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1.
J Environ Sci (China) ; 150: 25-35, 2025 Apr.
Article in English | MEDLINE | ID: mdl-39306400

ABSTRACT

Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor. An economical solid carbon source was developed by composition of polyvinyl alcohol, sodium alginate, and corncob, which was utilized as external carbon source in the anaerobic anoxic oxic (AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage, and the nitrogen removal was remarkably improved from 63.2% to 96.5%. Furthermore, the effluent chemical oxygen demand maintained at 35 mg/L or even lower, and the total nitrogen was reduced to less than 2 mg/L. Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides, respectively. The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO3--N to NO2--N conversion in both AAO and the biofilter reactors, thus enabled stable reaction. The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abundance of genes related to the tricarboxylic acid cycle, and then guaranteed efficient carbon metabolism. The results indicate that the composite carbon source is feasible for denitrification enhancement of AAO-biofilter, which contribute to the theoretical foundation for practical nitrogen removal application.


Subject(s)
Carbon , Denitrification , Metagenomics , Waste Disposal, Fluid , Carbon/metabolism , Waste Disposal, Fluid/methods , Nitrogen/metabolism , Bioreactors , Anaerobiosis , Sewage , Filtration/methods
2.
Sci Total Environ ; 954: 176273, 2024 Sep 14.
Article in English | MEDLINE | ID: mdl-39278478

ABSTRACT

The priming effect, i.e., the changes in soil organic matter (SOM) decomposition following fresh organic carbon (C) inputs is known to influence C storage in terrestrial ecosystems. Microplastics (particle size <5 mm) are ubiquitous in soils due to the increasing use and often inadequate end-of-life management of plastics. Conventional polyethylene and bio-degradable (PHBV) plastics contain large amounts of C within their molecular structure, which can be assimilated by microorganisms. However, the extent and direction of the potential priming effect induced by microplastics is unclear. As such, we added 14C-labeled glucose to investigate how background polyethylene and PHBV microplastics (1 %, w/w) affect SOM decomposition and its potential microbial mechanisms in a short-term. The cumulative CO2 emission in soil contaminated with PHBV was 42-53 % higher than under Polyethylene contaminated soil after 60-day incubation. Addition of glucose increased SOM decomposition and induced a positive priming effect, as a consequence, caused a negative net soil C balance (-59 to -132 µg C g-1 soil) regardless of microplastic types. K-strategists dominated in the PHBV-contaminated soils and induced 72 % higher positive priming effects as compared to Polyethylene-contaminated soils (160 vs. 92 µg C g-1 soil). This was attributed to the enhanced decomposition of recalcitrant SOM to acquire nitrogen. The stronger priming effect associated in PHBVs can be attributed to cooperative decomposition among fungi and bacteria, which metabolize more recalcitrant C in PHBV. Moreover, comparatively higher calorespirometric ratios, lower substrate use efficiency, and larger enzyme activity but shorter turnover time of enzymes indicated that soil contaminated with PHBV release more energy, and have a more efficient microbial catabolism and are more efficient in SOM decomposition and nutrient resource uptake. Overall, microplastics, (especially bio-degradable microplastics) can alter biogeochemical cycles with significant negative consequences for C sequestration via increasing SOM decomposition in agricultural soils and for regional and global C budgets.

