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1.
Spectrochim Acta A Mol Biomol Spectrosc ; 317: 124417, 2024 May 07.
Article En | MEDLINE | ID: mdl-38728850

The use of fluorescent carbon dots (CDs) as highly precise biolabeling probes has been widespread in the fields of live cell imaging and protein labeling due to their small size and excellent photoluminescence ability to accurately target specific molecules with surface chemical properties. However, there was a lack of research on the interaction between CDs and labeled molecules. In this work, we presented a novel investigation strategy, the fluorescence microscopy-surface plasmon resonance (FM-SPR) system, which combined the use of fluorescence microscopy and wavelength modulation surface plasmon resonance to study the interaction between CDs and labeled molecules in real-time. Using this system, simultaneously recorded the SPR signals and the fluorescence images on the surface of the FM-SPR sensor chip. We observed the dynamic curve and fluorescence images of the interaction between green emissive nitrogen-doped carbon dots (N-CDs) and silk fibroin (SF) in real-time. The kinetic parameters, the quantitative analysis, and the investigation of the binding could be achieved. The results showed a strong linear relationship between the change in SPR signals and the concentration of N-CDs, with a linear coefficient of 0.99913. The linear detection range was 2.5 µg/mL-100 µg/mL, and the real lowest detection limit reached 0.5 µg/mL. Additionally, the green fluorescence points in the imaging region on the FM-SPR sensor chip increased with the concentration of N-CDs, which was consistent with the change in SPR signals. Using this system we also acquired the association rate and dissociation rate of N-CDs to SF which were 2.65 × 10-5/s and 1.52 × 10-5/s, respectively. This demonstrated the effectiveness of our method in quantitatively analyzing SF labeled with N-CDs.

2.
BMC Cancer ; 24(1): 586, 2024 May 13.
Article En | MEDLINE | ID: mdl-38741062

BACKGROUND: Observational study investigated the association between pernicious anemia (PA) and cancers. However, with the exception of gastric cancer, the results are mostly contradictory. The purpose of this study was to investigate the potential causal relationship between PA and cancers through bidirectional two-sample Mendelian randomized (MR) analysis. METHODS: The European sample FinnGen project provided the genetic summary data for PA and 20 site-specific cancers. This bidirectional two-sample MR design mainly used the inverse variance weighting (IVW) method to evaluate the causal relationship between PA and cancer risk. Benjamini-Hochberg correction was performed to reduce the bias caused by multiple tests. RESULTS: Our study shows that there was a causal relationship between PA and gastric cancer, prostate cancer, testicular cancer and malignant melanoma of skin, and there was a reverse causal relationship between prostate cancer or gastric cancer and PA (P < 0.05). After Benjamini-Hochberg correction test, there was still a causal correlation between PA and gastric or prostate cancer (P' < 0.05), while there was only an implied causal association between PA and testicular cancer and malignant melanoma of skin (P'> 0.05). There was still a reverse causal relationship between gastric cancer and PA (P'< 0.05), while prostate cancer shows an implied reverse causal relationship(P'> 0.05). In addition, MR-Egger and MR-PRESSO tests showed no significant horizontal pleiotropy. CONCLUSIONS: PA may be genetically associated with testicular cancer, prostate cancer, gastric cancer, and malignant melanoma of skin.


Anemia, Pernicious , Mendelian Randomization Analysis , Humans , Anemia, Pernicious/genetics , Anemia, Pernicious/complications , Male , Stomach Neoplasms/genetics , Neoplasms/genetics , Testicular Neoplasms/genetics , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Prostatic Neoplasms/genetics , Female
3.
J Ethnopharmacol ; : 118231, 2024 May 06.
Article En | MEDLINE | ID: mdl-38718891

