQ)—is a cereal plant indigenous to Taiwan, known for its high nutrient value. However, its bran is considered a waste product and the nutrient value has never been analyzed. Methods In this study, we examined the proximate composition of RQ bran, specifically its soluble polysaccharide fractions. Results RQ bran exhibited high contents of protein (16.56%), ash (7.10%), carbohydrate (60.45%), total polyphenolics (1.85%), betaxanthin (9.91 mg/100 g of RQ bran), and indicaxanthin (7.27 mg/100 g of RQ bran). Specifically, it was rich in polyunsaturated fatty acids (PUFAs; 39.24%)—with an n-6/n-3 and PUFA/saturated fatty acid (SFA) ratio of 18.137 and 0.743, respectively. Four soluble polysaccharide fractions were also obtained: CF-1, CF-2, CF-3, and CF-4, with yields of 3.90%, 6.74%, 22.28%, and 0.06%, respectively, and molecular weights of 32.54, 24.93, 72.39, and 55.45 kDa, respectively. CF-1, CF-2, CF-3, and CF-4 had respectively 15.67%, 42.41%, 5.44%, and 14.52% peptide moiety content and 38.92%, 50.70%, 93.76%, and 19.80% carbohydrate moiety. In CF-2, the glucose content was 95.86 mol% and that of leucine was 16.23%, implicating the presence of a typical leucinoglucan. All four polysaccharide fractions lacked glutamic acid and hydroxyproline. The IC50 of CF-1, CF-2, and CF-3 was respectively 12.05, 3.98, and 14.5 mg/mL for DPPH free radical–scavenging ability; 5.77, 4.10, and 7.03 mg/mL for hydrogen peroxide–scavenging capability; 0.26, 0.05, and 0.19 mg/mL for O2− free radical–scavenging capability; and 100.41, 28.12, and 29.73 mg/mL for Fe2+ chelation. Conclusion Our results indicated that RQ bran has a large amount of nutrient compounds, and a cost-efficient process for their extraction is needed. Their biomedical application as nutraceuticals also warrants further investigation.
format: application/pdf
format: text/html
creator: Yaw-Bee Ker
creator: Hui-Ling Wu
creator: Kuan-Chou Chen
creator: Robert Y. Peng
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.13459
publisher: PeerJ Inc.
rights: © 2022 Ker et al.
abstract: Background Chenopodium formosanum Koidz. Amaranthaceae—also known as Djulis or red quinoa (RQ)—is a cereal plant indigenous to Taiwan, known for its high nutrient value. However, its bran is considered a waste product and the nutrient value has never been analyzed. Methods In this study, we examined the proximate composition of RQ bran, specifically its soluble polysaccharide fractions. Results RQ bran exhibited high contents of protein (16.56%), ash (7.10%), carbohydrate (60.45%), total polyphenolics (1.85%), betaxanthin (9.91 mg/100 g of RQ bran), and indicaxanthin (7.27 mg/100 g of RQ bran). Specifically, it was rich in polyunsaturated fatty acids (PUFAs; 39.24%)—with an n-6/n-3 and PUFA/saturated fatty acid (SFA) ratio of 18.137 and 0.743, respectively. Four soluble polysaccharide fractions were also obtained: CF-1, CF-2, CF-3, and CF-4, with yields of 3.90%, 6.74%, 22.28%, and 0.06%, respectively, and molecular weights of 32.54, 24.93, 72.39, and 55.45 kDa, respectively. CF-1, CF-2, CF-3, and CF-4 had respectively 15.67%, 42.41%, 5.44%, and 14.52% peptide moiety content and 38.92%, 50.70%, 93.76%, and 19.80% carbohydrate moiety. In CF-2, the glucose content was 95.86 mol% and that of leucine was 16.23%, implicating the presence of a typical leucinoglucan. All four polysaccharide fractions lacked glutamic acid and hydroxyproline. The IC50 of CF-1, CF-2, and CF-3 was respectively 12.05, 3.98, and 14.5 mg/mL for DPPH free radical–scavenging ability; 5.77, 4.10, and 7.03 mg/mL for hydrogen peroxide–scavenging capability; 0.26, 0.05, and 0.19 mg/mL for O2− free radical–scavenging capability; and 100.41, 28.12, and 29.73 mg/mL for Fe2+ chelation. Conclusion Our results indicated that RQ bran has a large amount of nutrient compounds, and a cost-efficient process for their extraction is needed. Their biomedical application as nutraceuticals also warrants further investigation.