3.
Front Neurosci ; 18: 1447743, 2024.
Article in English | MEDLINE | ID: mdl-39176380

ABSTRACT

Introduction: The fragile brain includes both the developing brain in childhood and the deteriorating brain in elderly. While the effects of general anesthesia on the myelin sheath of developing brain have been well-documented, limited research has explored its impact on degenerating brain in elderly individuals. Methods: In our study, aged marmosets in control group were only anesthetized with 6-8% sevoflurane and 100% oxygen (2 L/min) for 1-2 min for anesthesia induction. In addition to anesthesia induction, the anesthesia group was exposed to a clinical concentration of sevoflurane (1.5-2%) for 6 h to maintain anesthesia. After anesthesia, scanning electron microscopy (SEM) and artificial intelligence-assisted image analysis were utilized to observe the effects of general anesthesia on the myelin sheath in prefrontal cortex (PFC) of aged marmosets. Results: Compared with the control group, our findings revealed no evidence that 6 h of sevoflurane general anesthesia altered the thickness of myelin sheath, the diameter of myelinated axons, and the g-ratio in prefrontal cortex of aged marmosets. Conclusion: Clinical concentration of sevoflurane may have no short-term effect on the myelin sheath in prefrontal cortex of aged marmosets.

4.
J Fungi (Basel) ; 10(8)2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39194882

ABSTRACT

Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated in a different climatic zone. Using high-throughput sequencing, we aimed to assess fungal diversity patterns and investigate the primary environmental factors influencing fungal diversity. Our results indicate that soil fungal diversity exhibits different elevational distribution patterns on different mountains, highlighting the combined effects of climate, soil properties, and geographic topology. Notably, the total and available phosphorus contents in the soil emerged as key determinants in explaining the differences in diversity attributed to soil properties. Despite the varied responses of fungal diversity to elevational gradients among different trophic guilds and taxonomic levels, their primary environmental determinants remained remarkably consistent. In particular, total and available phosphorus contents showed significant correlations with the diversity of the majority of the trophic guilds and taxonomic levels. Our study reveals the absence of a uniform diversity pattern along elevational gradients, underscoring the general sensitivity of fungi to soil conditions. By enriching our understanding of fungal diversity dynamics, this research enhances our comprehension of the formation and maintenance of elevational fungal diversity and the response of microbial communities in mountain ecosystems to climate change. This study provides valuable insights for future ecological studies of similar biotic communities.

5.
Heliyon ; 10(11): e30950, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38947437

ABSTRACT

Understanding who adopt green production and why they choose this strategy is an important issue that needs to be addressed in the context of increasingly severe agricultural pollution. Previous studies have generally investigated subsistence-oriented smallholders, typically employing profit maximization or risk minimization models. However, Chinese farmers have differentiated, and have unique characteristics. This study collected data from 960 random samples of rice farmers and conducted quantitative analysis. The findings reveal that 94.9 % of the farmers had less than 2-ha rice-planting area, and 80.21 % of farmers reported that their purpose of planting rice was for family self-feeding. Furthermore, the new standard to define smallholder based on whether their production purpose is self-feeding or selling and found that non-smallholders had an overall advantage and passed the t-test. Even more non-smallholder (76.32 %) intentionally chose green pesticide than smallholders (66.1 %), but their decision-making logic was different. Binary logistic regression results show that three aspects of self-actualization (environmental, market, and personal) positively and significantly affected the green production behavior of smallholders, but not significant for non-smallholders. This study suggests that in China, where smallholders are the mainstay of agriculture production, green production by smallholders will greatly improve the ecological environment and provide high quality agricultural products.

6.
Plants (Basel) ; 13(13)2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38999577

ABSTRACT

Fungi as heterotrophs are key participants in the decomposition of organic materials and the transformation of nutrients in agroecosystems. Ditch-buried straw return as a novel conservation management strategy can improve soil fertility and alter hydrothermal processes. However, how ditch-buried straw return strategies affect the soil fungal community is still unclear. Herein, a 7-year field trial was conducted to test the influences of burial depth (0, 10, 20, 30, and 40 cm) and the amount of ditch-buried straw (half, full, double) on the diversity, composition, and predicted functions of a soil fungal community, as well as the activities of carbon-degraded enzymes. Under the full amount of straw burial, the abundance of phylum Ascomycota was 7.5% higher as compared to other burial amount treatments. This further increased the activity of cellobiohydrolase by 32%, as revealed by the positive correlation between Ascomycota and cellobiohydrolase. With deeper straw burial, however, the abundance of Ascomycota and ß-D-glucopyranoside activity decreased. Moreover, genus Alternaria and Fusarium increased while Mortierella decreased with straw burial amount and depth. FUNgild prediction showed that plant fungal pathogens were 1- to 2-fold higher, whilst arbuscular mycorrhizal fungi were 64% lower under straw buried with double the amount and at a depth of 40 cm. Collectively, these findings suggest that ditch-buried straw return with a full amount and buried at a depth less than 30 cm could improve soil nutrient cycles and health and may be beneficial to subsequent crop production.

