Gene Level Research Articles

PnNAC2 promotes the biosynthesis of Panax notoginseng saponins and induces early flowering.

PnNAC2 positively regulates saponin biosynthesis by binding the promoters of key biosynthetic genes, including PnSS, PnSE, and PnDS. PnNAC2 accelerates flowering through directly associating with the promoters of FT genes. NAC transcription factors play an important regulatory role in both terpenoid biosynthesis and flowering. Saponins with multiple pharmacological activities are recognized as the major active components of Panax notoginseng. The P. notoginseng flower is crucial for growth and used for medicinal and food purposes. However, the precise function of the P. notoginseng NAC transcription factor in the regulation of saponin biosynthesis and flowering remains largely unknown. Here, we conducted a comprehensive characterization of a specific NAC transcription factor, designated as PnNAC2, from P. notoginseng. PnNAC2 was identified as a nuclear-localized protein with transcription activator activity. The expression profile of PnNAC2 across various tissues mirrored the accumulation pattern of total saponins. Knockdown experiments of PnNAC2 in P. notoginseng calli revealed a significant reduction in saponin content and the expression level of pivotal saponin biosynthetic genes, including PnSS, PnSE, and PnDS. Subsequently, Y1H assays, dual-LUC assays, and electrophoretic mobility shift assays (EMSAs) demonstrated that PnNAC2 exhibits binding affinity to the promoters of PnSS, PnSE and PnDS, thereby activating their transcription. Additionally, an overexpression assay of PnNAC2 in Arabidopsis thaliana witnessed the acceleration of flowering and the induction of the FLOWERING LOCUS T (FT) gene expression. Furthermore, PnNAC2 demonstrated the ability to bind to the promoters of AtFT and PnFT genes, further activating their transcription. In summary, these results revealed that PnNAC2 acts as a multifunctional regulator, intricately involved in the modulation of triterpenoid saponin biosynthesis and flowering processes.

Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet (Pennisetum glaucum).

The apetala2/ethylene response factor (AP2/ERF) gene family plays a crucial role in regulating plant growth and development and responding to different abiotic stresses (e.g., drought, heat, cold, and salinity). However, the knowledge of the ERF family in pearl millet remains limited. Here, a total of 167 high-confidence PgERF genes are identified and divided into five subgroups based on gene-conserved structure and phylogenetic analysis. Forty-one pairs of segmental duplication are found using collinear analysis. Nucleotide substitution analysis reveals these duplicated pairs are under positive purification, indicating they are actively responding to natural selection. Comprehensive transcriptomic analysis reveals that PgERF genesare preferentially expressed in the imbibed seeds and stem (tilling stage) and respond to heat, drought, and salt stress. Prediction of the cis-regulatory element by the PlantCARE program indicates that PgERF genes are involved in responses to environmental stimuli. Using reverse transcription quantitative real-time PCR (RT-qPCR), expression profiles of eleven selected PgERF genes are monitored in various tissues and during different abiotic stresses. Transcript levels of each PgERF gene exhibit significant changes during stress treatments. Notably, the PgERF7 gene is the only candidate that can be induced by all adverse conditions. Furthermore, four PgERF genes (i.e., PgERF22, PgERF37, PgERF88, and PgERF155) are shown to be involved in the ABA-dependent signaling pathway. These results provide useful bioinformatic and transcriptional information for understanding the roles of the pearl millet ERF gene family in adaptation to climate change.

Polyethylene Glycol Priming Enhances the Seed Germination and Seedling Growth of Scutellaria baicalensis Georgi under Salt Stress.