ETHNOPHARMACOLOGICAL RELEVANCE: Radix Chimonanthi Pracecocis(RCP), also known as Tiekuaizi, widely used by the Miao community in Guizhou, exhibits diverse biological activities and holds promise for the treatment of osteoarthritis (OA). However, there is a lack of contemporary pharmacological research in this area. AIMS OF THE STUDY: This study aims to explore the potential of targets and mechanisms of RCP in the treatment of OA. MATERIALS AND METHODS: The chemical components of RCP were identified using UPLC-MS/MS, and active components were determined based on the Lipinski rule. RCP and OA-related targets were retrieved from public databases such as TCMSP and GeneCards. Network pharmacology approaches were employed to identify key genes. The limma package (version 3.40.2) in R 4.3.2 was used to screen for differentially expressed genes (DEGs) between OA and healthy individuals in GSE82107. DEGs were analyzed using an independent sample t-test and receiver operating characteristic analysis in GraphPad Prism 9.5.1. Additionally, molecular docking (SYBYL2.1.1) was used to analyze the binding interactions between the active components and target proteins. Finally, we established a papain-induced osteoarthritis (OA) rat model and treated it with RCP aqueous extract by gavage. We validated relevant indicators using real-time fluorescence quantitative polymerase chain reaction, western blot, immunohistochemistry, and enzyme-linked immunosorbent assays. RESULTS: Seven active components and 53 targets were identified. The results of GO and KEGG enrichment analyses confirmed the significant role of RCP in the regulation of pyroptosis. Hypoxia-inducible factor-1α (HIF-1α) was identified as a key gene involved in the main biological functions. Molecular docking analysis revealed that Praecoxin, Isofraxidin, Esculin, and Naringenin can bind to the nucleotide-binding domain, leucine-rich repeat, and pyrin domain-containing protein 3 (NLRP3) (T-Score > 5). Additionally, Praecoxin can bind to HIF-1α (T-Score > 5). In vivo experiments demonstrated that RCP significantly affects the NLRP3 inflammasome, which is regulated by the HIF-1α pathway. RCP inhibited pyroptosis and reduced synovial inflammation. CONCLUSIONS: This study confirmed the efficacy of RCP aqueous extract in the treatment of OA and identified seven active components (esculin, dihydrokaempferol, naringenin, praecoxin, carnosol, hydroxyvalerenic acid, isofraxidin) that may play an anti-pyroptosis role in the treatment of OA by downregulating the expression of HIF-1α and NLRP3 inflammasome.

4.
Neurosurg Rev ; 47(1): 202, 2024 May 03.
Article En | MEDLINE | ID: mdl-38700541

PURPOSE: Determine the prevalence and influencing factors of patient delay in stroke patients and explore variation in prevalence by country and delayed time. METHODS: PubMed, The Cochrane Library, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), Chinese Biomedical Database (CBM), Weipu database, and Wanfang database were comprehensively searched for observational studies from inception to April, 2023. The pooled prevalence, odds ratio (OR), and 95% confidence intervals (CI) were calculated with Stata 16.0 software. RESULTS: In total, 2721 articles were screened and data from 70 studies involving 85,468 subjects were used in meta-analysis. The pooled prevalence of patient delay in stroke patients was 59% (95% CI, 0.54-0.64). The estimates of pooled prevalence calculated for African, Asian, and European patient delay in stroke patients were 55% (0.29-0.81), 61% (0.56-0.66), and 49% (0.34-0.64).According to the patient delay time, the prevalence of 6 h, 5 h, 4.5 h, 3.5 h, 3 h and 2 h were 54% (0.47-0.61), 73% (0.61-0.86), 60% (0.49-0.71), 81% (0.68-0.93), 52% (0.42-0.62), 63% (0.19-1.07). Distance from the place of onset to the hospital > 10 km [OR=2.49, 95%CI (1.92, 3.24)], having medical insurance [OR = 0.45, 95%CI (0.26,0.80)], lack of stroke-related knowledge [OR = 1.56, 95%CI (1.08,2.26)], education level below junior high school [OR = 1.69, 95%CI (1.22,2.36)], non-emergency medical services (Non-EMS) [OR = 2.10, 95%CI (1.49,2.97)], living in rural areas [OR = 1.54, 95%CI (1.15,2.07)], disturbance of consciousness [OR = 0.60, 95%CI (0.39,0.93)], history of atrial fibrillation [OR = 0.53, 95%CI (0.47,0.59)], age ≥ 65 years [OR = 1.18, 95%CI (1.02,1.37)], National institutes of health stroke scale (NIHSS) ≤ 4 points [OR= 2.26, 95%CI (1.06,4.79)]were factors for patient delay in stroke patients. CONCLUSIONS: The prevalence of patient delay in stroke patients is high, we should pay attention to the influencing factors of patient delay in stroke patients and provide a theoretical basis for shortening the treatment time of stroke patients.