7.
BMC Plant Biol ; 24(1): 590, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38902595

ABSTRACT

BACKGROUND: The Prunus sibirica seeds with rich oils has great utilization, but contain amygdalin that can be hydrolyzed to release toxic HCN. Thus, how to effectively reduce seed amygdalin content of P. sibirica is an interesting question. Mandelonitrile is known as one key intermediate of amygdalin metabolism, but which mandelonitrile lyase (MDL) family member essential for its dissociation destined to low amygdalin accumulation in P. sibirica seeds still remains enigmatic. An integration of our recent 454 RNA-seq data, amygdalin and mandelonitrile content detection, qRT-PCR analysis and function determination is described as a critical attempt to determine key MDL and to highlight its function in governing mandelonitrile catabolism with low amygdalin accumulation in Prunus sibirica seeds for better developing edible oil and biodiesel in China. RESULTS: To identify key MDL and to unravel its function in governing seed mandelonitrile catabolism with low amygdalin accumulation in P. sibirica. Global identification of mandelonitrile catabolism-associated MDLs, integrated with the across-accessions/developing stages association of accumulative amount of amygdalin and mandelonitrile with transcriptional level of MDLs was performed on P. sibirica seeds of 5 accessions to determine crucial MDL2 for seed mandelonitrile catabolism of P. sibirica. MDL2 gene was cloned from the seeds of P. sibirica, and yeast eukaryotic expression revealed an ability of MDL2 to specifically catalyze the dissociation of mandelonitrile with the ideal values of Km (0.22 mM) and Vmax (178.57 U/mg). A combination of overexpression and mutation was conducted in Arabidopsis. Overexpression of PsMDL2 decreased seed mandelonitrile content with an increase of oil accumulation, upregulated transcript of mandelonitrile metabolic enzymes and oil synthesis enzymes (involving FA biosynthesis and TAG assembly), but exhibited an opposite situation in mdl2 mutant, revealing a role of PsMDL2-mediated regulation in seed amygdalin and oil biosynthesis. The PsMDL2 gene has shown as key molecular target for bioengineering high seed oil production with low amygdalin in oilseed plants. CONCLUSIONS: This work presents the first integrated assay of genome-wide identification of mandelonitrile catabolism-related MDLs and the comparative association of transcriptional level of MDLs with accumulative amount of amygdalin and mandelonitrile in the seeds across different germplasms and developmental periods of P. sibirica to determine MDL2 for mandelonitrile dissociation, and an effective combination of PsMDL2 expression and mutation, oil and mandelonitrile content detection and qRT-PCR assay was performed to unravel a mechanism of PsMDL2 for controlling amygdalin and oil production in P. sibirica seeds. These findings could offer new bioengineering strategy for high oil production with low amygdalin in oil plants.