Seed priming has become a practical pre-sowing strategy to deal with abiotic stresses. This study aims to explore the effects of polyethylene glycol (PEG) priming on seed germination and seedling growth of Scutellaria baicalensis Georgi under salt stress. Regardless of seed priming, salt stress significantly inhibited the seed germination and seedling growth of S. baicalensis. PEG priming significantly alleviates the inhibitory effects of salt stress on seed germination and seedling growth when compared to non-priming and water priming. Among all treatments, PEG priming exhibited the highest germination rate, germination potential, seed vigor index, fresh weight, dry weight, and plant length; the highest contents of proline, soluble sugar, and soluble protein; the highest K+/Na+ ratio and relative water content; the highest antioxidant activities and contents; but the lowest H2O2, malondialdehyde (MDA) content, and relative electrical conductivity in response to salt stress. In addition, PEG priming had the highest transcript levels of antioxidant-related genes among all treatments under NaCl stress. Taken together, the results demonstrated that seed priming with PEG could be recommended as an effective practice to enhance the germination and early seedling growth of S. baicalensis under saline conditions.

Biotic pathways of reciprocal responses between antibiotic resistance genes and inorganic nitrogen cycling genes in amoxicillin-stressed compost ecosystems

This study explored the transformation of inorganic nitrogen, the expression levels of antibiotic resistance genes (ARGs), and the regulatory mechanisms of key species on ARGs and inorganic nitrogen cycling genes (INCGs) under different levels of amoxicillin (AMX) stress. High level of AMX inhibited the accumulation of NH4+-N, which increased by 531 % relative to the initial. Moreover, AMX to some extent increased the levels of nirS and nirK, which could potentially result in nitrogen loss and the accumulation of NO2–. Actinobacteria might serve as potential hosts for ARGs during sludge composting. This stress induced a complex response between INCGs and ARGs more complex due to key species. Under high-level AMX pressure, most species associated with ARGs likely derived from nitrogen cycling functional species. To conclude, high levels of AMX stress might lead to nitrogen cycling imbalance and the dissemination of antibiotic resistance genes in composting systems.

CENPA promotes glutamine metabolism and tumor progression by up-regulating SLC38A1 in endometrial cancer

Glutamine addiction is a significant hallmark of metabolic reprogramming in tumors and is crucial to the progression of cancer. Nevertheless, the regulatory mechanisms of glutamine metabolism in endometrial cancer (EC) remains elusive. In this research, we found that elevated expression of CENPA and solute carrier family 38 member 1 (SLC38A1) were firmly associated with worse clinical stage and unfavorable outcomes in EC patients. In addition, ectopic overexpression or silencing of CENPA could either enhance or diminish glutamine metabolism and tumor progression in EC. Mechanistically, CENPA directly regulated the transcriptional activity of the target gene, SLC38A1, leading to enhanced glutamine uptake and metabolism, thereby promoting EC progression. Notably, a prognostic model utilizing the expression levels of CENPA and SLC38A1 genes independently emerged as a prognostic factor for EC. More importantly, CENPA and SLC38A1 were significantly elevated and positively correlated, as well as indicative of poor prognosis in multiple cancers. In brief, our study confirmed that CENPA is a critical transcription factor involved in glutamine metabolism and tumor progression through modulating SLC38A1. This revelation suggests that targeting CENPA could be an appealing therapeutic approach to address pan-cancer glutamine addiction.

Effect of Short Photoperiod on Behavior and Brain Plasticity in Mice Differing in Predisposition to Catalepsy: The Role of BDNF and Serotonin System.

Seasonal affective disorder is characterized by depression during fall/winter as a result of shorter daylight. Catalepsy is a syndrome of some grave mental diseases. Both the neurotransmitter serotonin (5-HT) and brain-derived neurotrophic factor (BDNF) are involved in the pathophysiological mechanisms underlying catalepsy and depressive disorders. The aim was to compare the response of behavior and brain plasticity to photoperiod alterations in catalepsy-resistant C57BL/6J and catalepsy-prone CBA/Lac male mice. Mice of both strains were exposed for six weeks to standard-day (14 h light/10 h darkness) or short-day (4 h light/20 h darkness) conditions. Short photoperiod increased depressive-like behavior in both strains. Only treated CBA/Lac mice demonstrated increased cataleptic immobility, decreased brain 5-HT level, and the expression of Tph2 gene encoding the key enzyme for 5-HT biosynthesis. Mice of both strains maintained under short-day conditions, compared to those under standard-day conditions, showed a region-specific decrease in the brain transcription of the Htr1a, Htr4, and Htr7 genes. After a short photoperiod exposure, the mRNA levels of the BDNF-related genes were reduced in CBA/Lac mice and were increased in the C57BL/6J mice. Thus, the predisposition to catalepsy considerably influences the photoperiodic changes in neuroplasticity, wherein both C57BL/6J and CBA/Lac mice can serve as a powerful tool for investigating the link between seasons and mood.

