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1.
Advancements in Reference Gene Selection for Fruit Trees: A Comprehensive Review.
Peng, S, Ali Sabir, I, Hu, X, Chen, J, Qin, Y
International journal of molecular sciences. 2024;(2)
Abstract
Real-time quantitative polymerase chain reaction (qRT-PCR) has been widely used in gene expression analyses due to its advantages of sensitivity, accuracy and high throughput. The stability of internal reference genes has progressively emerged as a major factor affecting the precision of qRT-PCR results. However, the stability of the expression of the reference genes needs to be determined further in different cells or organs, physiological and experimental conditions. Methods for evaluating these candidate internal reference genes have also evolved from simple single software evaluation to more reliable and accurate internal reference gene evaluation by combining different software tools in a comprehensive analysis. This study intends to provide a definitive reference for upcoming research that will be conducted on fruit trees. The primary focus of this review is to summarize the research progress in recent years regarding the selection and stability analysis of candidate reference genes for different fruit trees.
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2.
E. coli phage transport in porous media: Response to colloid types and water saturation.
Zhang, W, Li, S, Zhao, K, Chai, J, Wan, B, Qin, Y, Huan, H, Sun, S, Yang, Y, Jat Baloch, MY
The Science of the total environment. 2024;:167635
Abstract
Because of its long survival time, high migration ability and high pathogenicity, the migration of the virus in the subsurface environment deserves in-depth exploration and research. In this study we investigated the migration behavior of E. coli phage (VI) with organic colloids (HA) or inorganic colloids (SiO2) in the saturated or unsaturated bands and compared the differences in their migration mechanisms.The effects of different colloids on the surface characteristics of VI were analyzed according to particle size and zeta potential. Column experiments were conducted to simulate their migration in the subsurface environment. The results show that HA enhances the stability of VI-HA, promotes VI migration and plays a dominant role in its migration process under both saturated and unsaturated conditions. In contrast, SiO2 puts VI-SiO2 in an unstable state and is easily separated in the unsaturated state, thus promoting VI migration. Based on migration experiments, the extent of influence factors on VI migration was quantified and compared. The effect of colloids on VI migration is greater than that of moisture content, where the effect of HA is greater than that of SiO2. This study provides an experimental research idea to determine the dominant factors affecting virus migration, and provides a general direction and theoretical basis for the biological risk assessment of pathogenic microorganisms in complex underground environments, in order to enable the decision makers to make a response in time, accurately, and efficiently.
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3.
Occurrence, Risk Implications, Prevention and Control of CIT in Monascus Cheese: A Review.
Zhang, C, Cheng, Y, Qin, Y, Wang, C, Wang, H, Ablimit, A, Sun, Q, Dong, H, Wang, B, Wang, C
Journal of agricultural and food chemistry. 2024
Abstract
Monascus is a filamentous fungus that has been used in the food and pharmaceutical industries. When used as an auxiliary fermenting agent in the manufacturing of cheese, Monascus cheese is obtained. Citrinin (CIT) is a well-known hepatorenal toxin produced by Monascus that can harm the kidneys structurally and functionally and is frequently found in foods. However, CIT contamination in Monascus cheese is exacerbated by the metabolic ability of Monascus to product CIT, which is not lost during fermentation, and by the threat of contamination by Penicillium spp. that may be introduced during production and processing. Considering the safety of consumption and subsequent industrial development, the CIT contamination of Monascus cheese products needs to be addressed. This review aimed to examine its occurrence in Monascus cheese, risk implications, traditional control strategies, and new research advances in prevention and control to guide the application of biotechnology in the control of CIT contamination, providing more possibilities for the application of Monascus in the cheese industry.
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4.
SadNet: a novel multimodal fusion network for protein-ligand binding affinity prediction.