bibliographic citation: Ker et al. (2022) Nutrient composition of Chenopodium formosanum Koidz. bran: Fractionation and bioactivity of its soluble active polysaccharides. PeerJ 10:e13459 https://doi.org/10.7717/peerj.13459
date submitted: 2021-09-13
date accepted: 2022-04-27
issued: 2022-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ker
  given name: Yaw-Bee
author list: Agent
  family name: Wu
  given name: Hui-Ling
author list: Agent
  family name: Chen
  given name: Kuan-Chou
author list: Agent
  family name: Peng
  given name: Robert Y.
doi: 10.7717/peerj.13459
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-25
copyright: ©2022 Ker et al.
attribution name: Ker et al.

Phytochemical content, especially spermidine derivatives, presenting antioxidant and antilipoxygenase activities in Thai bee pollens
type: item
type: AcademicArticle
description: Background Bee pollen (BP) is full of useful nutrients and phytochemicals.Its chemical components and bioactivities depend mainly on the type of floral pollen. Methods Monofloral BP from Camellia sinensis L., Mimosa diplotricha, Helianthus annuus L., Nelumbo nucifera, Xyris complanata, and Ageratum conyzoides were harvested. Crude extraction and partition were performed to yield solvent-partitioned extracts of each BP. Total phenolic content (TPC) was assayed by the Folin-Ciocalteu method, while the flavonoid content (FC) was measured by the aluminium chloride colorimetric method. Antioxidant capacity was measured by the (i) 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, (ii) 2,2’-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) scavenging activity and its Trolox equivalent antioxidant capacity (TEAC), and (iii) ferric reducing antioxidant power (FRAP). All samples were tested for lipoxygenase inhibitory (LOXI) activity. The most active sample was enriched by silica gel 60 column chromatography (SiG60-CC) and high performance liquid chromatography (HPLC), observing the chemical pattern of each fraction using thin layer chromatography. Chemical structure of the most active compound was analyzed by proton nuclear magnetic resonance and mass spectrometry. Results Dichloromethane (DCM)-partitioned BP extracts of H. annuus L. and M. diplotricha (DCMMBP) showed a very high TPC, while DCMMBP had the highest FC. In addition, DCMMBP had the strongest DPPH and ABTS radical scavenging activities (as a TEAC value), as well as FRAP value. Also, DCMMBP (60 µg/mL) gave the highest LOXI activity (78.60 ± 2.81%). Hence, DCMMBP was chosen for further enrichment by SiG60-CC and HPLC. Following this, the most active fraction showed higher antioxidant andLOXI activities with an EC50 for DPPH and ABTS of 54.66 ± 3.45 µg/mL and 24.56 ± 2.99 µg/mL (with a TEAC value of 2,529.69 ± 142.16 µmole TE/g), respectively, and a FRAP value of 3,466.17 ± 81.30 µmole Fe2+/g…
format: application/pdf
format: text/html
creator: Phanthiwa Khongkarat
creator: Preecha Phuwapraisirisan
creator: Chanpen Chanchao
subject: Agricultural Science
subject: Biotechnology
description: doi:10.7717/peerj.13506
publisher: PeerJ Inc.
rights: © 2022 Khongkarat et al.