Efficient Biosynthesis of Difucosyllactose via De Novo GDP-l-Fucose Pathway in Metabolically Engineered Escherichia coli.

Difucosyllactose (DFL) is an important component of human milk oligosaccharides (HMOs) and has significant benefits for the growth and development of infants. So far, a few microbial cell factories have been constructed for the production of DFL, which still have problems of low production and high cost. Herein, a high-level de novo pathway DFL-producing strain was constructed by multistep optimization strategies in Escherichia coli BL21star(DE3). We first efficiently synthesized the intermediate 2'-fucosyllactose (2'-FL) in E. coli BL21star(DE3) by the advisable stepwise strategy. The truncated α-1,3/4-fucosyltransferase (Hp3/4FT) was then introduced into the engineered strain to achieve de novo biosynthesis of DFL. ATP-dependent protease (Lon) and GDP-mannose hydrolase (NudK) were deleted, and mannose-6-phosphate isomerase (ManA) was overexpressed to improve GDP-l-fucose accumulation. The regulator RcsA was overexpressed to fine-tune the expression level of pathway genes, thereby increasing the synthesis of DFL. The final strain produced 6.19 g/L of DFL in the shake flask and 33.45 g/L of DFL in the 5 L fermenter, which were the highest reported titers so far. This study provides a more economical, sustainable, and effective strategy to produce the fucosylated human milk oligosaccharides (HMOs).

Expression of FAT1 in Lung Adenocarcinoma and Its Relationship with Immune Cell Infiltration

Lung cancer is a leading cause of cancer-related deaths. Non-small cell lung cancer (NSCLC) is the most common pathological subtype, with adenocarcinoma being the predominant type. FAT atypical cadherin 1 (FAT1) is a receptor-like protein with a high frequency of mutations in lung adenocarcinoma. The protein encoded by FAT1 plays a crucial role in processes such as cell adhesion, proliferation, and differentiation. This study aims to investigate the expression of FAT1 in lung adenocarcinoma and its relationship with immune infiltration. Gene expression levels and relevant clinical information of 513 lung adenocarcinoma samples and 397 adjacent lung samples were obtained through The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data. The mRNA expression levels of the FAT1 gene in lung adenocarcinoma tissues were analyzed, along with its association with the prognosis of lung adenocarcinoma patients. Pathway enrichment analysis was conducted to explore the signaling pathways regulated by the FAT1 gene. Immunoblotting was used to detect the differential expression of FAT1 in lung epithelial cells and various lung cancer cell lines, while immunohistochemistry was employed to assess FAT1 expression in lung cancer and adjacent tissues. FAT1 gene mutations were identified in 14% of lung adenocarcinoma patients. TCGA database data revealed significantly higher FAT1 mRNA expression in lung adenocarcinoma tissues compared to adjacent lung tissues. Kaplan-Meier analysis indicated lower survival rates in lung adenocarcinoma patients with higher FAT gene expression. Pathway enrichment analysis suggested the involvement of FAT1 in tumor development pathways, and its expression was closely associated with immune cell infiltration. Immunohistochemical validation demonstrated significantly higher expression of FAT1 in cancer tissues compared to adjacent lung tissues. FAT1 mRNA is highly expressed in lung adenocarcinoma tissues, and elevated FAT1 mRNA expression is associated with poor prognosis in lung adenocarcinoma patients. FAT1 may serve as a potential biomarker for lung cancer.

Screening cotton genotypes for their drought tolerance ability based on the expression level of dehydration-responsive element-binding protein and proline biosynthesis-related genes and morpho-physio-biochemical responses.