Stroke , Time-to-Treatment , Humans , Stroke/epidemiology , Prevalence , Time Factors
6.
Cell Signal ; 119: 111167, 2024 Jul.
Article En | MEDLINE | ID: mdl-38604341

Autophagy is essential for eliminating aging and organelle damage that maintaining cellular homeostasis. However, the dysfunction of autophagy has been proven in hair loss such as AGA. Despite the crucial role of TRPML channels in regulating autophagy, their specific function in hair growth remains unclarified. To investigate the biological functions and associated molecular mechanisms of TRPMLs in hair growth, Animal experiments were conducted to confirm the function of TRLMLs activation in promoting hair growth. Subsequently, we analyzed molecular mechanisms in human dermal papilla cells (hDPCs) activated by TRPMLs through transcriptome sequencing analysis. MLSA1(a TRPML agonist) promoted hair regeneration and accelerated hair cycle transition in mice. The activation of TRPMLs upregulated calcium signaling inducing hDPCs to secrete hair growth promoting factors and decrease hair growth inhibiting factors. In addition, activation of TRPMLs triggered autophagy and reduced the generation of ROS, thereby delaying the senescence of hDPCs. All these findings suggested that TRPMLs activation could promote hair growth by regulating hDPCs secretion of hair growth-related factors. Moreover, it may play a prominent role in preventing hDPCs from ROS damage induced by H2O2 or DHT. Targeting TRPMLs may represent a promising therapeutic strategy for treating hair loss.


Autophagy , Hair , Animals , Mice , Humans , Autophagy/drug effects , Hair/growth & development , Hair/drug effects , Hair Follicle/drug effects , Hair Follicle/cytology , Reactive Oxygen Species/metabolism , Mice, Inbred C57BL , Dermis/cytology , Dermis/drug effects , Transient Receptor Potential Channels/metabolism , Calcium Signaling/drug effects
7.
J Hazard Mater ; 470: 134111, 2024 May 15.
Article En | MEDLINE | ID: mdl-38581870

Microplastics (MPs) pose a significant global concern, requiring a multifaceted approach to their risk assessment procedures, especially concerning their characteristics in the environment. The Horqin Left Middle Banner in Northeast China was chosen for the research region to investigate the abundance, composition, distribution, and ecological impact of MPs in surface agricultural soils. The concentrations of MPs ranged from 300 to 12800 items/kg, with a median concentration of 1550 items/kg (average = 1994 items/kg). The normal-sized MPs (500-5000 µm) had a higher relative abundance than small MPs (<500 µm). MPs were mainly derived from textiles and packaging and were affected by atmospheric transportation. Rayon and PET fibers were the main polymers identified. Furthermore, the potential environmental risks posed by the fundamental characteristics (abundance, chemical composition, and size) of MPs were quantified using multiple risk assessment models. The conditional fragmentation model indicated a propensity for MPs to degrade into smaller particles. Ecological risk assessments using pollution load index, pollution hazard index, and potential ecological risk index models revealed varying levels of risk. This study conducted a comprehensive assessment of the ecological risks of MPs based on their environmental characteristics, emphasizing the importance of considering multiple factors in the risk assessment process. ENVIRONMENT IMPLICATION: This study investigates the occurrence, distribution, and ecological risk of microplastics (MPs) in agricultural soils of the Northeast Plain of China, a major food production area. MPs are persistent organic pollutants that can pose threats to soil health, crop quality, and food security. By analyzing the composition, size, and source of MPs, as well as their fragmentation and stability in soil, this study provides valuable data for assessing the environmental risk of MPs in agricultural regions. The study also suggests strategies for mitigating MPs pollution and protecting soil ecosystems.