Subject(s)
Amygdalin , Prunus , Seeds , Amygdalin/metabolism , Prunus/genetics , Prunus/metabolism , Prunus/enzymology , Seeds/metabolism , Seeds/genetics , Plant Proteins/metabolism , Plant Proteins/genetics , Plant Oils/metabolism , Aldehyde-Lyases/metabolism , Aldehyde-Lyases/genetics , Gene Expression Regulation, Plant
8.
Mol Psychiatry ; 2024 May 04.
Article in English | MEDLINE | ID: mdl-38704506

ABSTRACT

Autism spectrum disorder (ASD) encompasses a range of neurodevelopmental conditions. Different mutations on a single ASD gene contribute to heterogeneity of disease phenotypes, possibly due to functional diversity of generated isoforms. SHANK2, a causative gene in ASD, demonstrates this phenomenon, but there is a scarcity of tools for studying endogenous SHANK2 proteins in an isoform-specific manner. Here, we report a point mutation on SHANK2, which is found in a patient with autism, located on exon of the SHANK2B transcript variant (NM_133266.5), hereby SHANK2BY29X. This mutation results in an early stop codon and an aberrant splicing event that impacts SHANK2 transcript variants distinctly. Induced pluripotent stem cells (iPSCs) carrying this mutation, from the patient or isogenic editing, fail to differentiate into functional dopamine (DA) neurons, which can be rescued by genetic correction. Available SMART-Seq single-cell data from human midbrain reveals the abundance of SHANK2B transcript in the ALDH1A1 negative DA neurons. We then show that SHANK2BY29X mutation primarily affects SHANK2B expression and ALDH1A1 negative DA neurons in vitro during early neuronal developmental stage. Mice knocked in with the identical mutation exhibit autistic-like behavior, decreased occupancy of ALDH1A1 negative DA neurons and decreased dopamine release in ventral tegmental area (VTA). Our study provides novel insights on a SHANK2 mutation derived from autism patient and highlights SHANK2B significance in ALDH1A1 negative DA neuron.

9.
J Org Chem ; 89(10): 7076-7083, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38701135

ABSTRACT

A method has been developed for the rapid synthesis of highly substituted 3-methylpyridones via the condensation of Baylis-Hillman amines and ketones under benzoic acid catalysis. The process features readily available starting materials, broad substrate scope, high functional group tolerance, excellent regioselectivity, and gram-scale synthesis. We envision that this on-demand construction of 3-methylpyridones will provide exciting opportunities in biological research, therapeutics, and material sciences.

10.
Org Lett ; 26(20): 4318-4322, 2024 May 24.
Article in English | MEDLINE | ID: mdl-38752547

ABSTRACT

Herein, we first report a γ-selective deuteration reaction of pyridines via H/D exchange without the need for preinstalled directing groups and transformable functional groups. The electrochemical process offers an attractive approach to producing γ-deuterated pyridines under gentle conditions. The broad substrate scope, excellent deuterium incorporation, and remarkable selectivity of the electrochemical method make it applicable for the late-stage modification of pharmaceutical molecules.

11.
Nat Commun ; 15(1): 3034, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589429

ABSTRACT

Chronic stress induces anxiety disorders via both neural pathways and circulating factors. Although many studies have elucidated the neural circuits involved in stress-coping behaviors, the origin and regulatory mechanism of peripheral cytokines in behavioural regulation under stress conditions are not fully understood. Here, we identified a serum cytokine, lipocalin 2 (LCN2), that was upregulated in participants with anxiety disorders. Using a mouse model of chronic restraint stress (CRS), circulating LCN2 was found to be related to stress-induced anxiety-like behaviour via modulation of neural activity in the medial prefrontal cortex (mPFC). These results suggest that stress increases hepatic LCN2 via a neural pathway, leading to disrupted cortical functions and behaviour.


Subject(s)
Anxiety , Prefrontal Cortex , Humans , Lipocalin-2/metabolism , Prefrontal Cortex/physiology , Anxiety/metabolism , Anxiety Disorders , Liver/metabolism
12.
Int J Mol Sci ; 25(6)2024 Mar 20.
Article in English | MEDLINE | ID: mdl-38542472