Drought stress adversely affects growth, development, productivity, and fiber quality of cotton (Gossypium hirsutum L). Breeding strategies to enhance drought tolerance require an improved knowledge of plant drought responses necessitating proper identification of drought-tolerant genotypes of crops, including cotton. The objective of this study was to classify the selected cotton genotypes for their drought tolerance ability based on morpho-physio-biochemical traits using Hierarchical Ward's cluster analysis. Five genotypes of cotton (Takfa 3, Takfa 6, Takfa 7, Takfa 84-4, and Takfa 86-5) were selected as plant materials, and were grown under well-watered (WW; 98 ± 2% field capacity) and water-deficit (WD; 50 ± 2% field capacity) conditions for 16days during the flower initiation stage. Data on morpho-physio-biochemical parameters and gene expression levels for these parameters were collected, and subsequently genotypes were classified either as a drought tolerant or drought susceptible one. Upregulation of GhPRP (proline-rich protein), GhP5CS (Δ1-pyrroline-5-carboxylate synthetase), and GhP5CR (Δ1-pyrroline-5-carboxylate reductase) in relation to free proline enrichment was observed in Takfa 3 genotype under WD condition. An accumulation of free proline, total soluble sugar, and potassium in plants under WD conditions was detected, which played a key role as major osmolytes controlling cellular osmotic potential. Magnesium and calcium concentrations were also enriched in leaves under WD conditions, functioning as essential elements and regulating photosynthetic abilities. Leaf greenness, net photosynthetic rate, stomatal conductance, and transpiration rate were also declined under WD conditions, leading to growth retardation, especially aboveground traits of Takfa 6, Takfa 7, Takfa 84-4, and Takfa 86-5 genotypes. An increase in leaf temperature (1.1 - 4.0°C) and crop water stress index (CWSI > 0.75) in relation to stomatal closure and reduced transpiration rate was recorded in cotton genotypes under WD conditions compared with WW conditions. Based on the increase of free proline, soluble sugar, leaf temperature, and CWSI, as well as the decrease of aboveground growth traits and physiological attributes, five genotypes were categorized into two cluster groups: drought tolerant (Takfa 3) and drought susceptible (Takfa 6, Takfa 7, Takfa 84-4, and Takfa 86-5). The identified drought-tolerant cotton genotype, namely, Takfa 3, may be grown in areas experiencing drought conditions. It is recommended to further validate the yield traits of Takfa 3 under rainfed field conditions in drought-prone environments.

The Role of miR-29a and miR-143 on the Anti-apoptotic MCL-1/cIAP-2 Genes Expression in EGFR Mutated Non-small Cell Lung Carcinoma Patients.

The survival rate of lung cancer is low due to the high frequency of drug resistance in patients with mutations in the driver genes. Overexpression of anti-apoptotic genes is one of the most prominent features of tumor drug resistance. EGFR signaling induces the expression of anti-apoptotic genes. Also, microRNAs (miRNAs) have a critical role in regulating biological functions such as apoptosis; a process mostly eluded in cancer progression. The mutation screening was performed on one thousand non-small cell lung carcinoma patients to enroll clinical samples in this study. Bioinformatics analysis predicted that miRNAs (miR-29a, miR-143) might regulate MCL-1 and cIAP-2 expression. We investigated the expression of MCL-1, cIAP-2, miR-29a, and miR-143 encoding genes in adenocarcinoma patients with or without EGFR mutations before treatment. The potential role of miR-29a and miR-143 on gene expression was evaluated by overexpression and luciferase assays in HEK-293T cells. EGFR mutations were found in 262 patients (26.2%) with a greater incidence in females (36.23% vs. 20.37%, P = 0.001). The expression levels of MCL-1 and cIAP-2 genes in patients with mutated EGFR were higher than those of wild-type EGFR. In contrast, compared to those of patients with wild-type EGFR, the expression levels of miR-29a and miR-143 were lower in the patients carrying EGFR mutations. In cell culture, overexpression of miR-29a and miR-143 significantly downregulated the expression of MCL-1 and cIAP-2. Dual-luciferase reporter experiments confirmed that miR-29a and miR-143 target MCL-1 and cIAP-2 mRNAs, respectively. Our results suggest that upregulation of EGFR signaling in lung cancer cells may increase anti-apoptotic MCL-1 and cIAP-2 gene expression, possibly through downregulation of miR-29a-3p and miR-143-3p.