abstract: Background Bee pollen (BP) is full of useful nutrients and phytochemicals.Its chemical components and bioactivities depend mainly on the type of floral pollen. Methods Monofloral BP from Camellia sinensis L., Mimosa diplotricha, Helianthus annuus L., Nelumbo nucifera, Xyris complanata, and Ageratum conyzoides were harvested. Crude extraction and partition were performed to yield solvent-partitioned extracts of each BP. Total phenolic content (TPC) was assayed by the Folin-Ciocalteu method, while the flavonoid content (FC) was measured by the aluminium chloride colorimetric method. Antioxidant capacity was measured by the (i) 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, (ii) 2,2’-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) scavenging activity and its Trolox equivalent antioxidant capacity (TEAC), and (iii) ferric reducing antioxidant power (FRAP). All samples were tested for lipoxygenase inhibitory (LOXI) activity. The most active sample was enriched by silica gel 60 column chromatography (SiG60-CC) and high performance liquid chromatography (HPLC), observing the chemical pattern of each fraction using thin layer chromatography. Chemical structure of the most active compound was analyzed by proton nuclear magnetic resonance and mass spectrometry. Results Dichloromethane (DCM)-partitioned BP extracts of H. annuus L. and M. diplotricha (DCMMBP) showed a very high TPC, while DCMMBP had the highest FC. In addition, DCMMBP had the strongest DPPH and ABTS radical scavenging activities (as a TEAC value), as well as FRAP value. Also, DCMMBP (60 µg/mL) gave the highest LOXI activity (78.60 ± 2.81%). Hence, DCMMBP was chosen for further enrichment by SiG60-CC and HPLC. Following this, the most active fraction showed higher antioxidant andLOXI activities with an EC50 for DPPH and ABTS of 54.66 ± 3.45 µg/mL and 24.56 ± 2.99 µg/mL (with a TEAC value of 2,529.69 ± 142.16 µmole TE/g), respectively, and a FRAP value of 3,466.17 ± 81.30 µmole Fe2+/g…
bibliographic citation: Khongkarat et al. (2022) Phytochemical content, especially spermidine derivatives, presenting antioxidant and antilipoxygenase activities in Thai bee pollens. PeerJ 10:e13506 https://doi.org/10.7717/peerj.13506
date submitted: 2022-01-31
date accepted: 2022-05-06
issued: 2022-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khongkarat
  given name: Phanthiwa
author list: Agent
  family name: Phuwapraisirisan
  given name: Preecha
author list: Agent
  family name: Chanchao
  given name: Chanpen
doi: 10.7717/peerj.13506
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-25
copyright: ©2022 Khongkarat et al.
attribution name: Khongkarat et al.

Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue
type: item
type: AcademicArticle
description: Background Fat accumulation in visceral adipose tissue (VAT) confers increased risk for metabolic disorders of obesity, whereas accumulation of subcutaneous adipose tissue (SAT) is associated with lower risk and may be protective. Previous studies have shed light on the gene expression profile differences between SAT and VAT; however, the chromatin accessibility landscape differences and how the cis-regulatory elements govern gene expression changes between SAT and VAT are unknown. Methods Pig were used to characterize the differences in chromatin accessibility between the two adipose depots-derived stromal vascular fractions (SVFs) using DNase-sequencing (DNase-seq). Using integrated data from DNase-seq, H3K27ac ChIP-sequencing (ChIP-seq), and RNA-sequencing (RNA-seq), we investigated how the regulatory locus complexity regulated gene expression changes between SAT and VAT and the possible impact that these changes may have on the different biological functions of these two adipose depots. Results SVFs form SAT and VAT (S-SVF and V-SVF) have differential chromatin accessibility landscapes. The differential DNase I hypersensitive site (DHS)-associated genes, which indicate dynamic chromatin accessibility, were mainly involved in metabolic processes and inflammatory responses. Additionally, the Krüppel-like factor family of transcription factors were enriched in the differential DHSs. Furthermore, the chromatin accessibility data were highly associated with differential gene expression as indicated using H3K27ac ChIP-seq and RNA-seq data, supporting the validity of the differential gene expression determined using DNase-seq. Moreover, by combining epigenetic and transcriptomic data, we identified two candidate genes, NR1D1 and CRYM, could be crucial to regulate distinct metabolic and inflammatory characteristics between SAT and VAT. Together, these results uncovered differences in the transcription regulatory network and enriched the mechanistic understanding of the …