8.
Front Public Health ; 12: 1268653, 2024.
Article En | MEDLINE | ID: mdl-38577277

Introduction: The cost-effectiveness study of syphilis screening in pregnant women has not been synthesized. This study aimed to synthesize the economic evidence on the cost-effectiveness of syphilis screening in pregnant women that might contribute to making recommendations on the future direction of syphilis screening approaches. Methods: We systematically searched MEDLINE, PubMed, and Web of Science databases for relevant studies published before 19 January 2023 and identified the cost-effectiveness analyses for syphilis screening in pregnant women. The methodological design quality was appraised by the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) 2022 checklist. Results: In total, 17 literature met the eligibility criteria for a full review. Of the 17 studies, four evaluated interventions using different screening methods, seven assessed a combination of syphilis testing and treatment interventions, three focused on repeat screening intervention, and four evaluated the interventions that integrated syphilis and HIV testing. The most cost-effective strategy appeared to be rapid syphilis testing with high treatment rates in pregnant women who were positive. Discussion: The cost-effectiveness of syphilis screening for pregnancy has been widely demonstrated. It is very essential to improve the compliance with maternal screening and the treatment rates for positive pregnant women while implementing screening.


Pregnancy Complications, Infectious , Syphilis , Female , Humans , Pregnancy , Cost-Benefit Analysis , Pregnancy Complications, Infectious/diagnosis , Pregnant Women , Syphilis/diagnosis
9.
Front Cell Infect Microbiol ; 14: 1327032, 2024.
Article En | MEDLINE | ID: mdl-38596649

Aim: Mendelian randomization (MR) analysis has been used in the exploration of the role of gut microbiota (GM) in type 2 diabetes mellitus (T2DM); however, it was limited to the genus level. This study herein aims to investigate the relationship of GM, especially at the species level, with T2DM in order to provide some evidence for further exploration of more specific GM taxa and pathway abundance in T2DM. Methods: This two-sample MR study was based on the summary statistics of GM from the available genome-wide association study (GWAS) meta-analysis conducted by the MiBioGen consortium as well as the Dutch Microbiome Project (DMP), whereas the summary statistics of T2DM were obtained from the FinnGen consortium released data. Inverse variance weighted (IVW), MR-Egger, strength test (F), and weighted median methods were used to examine the causal association between GM and the onset of T2DM. Cochran's Q statistics was employed to quantify the heterogeneity of instrumental variables. Bonferroni's correction was conducted to correct the bias of multiple testing. We also performed reverse causality analysis. Results: The corrected IVW estimates suggested the increased relative abundance of family Oxalobacteraceae (OR = 1.0704) and genus Oxalobacter (OR = 1.0874), respectively, were associated with higher odds of T2DM, while that of species faecis (OR = 0.9460) had a negative relationship with T2DM. The relationships of class Betaproteobacteria, family Lactobacillaceae, species finegoldii, and species longum with T2DM were also significant according to the IVW results (all P < 0.05). Conclusions: GM had a potential causal association with T2DM, especially species faecis, finegoldii, and longum. Further studies are still needed to clarify certain results that are contradictory with previous findings.


Diabetes Mellitus, Type 2 , Gastrointestinal Microbiome , Microbiota , Sulfalene , Humans , Diabetes Mellitus, Type 2/genetics , Gastrointestinal Microbiome/genetics , Genome-Wide Association Study , Mendelian Randomization Analysis , Meta-Analysis as Topic
10.
Hua Xi Kou Qiang Yi Xue Za Zhi ; 42(2): 242-248, 2024 Apr 01.
Article En, Zh | MEDLINE | ID: mdl-38597084

OBJECTIVES: This study aimed to observe the outcomes of iRoot BP Plus full pulpotomy in primary molars with partial irreversible pulpitis retrospectively. METHODS: Collect 102 cases of primary molars with partial irreversible pulpitis undergoing iRoot BP Plus full pulpotomy from January 2019 to August 2023, with a follow-up period of 24-47 months. Based on the presence of irreversible pulpitis symptoms before surgery, the included cases will be divided into asymptomatic group (n=53) and symptomatic group (n=49). Observe the clinical and imaging success rates of both groups. RESULTS: Clinical success rates were 96.2% and 97.9% in asymptomatic and symptomatic groups, and radiographic success rates were 96.2% and 93.9% respectively. CONCLUSIONS: iRoot BP Plus full pulpotomy can be used for the treatment of primary molars with partial irreversible pulpitis under an enhanced pulpotomy protocol.