Oncogenic miR-146a-PBX2 axis, a novel leukemic target in xenograft acute lymphoblastic leukemia model

Acute lymphoblastic leukemia (ALL) is one of the major hematological malignancies both in adults and children. Bone marrow biopsy is the main requirement for its accurate diagnostic and prognostic purpose till now that is a very painful process especially for children. The reluctance to go for bone marrow biopsy leads to delayed diagnosis treatment of ALL. MicroRNAs are emerging as diagnostic and therapeutic targets for cancer including ALL using less painful methods. The current study was conducted to evaluate the potential of miR-146a-PBX2 axis as a leukemic target of ALL using ALL-induced rabbit model. A total of 8 rabbits were divided into two groups: ALL-induced (diseased) and normal (control). The whole blood was collected from both groups and plasma isolation was performed. The levels of miR-146a and PBX2 gene in plasma of diseased and control samples were quantified by the real-time PCR (RT-qPCR). The normalized fold expression was calculated using miR-16 and the reference gene GAPDH. The results showed that there was a significant increase in miR-146a expression in diseased (ALL-induced) samples as compared to the control. Moreover, a significant upregulation of PBX2 gene was found in the diseased model as compared to that in the control. The results implied that miR-146a-PBX2 axis may be utilized as a potential target for ALL.

Dietary supplementation with short- and long-chain structured lipids alleviates obesity via regulating hepatic lipid metabolism, inflammation and gut microbiota in high-fat-diet-induced obese mice.

Obesity is closely associated with lipid accumulation, inflammation and intestinal microbiota dysbiosis. Short- and long-chain type structured lipids (SLCTs) are kinds of low-calorie structured lipids and demonstrate anti-obesity and hypolipidemia bioactivity. The objective of this study is to investigate the potential effects of dietary supplementation of SLCTs rich in short-chain fatty acids and polyunsaturated fatty acids on high-fat-diet-induced obesity and gut microbiota modulation in C57BL/6J mice. Results showed that SLCTs supplementation ameliorated body weight, dyslipidemia, liver lipid accumulation, liver injury and systemic inflammation in obese mice. As expected, immunohistochemical analysis showed that SLCTs significantly increased the expression of proliferator-activated receptor alpha and decreased the expression of Toll-like receptor 4 in liver tissue. Furthermore, SLCTs supplementation significantly downregulated the expression level of liver inflammation-related genes while upregulating the expression level of liver lipid metabolism-related genes. Additionally, SLCTssupplementation markedly enhanced the diversity of gut microbiota, reduced the Firmicutes/Bacteroidetes ratio and increased the diversity and richness of beneficial intestinal microorganisms, such as Bacteroides, Lactobacillus, Lachnospiraceae NK4A136 group, Alloprevotella and Ruminococcaceae UCG-014. Our work suggested that SLCTs may have the potential to reduce obesity associated with a high-fat diet by regulating liver metabolism, inflammation and gut microbiota. © 2024 Society of Chemical Industry.

Dietary pterostilbene exerts potential protective effects by regulating lipid metabolism and enhancing antioxidant capacity on liver in broilers.

Intensive breeding of broilers met the increasing demands of human for broiler products, but it raised their increased susceptibility to various stressors resulting in the disorder of lipid metabolism. Pterostilbene, the methoxylated analogue of resveratrol, exhibits astonishing functions of antioxidant, anti-inflammatory and glycolipid regulatory. The study aimed to elucidate the protective effects of pterostilbene on broiler liver and to explore the potential mechanisms. A total of 480 one-day-old male Arbor Acres (AA) broilers were randomly divided into four groups: the control group (basal diet) and pterostilbene groups (PT200, PT400, and PT600 feeding with basal diet containing 200, 400 and 600 mg/kg pterostilbene, respectively). The results showed that the dietary pterostilbene supplementation significantly improved the ADG of broilers. Dietary pterostilbene supplementation regulated the expression levels of the genes Sirt1 and AMPK and the downstream genes related to lipid metabolism to protect liver function and reduce lipid accumulation in broilers. Dietary pterostilbene supplementation upregulated the expression levels of the Nrf2 gene and its downstream antioxidant genes (SOD, CAT, HO-1, NQO-1, GPX) and phase II detoxification enzyme-related genes (GST, GCLM, GCLC). Collectively, pterostilbene was confirmed the positive effects as a feed additive on lipid metabolism and antioxidant via regulating Sirt1/AMPK and Nrf2 signalling pathways in broilers.