format: application/pdf
format: text/html
creator: Wenyang Sun
creator: Tinghuan Zhang
creator: Silu Hu
creator: Qianzi Tang
creator: Xi Long
creator: Xu Yang
creator: Shuangbao Gun
creator: Lei Chen
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.13250
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Background Fat accumulation in visceral adipose tissue (VAT) confers increased risk for metabolic disorders of obesity, whereas accumulation of subcutaneous adipose tissue (SAT) is associated with lower risk and may be protective. Previous studies have shed light on the gene expression profile differences between SAT and VAT; however, the chromatin accessibility landscape differences and how the cis-regulatory elements govern gene expression changes between SAT and VAT are unknown. Methods Pig were used to characterize the differences in chromatin accessibility between the two adipose depots-derived stromal vascular fractions (SVFs) using DNase-sequencing (DNase-seq). Using integrated data from DNase-seq, H3K27ac ChIP-sequencing (ChIP-seq), and RNA-sequencing (RNA-seq), we investigated how the regulatory locus complexity regulated gene expression changes between SAT and VAT and the possible impact that these changes may have on the different biological functions of these two adipose depots. Results SVFs form SAT and VAT (S-SVF and V-SVF) have differential chromatin accessibility landscapes. The differential DNase I hypersensitive site (DHS)-associated genes, which indicate dynamic chromatin accessibility, were mainly involved in metabolic processes and inflammatory responses. Additionally, the Krüppel-like factor family of transcription factors were enriched in the differential DHSs. Furthermore, the chromatin accessibility data were highly associated with differential gene expression as indicated using H3K27ac ChIP-seq and RNA-seq data, supporting the validity of the differential gene expression determined using DNase-seq. Moreover, by combining epigenetic and transcriptomic data, we identified two candidate genes, NR1D1 and CRYM, could be crucial to regulate distinct metabolic and inflammatory characteristics between SAT and VAT. Together, these results uncovered differences in the transcription regulatory network and enriched the mechanistic understanding of the …
bibliographic citation: Sun et al. (2022) Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue. PeerJ 10:e13250 https://doi.org/10.7717/peerj.13250
date submitted: 2021-11-12
date accepted: 2022-03-21
issued: 2022-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Wenyang
author list: Agent
  family name: Zhang
  given name: Tinghuan
author list: Agent
  family name: Hu
  given name: Silu
author list: Agent
  family name: Tang
  given name: Qianzi
author list: Agent
  family name: Long
  given name: Xi
author list: Agent
  family name: Yang
  given name: Xu
author list: Agent
  family name: Gun
  given name: Shuangbao
author list: Agent
  family name: Chen
  given name: Lei
doi: 10.7717/peerj.13250
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-24
copyright: ©2022 Sun et al.
attribution name: Sun et al.

Effect of a cover crop on the aphid incidence is not explained by increased top-down regulation
type: item
type: AcademicArticle
description: Background Cover crops can be used as a habitat management strategy to enhance the natural enemies and their temporal synchronization with a target pest. We examined the effect of winter oat intercropping within organic plum orchards on the natural enemy abundance and seasonal dynamics on the biological control of plum aphids in spring in Central Chile. Methods We compared the incidence and abundance of natural enemies and aphid pests from winter to the end of spring using two treatments: (1) plum trees with an oat cover crop (OCC) and (2) plum trees without a cover crop but with spontaneous vegetation (SV). We hypothesized that cover crops allow the development of winter cereal aphids, promoting the early arrival of natural enemies in spring, resulting in an earlier control of plum aphids. Results Winter cereal aphids developed well on the OCC, and as a result, a lower plum aphid incidence in spring was observed when compared to the SV. However, the abundance of natural enemies and the parasitism rates cannot explain the positive impacts of the oat cover crop on the aphid populations as there were no differences between treatments. A potential effect of the oat due to chemical and/or physical stimuli (bottom-up effects) could help to explain these results.