Hong, Q, Zhou, G, Qin, Y, Shen, J, Li, H
Physical chemistry chemical physics : PCCP. 2024;(16):12880-12891
Abstract
Protein-ligand binding affinity prediction plays an important role in the field of drug discovery. Existing deep learning-based approaches have significantly improved the efficiency of protein-ligand binding affinity prediction through their excellent inductive bias capability. However, these methods only focus on fragmented three-dimensional data, which truncates the integrity of pocket data, leading to the neglect of potential long-range interactions. In this paper, we propose a dual-stream framework, with amino acid sequence assisting the atomic data fusion for graph neural network (termed SadNet), to fuse both 3D atomic data and sequence data for more accurate prediction results. In detail, SadNet consists of a pocket module and a sequence module. The sequence module expands the "receptive field" of the pocket module through a mid-term virtual node fusion. To better integrate sequence-level information from the sequence module and 3D structural information from the pocket module, we incorporate structural information for each amino acid within the sequence module. Besides, to better understand the intrinsic relationship between sequences and 3D atomic information, our SadNet utilizes information stacking from both the early stage and later stage. Experimental results on publicly available benchmark datasets demonstrate the superiority of the proposed dual-stream approach over the state-of-the-art alternatives. The code of this work is available online at https://github.com/wardhong/SadNet.
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5.
Recent advances in the therapeutic potential of nobiletin against respiratory diseases.
Qin, Y, Yang, J, Li, H, Li, J
Phytomedicine : international journal of phytotherapy and phytopharmacology. 2024;:155506
Abstract
BACKGROUND Nobiletin is a natural polymethoxylated flavonoid widely present in citrus fruit peels. It has been demonstrated to exert the effects of anti-tumor, anti-inflammation, anti-oxidative, anti-apoptotic and improve cardiovascular function. Increasing evidences suggest that nobiletin plays an important role in respiratory diseases (RDs) treatment. OBJECTIVE This review aimed to investigate the therapeutic potential of nobiletin against RDs, such as lung cancer, COPD, pulmonary fibrosis, asthma, pulmonary infection, acute lung injury, coronavirus disease 2019, and pulmonary arterial hypertension. METHODS We retrieved extensive literature of relevant literatures in English until June 26, 2023 from the database of PubMed, Web of Science, and Scopus databases. The keywords of "nobiletin and lung", "nobiletin and respiratory disease", "nobiletin and chronic respiratory diseases", "nobiletin and metabolites", "nobiletin and pharmacokinetics", "nobiletin and toxicity" were searched in pairs. A total of 298 literatures were retrieved from the above database. After excluding the duplicates and reviews, 53 were included in the current review. RESULTS We found that the therapeutic mechanisms are based on different signaling pathways. Firstly, nobiletin inhibited the proliferation and suppressed the invasion and migration of cancer cells by regulating the related pathway or key target, like Bcl-2, PD-L1, PARP, and Akt/GSK3β/β-catenin in lung cancer treatment. Secondly, nobiletin treats COPD and ALI by targeting classical signaling pathway mediating inflammation. Besides, the available findings show that nobiletin exerts the effect of PF treatment via regulating mTOR pathway. CONCLUSIONS With the wide range of pharmacological activities, high efficiency and low toxicity, nobiletin can be used as a potential agent for preventing and treating RDs. These findings will contribute to further research on the molecular mechanisms of nobiletin and facilitate in-depth studies on nobiletin at both preclinical and clinical levels for the treatment of RDs.
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6.
Effects of human milk odor stimulation on feeding in premature infants: a systematic review and meta-analysis.