Decreasing SIL1-R2 concentration could enhance the expression oftranscription factors on the gene level

By the time you opened this document, an individual somewhere in the world has developed Alzheimer’s disease. With over 6 million cases in the United States alone and a global total exceeding 50 million, Alzheimer’s contributes to around one-third of senior fatalities. Horrifyingly, according to the United Nations, the number of patients doubles every two decades if a breakthrough is not discovered. Therefore, it is imperative to the survival of the human species to address and attempt to solve this issue before it can escalate any further. In this work, I have designed a few experiments that could be monumental to developing future Alzheimer’s vaccines and medicine. The primary focus of the trials above is to explore the possible role of the IL-1 signaling protein in the Bace-1- 1 deletion process to the potential prevention of DAM-2 formation, which, in turn, could worsen Alzheimer’s symptoms. The overall prediction can be summed up in the following: The activation of the IL-1 signaling pathway will enhance the activity of TF and lead to the up-regulation of TF gene expression. If my assumption is proven correct, it could pave the way for future Alzheimer’s medication to include drugs that moderate IL-1 signaling, which could save countless amount of lives.

Mouse Type-I Interferon-Mannosylated Albumin Fusion Protein for the Treatment of Chronic Hepatitis.

Although a lot of effort has been put into creating drugs and combination therapies against chronic hepatitis, no effective treatment has been established. Type-I interferon is a promising therapeutic for chronic hepatitis due to its excellent anti-inflammatory effects through interferon receptors on hepatic macrophages. To develop a type-I IFN equipped with the ability to target hepatic macrophages through the macrophage mannose receptor, the present study designed a mouse type-I interferon-mannosylated albumin fusion protein using site-specific mutagenesis and albumin fusion technology. This fusion protein exhibited the induction of anti-inflammatory molecules, such as IL-10, IL-1Ra, and PD-1, in RAW264.7 cells, or hepatoprotective effects on carbon tetrachloride-induced chronic hepatitis mice. As expected, such biological and hepatoprotective actions were significantly superior to those of human fusion proteins. Furthermore, the repeated administration of mouse fusion protein to carbon tetrachloride-induced chronic hepatitis mice clearly suppressed the area of liver fibrosis and hepatic hydroxyproline contents, not only with a reduction in the levels of inflammatory cytokine (TNF-α) and fibrosis-related genes (TGF-β, Fibronectin, Snail, and Collagen 1α2), but also with a shift in the hepatic macrophage phenotype from inflammatory to anti-inflammatory. Therefore, type-I interferon-mannosylated albumin fusion protein has the potential as a new therapeutic agent for chronic hepatitis.

Identification of Isthmin-1 in common carp (Cyprinus carpio L.) and the effects on glucose metabolism in vivo and in vitro.

Isthmin-1 (Ism1) plays roles in glucose uptake in mammals as an adipokine. To investigate its role in the glucose metabolism of common carp (Cyprinus carpio. L), the Ism1 sequence was cloned, and its expression and distribution in tissues were detected. In addition, we prepared and purified the recombinant Ism1 protein using the E. coli expression system and assessed changes in the expression of key genes related to glucose metabolism through both in vivo injection experiments and primary hepatocyte experiments in vitro. The results revealed that the open reading frame of Ism1 was 1377 bp long, encoding 458 amino acids. Similarity analysis indicated that Ism1 exhibited a close evolutionary relationship with goldfish (Carassius auratus), sharing 98.35% amino acid similarity. Ism1 was expressed in all tissues of common carp, with the highest level observed in the heart, followed by the gill, head kidney, and hepatopancreas. Distinct patterns of Ism1 expression were identified during the oral glucose tolerance test and long-term high-carbohydrate and high-fat diet feeding experiments. In vivo studies demonstrated that the serum glucose concentration was reduced on treatment with Ism1, accompanied by a significant upregulation of mRNA levels for gk, hk, and pfk genes in hepatopancreas; conversely pepck and g6pase mRNA levels were significantly downregulated in the hepatopancreas under these conditions as well. Furthermore, our primary hepatocyte experiment confirmed that Ism1 could inhibit pepck and g6pase mRNA expression, while promoting gk, hk, and pfk mRNA expression levels. In conclusion, Ism1, in common carp, could participate in the glucose metabolism, which provides essential information for future studies on the function of Ism1.