format: application/pdf
format: text/html
creator: Jeniffer K. Alvarez-Baca
creator: Xiomara Montealegre
creator: Cécile Le Lann
creator: Joan Van Baaren
creator: Blas Lavandero
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.13299
publisher: PeerJ Inc.
rights: © 2022 Alvarez-Baca et al.
abstract: Background Cover crops can be used as a habitat management strategy to enhance the natural enemies and their temporal synchronization with a target pest. We examined the effect of winter oat intercropping within organic plum orchards on the natural enemy abundance and seasonal dynamics on the biological control of plum aphids in spring in Central Chile. Methods We compared the incidence and abundance of natural enemies and aphid pests from winter to the end of spring using two treatments: (1) plum trees with an oat cover crop (OCC) and (2) plum trees without a cover crop but with spontaneous vegetation (SV). We hypothesized that cover crops allow the development of winter cereal aphids, promoting the early arrival of natural enemies in spring, resulting in an earlier control of plum aphids. Results Winter cereal aphids developed well on the OCC, and as a result, a lower plum aphid incidence in spring was observed when compared to the SV. However, the abundance of natural enemies and the parasitism rates cannot explain the positive impacts of the oat cover crop on the aphid populations as there were no differences between treatments. A potential effect of the oat due to chemical and/or physical stimuli (bottom-up effects) could help to explain these results.
bibliographic citation: Alvarez-Baca et al. (2022) Effect of a cover crop on the aphid incidence is not explained by increased top-down regulation. PeerJ 10:e13299 https://doi.org/10.7717/peerj.13299
date submitted: 2021-10-01
date accepted: 2022-03-29
issued: 2022-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alvarez-Baca
  given name: Jeniffer K.
author list: Agent
  family name: Montealegre
  given name: Xiomara
author list: Agent
  family name: Le Lann
  given name: Cécile
author list: Agent
  family name: Van Baaren
  given name: Joan
author list: Agent
  family name: Lavandero
  given name: Blas
doi: 10.7717/peerj.13299
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-24
copyright: ©2022 Alvarez-Baca et al.
attribution name: Alvarez-Baca et al.

Down-regulated NEDD4L facilitates tumor progression through activating Notch signaling in lung adenocarcinoma
type: item
type: AcademicArticle
description: Neural precursor cell expressed developmentally down-regulated 4-like protein (NEDD4L), an E3 ubiquitin ligase, exerts an important role in diverse biological processes including development, tumorigenesis, and tumor progression. Although the role of NEDD4L in the pathogenesis of lung adenocarcinoma (LUAD) has been described, the mechanism by which NEDD4L promotes LUAD progression remains poorly understood. In the study, the correlation between NEDD4L level and clinical outcome in LUAD patients was analysed using the data from The Cancer Genome Atlas (TCGA) database. NEDD4L expression in LUAD cell lines and tissue samples was assessed through quantitative real-time PCR (qRT-PCR). The biological function of NEDD4L on regulating LUAD cell proliferation was tested with Cell Counting Kit-8 (CCK-8) assay in vitro, and mouse xenograft tumor model in vivo. We found that NEDD4L expression was significantly decreased in LUAD tissues and cell lines. Lower expression of NEDD4L exhibited a significantly poorer overall survival. Functionally, NEDD4L knockdown in H1299 cells accelerated cell growth, whereas NEDD4L overexpression in A549 cells repressed cell proliferation. NEDD4L overexpression also inhibited tumor xenograft growth in vivo. Mechanistically, NEDD4L decreased the protein stability of notch receptor 2 (Notch2) through facilitating its ubiquitination and degradation by ubiquitin-proteasome system. Consequently, NEDD4L negatively regulated Notch signaling activation in LUAD cells, and RO4929097 (a Notch inhibitor) treatment effectively repressed the effect of NEDD4L knockdown on LUAD cell proliferation. Taken together, these results demonstrate that down-regulated NEDD4L facilitates LUAD progression by activating Notch signaling, and NEDD4L may be a promising target to treat LUAD.
