Overexpression of AmCBF1 enhances drought and cold stress tolerance, and improves photosynthesis in transgenic cotton
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.
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
Influence of hot air drying on capsaicinoids, phenolics, flavonoids and antioxidant activities of ‘Super Hot’ chilies
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.
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
Heat stress response in Chinese cabbage (Brassica rapa L.) revealed by transcriptome and physiological analysis
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.
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
Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing
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.
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
Nutrient composition of Chenopodium formosanum Koidz. bran: Fractionation and bioactivity of its soluble active polysaccharides
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.
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
Phytochemical content, especially spermidine derivatives, presenting antioxidant and antilipoxygenase activities in Thai bee pollens
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 and an IC50 for LOXI activity of 12.11 ± 0.36 µg/mL. Triferuloyl spermidines were revealed to be the likely main active components. Conclusions TPC, FC, and spermidine derivatives played an important role in the antioxidant and antilipoxygenase activities in M. diplotricha bee pollen.
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
Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue
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 different biological functions between SAT and VAT.
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
Effect of a cover crop on the aphid incidence is not explained by increased top-down regulation
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.
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
Down-regulated NEDD4L facilitates tumor progression through activating Notch signaling in lung adenocarcinoma
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.
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
Fisetin glycosides synthesized by cyclodextrin glycosyltransferase from Paenibacillus sp. RB01: characterization, molecular docking, and antioxidant activity
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.
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