Effects and Underlying Mechanisms of Rice-Paddy-Upland Rotation Combined with Bacterial Fertilizer for the Abatement of Radix pseudostellariae Continuous Cropping Obstacles

Radix pseudostellariae is one of the well-known genuine medicinal herbs in Fujian province, China. However, the continuous cropping obstacles with respect to R. pseudostellariae have seriously affected the sustainable utilization of medicinal resources and the development of related industrial systems. The occurrence of continuous cropping obstacles is a comprehensive effect of multiple deteriorating biological and abiotic factors in the rhizosphere soil. Therefore, intensive ecological methods have been the key to abating such obstacles. In this study, four treatments were set up, i.e., fallow (RP-F), fallow + bacterial fertilizer (RP-F-BF), rice-paddy-upland rotation (RP-R), and rice-paddy-upland rotation + bacterial fertilizer (RP-R-BF), during the interval between two plantings of R. pseudostellariae, with a newly planted (NP) treatment as the control. The results show that the yield of R. pseudostellariae under the RP-F treatment decreased by 46.25% compared to the NP treatment. Compared with the RP-F treatment, the yields of the RP-F-BF, RP-R, and RP-R-BF treatments significantly increased by 14.11%, 27.79%, and 62.51%, respectively. The medicinal quality of R. pseudostellariae treated with RP-R-BF was superior to that achieved with the other treatments, with the total saponin and polysaccharide contents increasing by 8.54% and 27.23%, respectively, compared to the RP-F treatment. The ecological intensive treatment of RP-R-BF significantly increased the soil pH, content of organic matter, abundance of beneficial microbial populations, and soil enzyme activity, thus remediating the deteriorating environment of continuous cropping soil. On this basis, the ecological intensive treatment RP-R-BF significantly increased the activity of protective enzymes and the expression levels of genes related to disease and stress resistance in leaves and root tubers. Redundancy and Pearson correlation analyses indicated that rice-paddy-upland rotation improved the soil structure, promoted the growth of eutrophic r-strategy bacterial communities, enhanced compound oxidation and reduction, broke the relationship between the deteriorating environment and harmful biological factors, and eventually weakened the intensity of harmful factors. The subsequent application of bacterial fertilizer improved the beneficial biological and abiotic factors, activated various ecological functions of the soil, enhanced the ecological relationship between various biological and abiotic factors, and reduced the stress intensity of R. pseudostellariae, thereby improving its disease and stress resistance, and ultimately reflecting the recovery of yield and quality. The results indirectly prove that the intensive ecological amelioration of the soil environment was the main factor for the yield recovery of R. pseudostellariae under continuous cropping.

Predicting the role of the human gut microbiome in type 1 diabetes using machine-learning methods.