Pulpitis , Pulpotomy , Humans , Pulpotomy/methods , Pulpitis/surgery , Pulpitis/drug therapy , Retrospective Studies , Silicates/therapeutic use , Molar/surgery , Treatment Outcome , Calcium Compounds/therapeutic use
11.
Cancer Sci ; 2024 Apr 23.
Article En | MEDLINE | ID: mdl-38651282

Ubiquitination and deubiquitylation are pivotal posttranslational modifications essential for regulating cellular protein homeostasis and are implicated in the development of human diseases. Ubiquitin-specific protease 3 (USP3), a member of the ubiquitin-specific protease family, serves as a key deubiquitylation enzyme, playing a critical role in diverse cellular processes including the DNA damage response, cell cycle regulation, carcinogenesis, tumor cell proliferation, migration, and invasion. Despite notable research efforts, our current understanding of the intricate and context-dependent regulatory networks governing USP3 remains incomplete. This review aims to comprehensively synthesize existing published works on USP3, elucidating its multifaceted roles, functions, and regulatory mechanisms, while offering insights for future investigations. By delving into the complexities of USP3, this review strives to provide a foundation for a more nuanced understanding of its specific roles in various cellular processes. Furthermore, the exploration of USP3's regulatory networks may uncover novel therapeutic strategies targeting this enzyme in diverse human diseases, thereby holding promising clinical implications. Overall, an in-depth comprehension of USP3's functions and regulatory pathways is crucial for advancing our knowledge and developing targeted therapeutic approaches for human diseases.

12.
Skin Res Technol ; 30(4): e13696, 2024 Apr.
Article En | MEDLINE | ID: mdl-38602262

BACKGROUND: Female pattern hair loss (FPHL) is the most prevalent type of alopecia among adult women. Presently, topical minoxidil stands as the sole treatment endorsed by the FDA. Addressing cases of FPHL in individuals who develop contact dermatitis in response to minoxidil can pose a challenge for dermatologists. OBJECTIVE: To assess the efficacy and safety of subcutaneous injections of Botulinum Toxin Type A (BTA) in treating FPHL. METHODS: Enrolled outpatients with FPHL who exhibited an allergic reaction to minoxidil solution. Diagnosis of FPHL was established through clinical examination and trichoscopy. Inclusion criteria involved patients with no prior treatment within the last year and without any comorbidities. BTA, specifically 100 units, was mixed with 2 mL of 0.9% normal saline. Twenty injection target sites, spaced 2-3 cm apart, were symmetrically marked on the hairless area of the scalp. A dosage of five units was intradermally injected at each target site. Representative photographs and dermoscopic images of the scalp were captured before and after 3 months of treatment. RESULTS: A total of 10 FPHL, aged between 26 and 40 years, were included. The average age was 30.3 ± 4.64 years, and all patients had a positive family history of Androgenetic Alopecia. The average duration of the disease was 3.70 ± 1.42 years. According to patients' self-assessment, after 1 month of treatment, 10 FPHL patients reported experiencing moderate to marked improvement in symptoms related to scalp oil secretion. Three months later, dermatological assessments showed that three had mild improvement, six had no change, and one had a worsening condition. No adverse effects were observed. CONCLUSIONS: Our study suggests that the effectiveness of BTA for FPHL is limited to 3 months. However, it can be considered for tentative use after effective communication with patients. The long-term efficacy and safety of BTA in treating FPHL require further observation and study.