Qin, Y, Liu, S, Yang, Y, Zhong, Y, Hao, D, Han, H
Scientific reports. 2024;(1):8964
Abstract
Previous studies suggested odor stimulation may influence feeding of premature neonates. Therefore, this systematic review and meta-analysis of randomized controlled trials was conducted to assess the effect of human milk odor stimulation on feeding of premature infants. All randomized controlled trials related to human milk odor stimulation on feeding in premature infants published in PubMed, Cochrane, Library, Medline, Embase, Web of science databases and Chinese biomedical literature databases, China National Knowledge Infrastructure, China Science and Technology Journal Database (VIP) and Wanfang Chinese databases were searched, and The Cochrane Handbook 5.1.0 was used to evaluate the quality and authenticity of the literature. Relevant information of the included studies was extracted and summarized, and the evaluation indexes were analyzed using ReviewManager5.3. The retrieval time was from the establishment of the database to July 28, 2022.12 articles were assessed for eligibility, and six randomized controlled studies were eventually included in the meta-analysis (PRISMA). A total of 6 randomized controlled studies with 763 patients were finally included in the study, and the quality evaluation of literatures were all grade B. Human milk odor stimulation reduced the transition time to oral feeding in premature infants [SMD = - 0.48, 95% CI (- 0.69, - 0.27), Z = 4.54, P < 0.00001] and shortened the duration of parenteral nutrition [MD = - 1.01, 95% CI (- 1.70, - 0.32), Z = 2.88, P = 0.004]. However, it did not change the length of hospitalization for premature infants [MD = - 0.03, 95% CI (- 0.41, 0.35), Z = 0.17, P = 0.86]. The implementation of human milk odor stimulation can reduce the transition time to oral feeding and the duration of parenteral nutrition in premature infants, but further studies are needed to determine whether it can reduce the length of hospital stay in premature infants. More high-quality, large-sample studies are needed to investigate the effect of human milk odor stimulation on the feeding process and other outcomes in premature infants.
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7.
Assessment of the impact of a personalised nutrition intervention in impaired glucose regulation over 26 weeks: a randomised controlled trial.
Karvela, M, Golden, CT, Bell, N, Martin-Li, S, Bedzo-Nutakor, J, Bosnic, N, DeBeaudrap, P, de Mateo-Lopez, S, Alajrami, A, Qin, Y, et al
Scientific reports. 2024;(1):5428
Abstract
Dietary interventions can reduce progression to type 2 diabetes mellitus (T2DM) in people with non-diabetic hyperglycaemia. In this study we aimed to determine the impact of a DNA-personalised nutrition intervention in people with non-diabetic hyperglycaemia over 26 weeks. ASPIRE-DNA was a pilot study. Participants were randomised into three arms to receive either (i) Control arm: standard care (NICE guidelines) (n = 51), (ii) Intervention arm: DNA-personalised dietary advice (n = 50), or (iii) Exploratory arm: DNA-personalised dietary advice via a self-guided app and wearable device (n = 46). The primary outcome was the difference in fasting plasma glucose (FPG) between the Control and Intervention arms after 6 weeks. 180 people were recruited, of whom 148 people were randomised, mean age of 59 years (SD = 11), 69% of whom were female. There was no significant difference in the FPG change between the Control and Intervention arms at 6 weeks (- 0.13 mmol/L (95% CI [- 0.37, 0.11]), p = 0.29), however, we found that a DNA-personalised dietary intervention led to a significant reduction of FPG at 26 weeks in the Intervention arm when compared to standard care (- 0.019 (SD = 0.008), p = 0.01), as did the Exploratory arm (- 0.021 (SD = 0.008), p = 0.006). HbA1c at 26 weeks was significantly reduced in the Intervention arm when compared to standard care (- 0.038 (SD = 0.018), p = 0.04). There was some evidence suggesting prevention of progression to T2DM across the groups that received a DNA-based intervention (p = 0.06). Personalisation of dietary advice based on DNA did not result in glucose changes within the first 6 weeks but was associated with significant reduction of FPG and HbA1c at 26 weeks when compared to standard care. The DNA-based diet was effective regardless of intervention type, though results should be interpreted with caution due to the low sample size. These findings suggest that DNA-based dietary guidance is an effective intervention compared to standard care, but there is still a minimum timeframe of adherence to the intervention before changes in clinical outcomes become apparent.Trial Registration: www.clinicaltrials.gov.uk Ref: NCT03702465.
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8.
Changes in root metabolites and soil microbial community structures in rhizospheres of sugarcanes under different propagation methods.