Gut microbes is a crucial factor in the pathogenesis of type 1 diabetes (T1D). However, it is still unclear which gut microbiota are the key factors affecting T1D and their influence on the development and progression of the disease. To fill these knowledge gaps, we constructed a model to find biomarker from gut microbiota in patients with T1D. We first identified microbial markers using Linear discriminant analysis Effect Size (LEfSe) and random forest (RF) methods. Furthermore, by constructing co-occurrence networks for gut microbes in T1D, we aimed to reveal all gut microbial interactions as well as major beneficial and pathogenic bacteria in healthy populations and type 1 diabetic patients. Finally, PICRUST2 was used to predict Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways and KO gene levels of microbial markers to investigate the biological role. Our study revealed that 21 identified microbial genera are important biomarker for T1D. Their AUC values are 0.962 and 0.745 on discovery set and validation set. Functional analysis showed that 10 microbial genera were significantly positively associated with D-arginine and D-ornithine metabolism, spliceosome in transcription, steroid hormone biosynthesis and glycosaminoglycan degradation. These genera were significantly negatively correlated with steroid biosynthesis, cyanoamino acid metabolism and drug metabolism. The other 11 genera displayed an inverse correlation. In summary, our research identified a comprehensive set of T1D gut biomarkers with universal applicability and have revealed the biological consequences of alterations in gut microbiota and their interplay. These findings offer significant prospects for individualized management and treatment of T1D.

Analysis of the lncRNA-miRNA-mRNA network to explore the regulation mechanism in human traumatic brain injury.

Traumatic brain injury (TBI) refers to brain dysfunction with or without traumatic structural injury induced by an external force. Nevertheless, the molecular mechanism of TBI remains undefined. Differentially expressed (DE) lncRNAs, DEmRNAs and DEmiRNAs were selected between human TBI tissues and the adjacent histologically normal tissue by high-throughput sequencing. Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis of overlapping DEmRNAs between predicted mRNAs of DEmiRNAs and DEmRNAs. The competitive endogenous RNA (ceRNA) network of lncRNA-miRNA-mRNA was established in light of the ceRNA theory. In the ceRNA network, the key lncRNAs were screened out. Then key lncRNAs related ceRNA subnetwork was constructed. After that, qRT-PCR was applied to validate the expression levels of hub genes. 114 DElncRNAs, 1807 DEmRNAs and 6 DEmiRNAs were DE in TBI. The TBI-related ceRNA network was built with 73 lncRNA nodes, 81 mRNA nodes and 6 miRNAs. According to topological analysis, two hub lncRNAs (ENST00000562897 and ENST00000640877) were selected to construct the ceRNA subnetwork. Subsequently, key lncRNA-miRNA-mRNA regulatory axes constructed by two lncRNAs including ENST00000562897 and ENST00000640877, two miRNAs including miR-6721-5p and miR-129-1-3p, two mRNAs including ketohexokinase (KHK) and cyclic nucleotide-gated channel beta1 (CNGB1), were identified. Furthermore, qRT-PCR results displayed that the expression of ENST00000562897, KHK and CNGB1 were significantly decreased in TBI, while the miR-6721-5p expression levels were markedly increased in TBI. The results of our study reveal a new insight into understanding the ceRNA regulation mechanism in TBI and select key lncRNA-miRNA-mRNA axes for prevention and treatment of TBI.

Drosophila melanogaster Sting mediates Coxiella burnetii infection by reducing accumulation of reactive oxygen species.

The Gram-negative bacterium Coxiella burnetii is the causative agent of query fever in humans and coxiellosis in livestock. C. burnetii infects a variety of cell types, tissues, and animal species including mammals and arthropods, but there is much left to be understood about the molecular mechanisms at play during infection in distinct species. Human stimulator of interferon genes (STING) induces an innate immune response through the induction of type I interferons (IFNs), and IFN promotes or suppresses C. burnetii replication, depending on tissue type. Drosophila melanogaster contains a functional STING ortholog (Sting) which activates NF-κB signaling and autophagy. Here, we sought to address the role of D. melanogaster Sting during C. burnetii infection to uncover how Sting regulates C. burnetii infection in flies. We show that Sting-null flies exhibit higher mortality and reduced induction of antimicrobial peptides following C. burnetii infection compared to control flies. Additionally, Sting-null flies induce lower levels of oxidative stress genes during infection, but the provision of N-acetyl-cysteine (NAC) in food rescues Sting-null host survival. Lastly, we find that reactive oxygen species levels during C. burnetii infection are higher in Drosophila S2 cells knocked down for Sting compared to control cells. Our results show that at the host level, NAC provides protection against C. burnetii infection in the absence of Sting, thus establishing a role for Sting in protection against oxidative stress during C. burnetii infection.