Botulinum Toxins, Type A , Minoxidil , Adult , Female , Humans , Minoxidil/therapeutic use , Botulinum Toxins, Type A/adverse effects , Alopecia/drug therapy , Scalp
13.
Sci Data ; 11(1): 356, 2024 Apr 08.
Article En | MEDLINE | ID: mdl-38589398

Rapeseed is a critical cash crop globally, and understanding its distribution can assist in refined agricultural management, ensuring a sustainable vegetable oil supply, and informing government decisions. China is the leading consumer and third-largest producer of rapeseed. However, there is a lack of widely available, long-term, and large-scale remotely sensed maps on rapeseed cultivation in China. Here this study utilizes multi-source data such as satellite images, GLDAS environmental variables, land cover maps, and terrain data to create the China annual rapeseed maps at 30 m spatial resolution from 2000 to 2022 (CARM30). Our product was validated using independent samples and showed average F1 scores of 0.869 and 0.971 for winter and spring rapeseed. The CARM30 has high spatial consistency with existing 10 m and 20 m rapeseed maps. Additionally, the CARM30-derived rapeseed planted area was significantly correlated with agricultural statistics (R2 = 0.65-0.86; p < 0.001). The obtained rapeseed distribution information can serve as a reference for stakeholders such as farmers, scientific communities, and decision-makers.


Brassica napus , Agriculture , China
14.
PLoS One ; 19(4): e0301585, 2024.
Article En | MEDLINE | ID: mdl-38625891

In order to solve the problem of coordinated development among mining economy, social governance and environmental conservation in global resource-based cities, we choose Guangxi Zhuang Autonomous Region as the research area. The advantage of resource endowment and resource industry was measured by location quotient and input-output method. The panel data related to mining governance from 2010 to 2021 were selected to build the evaluation and coupling analysis model between mining economic, social governance and environmental conservation, and the spatial-temporal heterogeneity and coupling effect of them were analyzed by comprehensive empowerment evaluation, spatial autocorrelation analysis and barrier degree methods. The results show that: (1) Except for the overall upward trend of social governance, the development level of mining economy and environmental conservation are basically stable; (2) The resource-rich areas have obvious mining economic advantages, and the central cities have good social governance capabilities, and the environmental conservation effectiveness is uncertain; (3) The coupling effect between mining economy and social governance is stronger than that between mining economy and environment conservation, and the synergistic coupling effect of the three is relatively random. Finally, we put forward some policy response strategies to Guangxi, and theoretical and practical reference would be provided for resource-based cities around the world.


Economic Development , Urbanization , China , Cities , Industry , Conservation of Natural Resources
15.
Heliyon ; 10(7): e28274, 2024 Apr 15.
Article En | MEDLINE | ID: mdl-38560183

Kuiper's statistic is a good measure for the difference of ideal distribution and empirical distribution in the goodness-of-fit test. However, it is a challenging problem to solve the critical value and upper tail quantile, or simply Kuiper pair, of Kuiper's statistics due to the difficulties of solving the nonlinear equation and reasonable approximation of infinite series. In this work, the contributions lie in three perspectives: firstly, the second order approximation for the infinite series of the cumulative distribution of the critical value is used to achieve higher precision; secondly, the principles and fixed-point algorithms for solving the Kuiper pair are presented with details; finally, finally, a mistake about the critical value cnα for (α,n)=(0.01,30) in Kuiper's distribution table has been labeled and corrected where n is the sample capacity and α is the upper tail quantile. The algorithms are verified and validated by comparing with the table provided by Kuiper. The methods and algorithms proposed are enlightening and worth of introducing to the college students, computer programmers, engineers, experimental psychologists and so on.