Lin, X, Yang, D, Zhu, Y, Qin, Y, Liang, T, Yang, S, Tan, H
Microbial biotechnology. 2024;(1):e14372
Abstract
Root metabolites and soil microbial community structure in the rhizosphere play critical roles in crop growth. Here, we assessed the efficiency of conventional and tissue culture propagation methods in modulating the soil health and microbiota in the rhizosphere of sugarcane (Saccharum officinarum L.) plants. The seeding canes were obtained using newly planted and two-year ratooned canes propagated by conventional (CSN and CSR) or tissue culture (TCN and TCR) methods. Changes in soil fertility, root metabolites and soil microbial community structure in the rhizosphere of sugarcane plants obtained using these canes were assessed. The activities of soil β-glucosidase and aminopeptidase, soil microbial biomass nitrogen, and abundances of soil beneficial microbes, both at phyla and genera levels, were significantly higher in the rhizosphere of sugarcane plants in TCN and TCR treatments than those in that of plants in CSN and CSR treatments. Furthermore, flavonoid and flavonol biosynthesis and alanine, aspartate and glutamate metabolism were significantly upregulated in the roots of TCR and TCN plants compared with those in the roots of CSN and CSR plants. These results suggest that the tissue culture propagation method is a sustainable method for sugarcane cultivation to improve soil fertility and health in sugarcane rhizosphere.
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9.
The enzymes of serine synthesis pathway in cancer metastasis.
Li, L, Qin, Y, Chen, Y
Biochimica et biophysica acta. Molecular cell research. 2024;(4):119697
Abstract
Metastasis, the major cause of cancer mortality, requires cancer cells to reprogram their metabolism to adapt to and thrive in different environments, thereby leaving metastatic cells metabolic characteristics different from their parental cells. Mounting research has revealed that the de novo serine synthesis pathway (SSP), a glycolytic branching pathway that consumes glucose carbons for serine makeup and α-ketoglutarate generation and thus supports the proliferation, survival, and motility of cancer cells, is one such reprogrammed metabolic pathway. During different metastatic cascades, the SSP enzyme proteins or their enzymatic activity are both dynamically altered; manipulating their expression or catalytic activity could effectively prevent the progression of cancer metastasis; and the SSP enzymatic proteins could even conduce to metastasis via their nonenzymatic functions. In this article we overview the SSP dynamics during cancer metastasis and put the focuses on the regulatory role of the SSP in metastasis and the underlying mechanisms that mainly involve cellular anabolism/catabolism, redox balance, and epigenetics, aiming to provide a theoretical basis for the development of therapeutic strategies for targeting metastatic lesions.
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10.
Dietary regulation of the SIgA-gut microbiota interaction.
Han, X, Guo, J, Qin, Y, Huang, W, You, Y, Zhan, J
Critical reviews in food science and nutrition. 2023;(23):6379-6392
Abstract
Gut microbiota (GM) is essential for host health, and changes in the GM are related to the development of various diseases. Recently, secretory immunoglobulin A (SIgA), the most abundant immunoglobulin isotype in the intestinal mucosa, has been found to play an essential role in controlling GM. SIgA dysfunction can lead to changes in the GM and is associated with the development of various GM-related diseases. Although in early stage, recent studies have shown that assorted dietary interventions, including vitamins, amino acids, fatty acids, polyphenols, oligo/polysaccharides, and probiotics, can influence the intestinal SIgA response and SIgA-GM interaction. Dietary intervention can enhance the SIgA response by directly regulating it (from top to bottom) or by regulating the GM structure or gene expression (from bottom to top). Furthermore, intensive studies involving the particular influence of dietary intervention on SIgA-binding to the GM and SIgA repertoire and the precise regulation of the SIgA response via dietary intervention are still exceedingly scarce and merit further consideration. This review summarizes the existing knowledge and (possible) mechanisms of the influence of dietary intervention on the SIgA-GM interaction. Key issues are considered, and the approaches in addressing these issues in future studies are also discussed.