format: application/pdf
format: text/html
creator: Liping Lin
creator: Xuan Wu
creator: Yuanxue Jiang
creator: Caijiu Deng
creator: Xi Luo
creator: Jianjun Han
creator: Jiazhu Hu
creator: Xiaolong Cao
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13402
publisher: PeerJ Inc.
rights: © 2022 Lin et al.
abstract: Neural precursor cell expressed developmentally down-regulated 4-like protein (NEDD4L), an E3 ubiquitin ligase, exerts an important role in diverse biological processes including development, tumorigenesis, and tumor progression. Although the role of NEDD4L in the pathogenesis of lung adenocarcinoma (LUAD) has been described, the mechanism by which NEDD4L promotes LUAD progression remains poorly understood. In the study, the correlation between NEDD4L level and clinical outcome in LUAD patients was analysed using the data from The Cancer Genome Atlas (TCGA) database. NEDD4L expression in LUAD cell lines and tissue samples was assessed through quantitative real-time PCR (qRT-PCR). The biological function of NEDD4L on regulating LUAD cell proliferation was tested with Cell Counting Kit-8 (CCK-8) assay in vitro, and mouse xenograft tumor model in vivo. We found that NEDD4L expression was significantly decreased in LUAD tissues and cell lines. Lower expression of NEDD4L exhibited a significantly poorer overall survival. Functionally, NEDD4L knockdown in H1299 cells accelerated cell growth, whereas NEDD4L overexpression in A549 cells repressed cell proliferation. NEDD4L overexpression also inhibited tumor xenograft growth in vivo. Mechanistically, NEDD4L decreased the protein stability of notch receptor 2 (Notch2) through facilitating its ubiquitination and degradation by ubiquitin-proteasome system. Consequently, NEDD4L negatively regulated Notch signaling activation in LUAD cells, and RO4929097 (a Notch inhibitor) treatment effectively repressed the effect of NEDD4L knockdown on LUAD cell proliferation. Taken together, these results demonstrate that down-regulated NEDD4L facilitates LUAD progression by activating Notch signaling, and NEDD4L may be a promising target to treat LUAD.
bibliographic citation: Lin et al. (2022) Down-regulated NEDD4L facilitates tumor progression through activating Notch signaling in lung adenocarcinoma. PeerJ 10:e13402 https://doi.org/10.7717/peerj.13402
date submitted: 2021-12-21
date accepted: 2022-04-17
issued: 2022-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Liping
author list: Agent
  family name: Wu
  given name: Xuan
author list: Agent
  family name: Jiang
  given name: Yuanxue
author list: Agent
  family name: Deng
  given name: Caijiu
author list: Agent
  family name: Luo
  given name: Xi
author list: Agent
  family name: Han
  given name: Jianjun
author list: Agent
  family name: Hu
  given name: Jiazhu
author list: Agent
  family name: Cao
  given name: Xiaolong
doi: 10.7717/peerj.13402
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-24
copyright: © 2022 Lin et al.
attribution name: Lin et al.