ABSTRACT

In recent years, the field of biology has witnessed a surge of interest in genomics research due to the advancements in biotechnology. Gene expression pattern analysis plays a crucial role in this research, as it enables us to understand the regulatory mechanism of gene expression and the associated biological processes. Real-time quantitative polymerase chain reaction (q-PCR) is an efficient method to analyze the gene expression patterns, for which accuracy relies on the standardized analysis of reference genes. However, numerous studies have shown that no reference gene is universal in all conditions, so screening a suitable reference gene under certain conditions is of great importance. Cinnamomum burmannii (C. burmannii) is rich in volatile components and has high medicinal and economic value. However, knowledge of the screening of reference genes for the gene expression analysis of C. burmannii is insufficient. Aiming at this problem, we evaluated and screened the reference genes in C. burmannii under different experimental conditions, including different abiotic stresses (Cold-treated, PEG-treated and Nacl-treated), different tissues, leaves at different developmental stages and different chemical types. In this study, different algorithms (∆Ct, geNorm, NormFinder and BestKeeper) were used to evaluate the stability of the candidate reference genes, and RefFinder further merged the output data to screen out the optimum reference gene under various experimental conditions in C. burmannii. The results showed that the optimal reference gene number for gene standardization was 2 under different experimental conditions. RPL27|RPS15 was the most suitable combination under the Nacl-treated and PEG-treated samples. RPL27|APT was the optimum combination under the Cold-treated samples. The optimal combinations of other samples were EF1α|ACT7 for different tissues, eIF-5A|Gllα for different borneol clones in C. burmannii, RPS15|ACT7 for leaves at different developmental stages and RPS15|TATA for all samples. Additionally, two terpenoid synthesis-related genes (CbWRKY4 and CbDXS2) were standardized to verify the feasibility of the selected reference genes under different experimental conditions. This study will be helpful for the subsequent molecular genetic mechanism study of C. burmannii.


Subject(s)
Cinnamomum , Gene Expression Regulation, Plant , Sodium Chloride , Cinnamomum/genetics , Gene Expression Profiling , Real-Time Polymerase Chain Reaction/methods , Reference Standards
13.
Int J Mol Sci ; 25(5)2024 Mar 06.
Article in English | MEDLINE | ID: mdl-38474323

ABSTRACT

This work aimed to identify the chemical compounds of Cinnamomum burmannii leaf essential oil (CBLEO) and to unravel the antibacterial mechanism of CBLEO at the molecular level for developing antimicrobials. CBLEO had 37 volatile compounds with abundant borneol (28.40%) and showed good potential to control foodborne pathogens, of which Staphylococcus aureus had the greatest inhibition zone diameter (28.72 mm) with the lowest values of minimum inhibitory concentration (1.0 µg/mL) and bactericidal concentration (2.0 µg/mL). To unravel the antibacterial action of CBLEO on S. aureus, a dynamic exploration of antibacterial growth, material leakage, ROS formation, protein oxidation, cell morphology, and interaction with genome DNA was conducted on S. aureus exposed to CBLEO at different doses (1/2-2×MIC) and times (0-24 h), indicating that CBLEO acts as an inducer for ROS production and the oxidative stress of S. aureus. To highlight the antibacterial action of CBLEO on S. aureus at the molecular level, we performed a comparative association of ROS accumulation with some key virulence-related gene (sigB/agrA/sarA/icaA/cidA/rsbU) transcription, protease production, and biofilm formation in S. aureus subjected to CBLEO at different levels and times, revealing that CBLEO-induced oxidative stress caused transcript suppression of virulence regulators (RsbU and SigB) and its targeted genes, causing a protease level increase destined for the biofilm formation and growth inhibition of S. aureus, which may be a key bactericidal action. Our findings provide valuable information for studying the antibacterial mechanism of essential oil against pathogens.


Subject(s)
Cinnamomum , Oils, Volatile , Oils, Volatile/pharmacology , Cinnamomum/genetics , Staphylococcus aureus/physiology , Virulence , Reactive Oxygen Species , Anti-Bacterial Agents/pharmacology , Biofilms , Oxidative Stress , Transcription, Genetic , Peptide Hydrolases/genetics , Microbial Sensitivity Tests
14.
Int J Biol Macromol ; 264(Pt 2): 130763, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38467223

ABSTRACT

Lindera glauca with rich resource and fruit terpene has emerged as potential material for utilization in China, but different germplasms show a variation for essential oil content and volatile profiling. This work aimed to determine key regulators (enzymes or transporters) and unravel mechanism of governing high production of essential oil of L. glauca fruit (EO-LGF). Temporal analysis of fruit growth and EO-LGF accumulation (yield, volatile compounds and contents) during development revealed a notable change in the contents of EO-LGF and its 45 compounds in developing fruits, and the major groups were monoterpene and sesquiterpene, showing good antioxidant and antimicrobial activities. To highlight molecular mechanism that govern such difference in terpene content and compound in developing fruits, Genome-wide assay was used to annotate 104 genes for terpene-synthesis pathway based on recent transcriptome data, and the comparative associations of terpene accumulative amount with gene transcriptional level were conducted on developing fruits to identify some crucial determinants (enzymes and transporters) with metabolic regulation model for high-quality terpene accumulation, involving in carbon allocation (sucrose cleavage, glycolysis and OPP pathway), metabolite transport, isoprene precursor production, C5-unit formation (MEP and MVA pathways), and mono-/sesqui-terpene synthesis. Our findings may present strategy for engineering terpene accumulation for utilization.


Subject(s)
Lindera , Oils, Volatile , Terpenes/metabolism , Fruit , Lindera/genetics , Lindera/metabolism , Oils, Volatile/metabolism , Monoterpenes/metabolism
15.
Int J Mol Sci ; 25(4)2024 Feb 11.
Article in English | MEDLINE | ID: mdl-38396847

ABSTRACT

Schima superba is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in S. superba growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 S. superba individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including Ss4CL2, SsCSL1, and SsCSL2, and transcription factors, including SsDELLA2 (SsSLR), SsDELLA3 (SsSLN), SsDELLA5 (SsGAI-like2), and SsNAM1, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of S. superba. The results not merely provide candidate functional genes related to S. superba growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species.


Subject(s)
MicroRNAs , RNA, Long Noncoding , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Circular/genetics , RNA, Long Noncoding/genetics , Plant Breeding , Gene Regulatory Networks
16.
J Exp Bot ; 75(8): 2545-2557, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38271585

ABSTRACT

Non-structural carbohydrates (NSCs) are building blocks for biomass and fuel metabolic processes. However, it remains unclear how tropical forests mobilize, export, and transport NSCs to cope with extreme droughts. We combined drought manipulation and ecosystem 13CO2 pulse-labeling in an enclosed rainforest at Biosphere 2, assessed changes in NSCs, and traced newly assimilated carbohydrates in plant species with diverse hydraulic traits and canopy positions. We show that drought caused a depletion of leaf starch reserves and slowed export and transport of newly assimilated carbohydrates below ground. Drought effects were more pronounced in conservative canopy trees with limited supply of new photosynthates and relatively constant water status than in those with continual photosynthetic supply and deteriorated water status. We provide experimental evidence that local utilization, export, and transport of newly assimilated carbon are closely coupled with plant water use in canopy trees. We highlight that these processes are critical for understanding and predicting tree resistance and ecosystem fluxes in tropical forest under drought.