Fisetin glycosides synthesized by cyclodextrin glycosyltransferase from Paenibacillus sp. RB01: characterization, molecular docking, and antioxidant activity
type: item
type: AcademicArticle
description: Fisetin is a flavonoid that exhibits high antioxidant activity and is widely employed in the pharmacological industries. However, the application of fisetin is limited due to its low water solubility. In this study, glycoside derivatives of fisetin were synthesized by an enzymatic reaction using cyclodextrin glycosyltransferase (CGTase) from Paenibacillus sp. RB01 in order to improve the water solubility of fisetin. Under optimal conditions, CGTase was able to convert more than 400 mg/L of fisetin to its glycoside derivatives, which is significantly higher than the previous biosynthesis using engineered E. coli. Product characterization by HPLC and LC-MS/MS revealed that the transglycosylated products consisted of at least five fisetin glycoside derivatives, including fisetin mono-, di- and triglucosides, as well as their isomers. Enzymatic analysis by glucoamylase and α-glucosidase showed that these fisetin glycosides were formed by α-1,4-glycosidic linkages. Molecular docking demonstrated that there are two possible binding modes of fisetin in the enzyme active site containing CGTase-glysosyl intermediate, in which O7 and O4’ atoms of fisetin positioned close to the C1 of glycoside donor, corresponding to the isomers of the obtained fisetin monoglucosides. In addition, the water solubility and the antioxidant activity of the fisetin monoglucosides were tested. It was found that their water solubility was increased at least 800 times when compared to that of their parent molecule while still maintaining the antioxidant activity. This study revealed the potential application of CGTase to improve the solubility of flavonoids.
format: application/pdf
format: text/html
creator: Nattawadee Lorthongpanich
creator: Panupong Mahalapbutr
creator: Thanyada Rungrotmongkol
creator: Thanapon Charoenwongpaiboon
creator: Manchumas Hengsakul Prousoontorn
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.13467
publisher: PeerJ Inc.
rights: © 2022 Lorthongpanich et al.
abstract: Fisetin is a flavonoid that exhibits high antioxidant activity and is widely employed in the pharmacological industries. However, the application of fisetin is limited due to its low water solubility. In this study, glycoside derivatives of fisetin were synthesized by an enzymatic reaction using cyclodextrin glycosyltransferase (CGTase) from Paenibacillus sp. RB01 in order to improve the water solubility of fisetin. Under optimal conditions, CGTase was able to convert more than 400 mg/L of fisetin to its glycoside derivatives, which is significantly higher than the previous biosynthesis using engineered E. coli. Product characterization by HPLC and LC-MS/MS revealed that the transglycosylated products consisted of at least five fisetin glycoside derivatives, including fisetin mono-, di- and triglucosides, as well as their isomers. Enzymatic analysis by glucoamylase and α-glucosidase showed that these fisetin glycosides were formed by α-1,4-glycosidic linkages. Molecular docking demonstrated that there are two possible binding modes of fisetin in the enzyme active site containing CGTase-glysosyl intermediate, in which O7 and O4’ atoms of fisetin positioned close to the C1 of glycoside donor, corresponding to the isomers of the obtained fisetin monoglucosides. In addition, the water solubility and the antioxidant activity of the fisetin monoglucosides were tested. It was found that their water solubility was increased at least 800 times when compared to that of their parent molecule while still maintaining the antioxidant activity. This study revealed the potential application of CGTase to improve the solubility of flavonoids.
bibliographic citation: Lorthongpanich et al. (2022) Fisetin glycosides synthesized by cyclodextrin glycosyltransferase from Paenibacillus sp. RB01: characterization, molecular docking, and antioxidant activity. PeerJ 10:e13467 https://doi.org/10.7717/peerj.13467
date submitted: 2021-11-18
date accepted: 2022-04-29
issued: 2022-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lorthongpanich
  given name: Nattawadee
author list: Agent
  family name: Mahalapbutr
  given name: Panupong
author list: Agent
  family name: Rungrotmongkol
  given name: Thanyada
author list: Agent
  family name: Charoenwongpaiboon
  given name: Thanapon
author list: Agent
  family name: Prousoontorn
  given name: Manchumas Hengsakul
doi: 10.7717/peerj.13467
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-24
copyright: © 2022 Lorthongpanich et al.
attribution name: Lorthongpanich et al.

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