Subject(s)
Carbon , Rainforest , Carbon/metabolism , Ecosystem , Droughts , Water/metabolism , Trees/metabolism , Carbohydrates , Plant Leaves/metabolism
17.
Nucleic Acids Res ; 52(D1): D1588-D1596, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37933857

ABSTRACT

Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.cncb.ac.cn/ppgr/) to address this critical gap, by collecting, integrating, analyzing and visualizing genomic, gene regulation and functional data of perennial plants. PPGR currently includes 60 species, 847 million protein-protein/TF (transcription factor)-target interactions, 9016 transcriptome samples under various environmental conditions and genetic backgrounds. Noteworthy is the focus on genes that regulate wood production, seasonal dormancy, terpene biosynthesis and leaf senescence representing a wealth of information derived from experimental data, literature mining, public databases and genomic predictions. Furthermore, PPGR incorporates a range of multi-omics search and analysis tools to facilitate browsing and application of these extensive datasets. PPGR represents a comprehensive and high-quality resource for perennial plants, substantiated by an illustrative case study that demonstrates its capacity in unraveling gene functions and shedding light on potential regulatory processes.


Subject(s)
Databases, Genetic , Genome, Plant , Genomics , Plants/genetics , Transcriptome
19.
Sci Rep ; 13(1): 21607, 2023 12 07.
Article in English | MEDLINE | ID: mdl-38062199

ABSTRACT

The recently discovered APRO (anti-proliferative protein) family encodes a group of trans-membrane glycoproteins and includes 6 members: TOB1, TOB2, BTG1, BTG2, BTG3 and BTG4. The APRO family is reportedly associated with the initiation and progression of cancers. This study aims to undertake a comprehensive investigation of the APRO family of proteins as a prognostic biomarker in various human tumors. We performed a pan-cancer analysis of the APRO family based on The Cancer Genome Atlas (TCGA). With the bioinformatics methods, we explored the prognostic value of the APRO family and the correlation between APRO family expression and tumor mutation burden (TMB), microsatellite instability (MSI), drug sensitivity, and immunotherapy in numerous cancers. Our results show that the APRO family was primarily down-regulated in cancer samples. The expression of APRO family members was linked with patient prognosis. In addition, APRO family genes showed significant association with immune infiltrate subtypes, tumor microenvironment, and tumor cell stemness. Finally, our study also demonstrated the relationship between APRO family genes and drug sensitivity. This study provides comprehensive information to understand the APRO family's role as an oncogene and predictor of survival in some tumor types.


Subject(s)
Immediate-Early Proteins , Neoplasms , Humans , Oncogenes , Immunotherapy , Cognition , Computational Biology , Neoplasms/drug therapy , Neoplasms/genetics , Tumor Microenvironment/genetics , Tumor Suppressor Proteins/genetics
20.
J Mater Chem B ; 11(40): 9757-9764, 2023 10 18.
Article in English | MEDLINE | ID: mdl-37807767

ABSTRACT

Stimuli-responsive/smart drug delivery systems (DDSs), particularly those that use temperature as a stimuli-response factor to activate drug release, are the subject of recent research. A phase change material (PCM) is a popular thermally responsive material that can be used as a drug carrier and only when the system temperature is above the phase change point is the drug released following the phase change material changing from solid to liquid. In this study, a novel NIR light-triggered temperature-sensitive drug delivery system is developed for controllable release of acyclovir (ACV). For this purpose, a mixture of a phase change material (T38) and an ACV compound is first emulsified with copper oxide nanoparticles (CuO NPs) as a Pickering stabilizer and a photothermal conversion material, and then encapsulated with SiO2 to form a photothermal stimuli-responsive delivery system. This system shows a uniform spherical shape with a well-distinct core-shell structure, and is further experimentally proven to be able to controllably release drugs with solid-liquid transition of the phase change carrier upon temperature change. These results indicate that cumulative release of ACV can reach 51.2% at 40 °C within 20 hours, which is much higher than 27.3% release achieved below the melting point of T38. In addition, CuO NPs with excellent photothermal conversion ability endow the system with precisely controllable drug delivery via NIR light stimulation, where the cumulative drug release can reach 83.6% after 7 cycles of light stimulation, allowing controlled release at a specific time or location.


Subject(s)
Doxorubicin , Silicon Dioxide , Temperature , Capsules , Doxorubicin/chemistry , Drug Delivery Systems/methods
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