16.
Allergy Asthma Clin Immunol ; 20(1): 32, 2024 Apr 27.
Article En | MEDLINE | ID: mdl-38678274

BACKGROUND: Alopecia areata (AA), a prevalent form of autoimmune hair loss, has a not well-defined relationship with atopic and allergic disorders, including eczema, hay fever, and asthma. OBJECTIVES: This study aims to elucidate the genetic relationship between atopy, allergies, and alopecia areata (AA) using Mendelian randomization. We hypothesize that atopic and allergic conditions contribute to the genetic predisposition of AA. METHODS: We analyzed extensive genetic data from Genome-wide Association Studies (GWAS) involving over one million individuals. This analysis focused on assessing the genetic correlation between AA and various allergic conditions, including hay fever, eczema, asthma, and allergies to pollen, dust, and cats. The inverse variance weighted method served as our primary analytical tool, complemented by sensitivity analyses to verify the robustness of our results. RESULTS: Our findings reveal a significant genetic correlation between atopy/allergies and an increased risk of AA. Notably, strong associations were observed for hay fever, eczema, asthma, and specific allergies (pollen, dust, and cats). The sensitivity analyses corroborated these associations, reinforcing the reliability of our primary results. CONCLUSIONS: This study provides compelling genetic evidence of an association between atopic and allergic conditions and the development of AA. These findings suggest that individuals with such conditions may benefit from enhanced surveillance for early signs of AA.

17.
Genes (Basel) ; 15(4)2024 Mar 26.
Article En | MEDLINE | ID: mdl-38674339

The precise identification of splice sites is essential for unraveling the structure and function of genes, constituting a pivotal step in the gene annotation process. In this study, we developed a novel deep learning model, DRANetSplicer, that integrates residual learning and attention mechanisms for enhanced accuracy in capturing the intricate features of splice sites. We constructed multiple datasets using the most recent versions of genomic data from three different organisms, Oryza sativa japonica, Arabidopsis thaliana and Homo sapiens. This approach allows us to train models with a richer set of high-quality data. DRANetSplicer outperformed benchmark methods on donor and acceptor splice site datasets, achieving an average accuracy of (96.57%, 95.82%) across the three organisms. Comparative analyses with benchmark methods, including SpliceFinder, Splice2Deep, Deep Splicer, EnsembleSplice, and DNABERT, revealed DRANetSplicer's superior predictive performance, resulting in at least a (4.2%, 11.6%) relative reduction in average error rate. We utilized the DRANetSplicer model trained on O. sativa japonica data to predict splice sites in A. thaliana, achieving accuracies for donor and acceptor sites of (94.89%, 94.25%). These results indicate that DRANetSplicer possesses excellent cross-organism predictive capabilities, with its performance in cross-organism predictions even surpassing that of benchmark methods in non-cross-organism predictions. Cross-organism validation showcased DRANetSplicer's excellence in predicting splice sites across similar organisms, supporting its applicability in gene annotation for understudied organisms. We employed multiple methods to visualize the decision-making process of the model. The visualization results indicate that DRANetSplicer can learn and interpret well-known biological features, further validating its overall performance. Our study systematically examined and confirmed the predictive ability of DRANetSplicer from various levels and perspectives, indicating that its practical application in gene annotation is justified.


Arabidopsis , Oryza , RNA Splice Sites , Arabidopsis/genetics , RNA Splice Sites/genetics , Humans , Oryza/genetics , Deep Learning , Software , RNA Splicing , Computational Biology/methods
18.
Microorganisms ; 12(4)2024 Apr 22.
Article En | MEDLINE | ID: mdl-38674785

Microbial degradation of feathers offers potential for bioremediation, yet the microbial response mechanisms warrant additional investigation. In prior work, Pseudomonas aeruginosa Gxun-7, which demonstrated robust degradation of feathers at elevated concentrations, was isolated. However, the molecular mechanism of this degradation remains only partially understood. To investigate this, we used RNA sequencing (RNA-seq) to examine the genes that were expressed differentially in P. aeruginosa Gxun-7 when exposed to 25 g/L of feather substrate. The RNA-seq analysis identified 5571 differentially expressed genes; of these, 795 were upregulated and 603 were downregulated. Upregulated genes primarily participated in proteolysis, amino acid, and pyruvate metabolism. Genes encoding proteases, as well as those involved in sulfur metabolism, phenazine synthesis, and type VI secretion systems, were notably elevated, highlighting their crucial function in feather decomposition. Integration of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) taxonomies, combined with a review of the literature, led us to propose that metabolic feather degradation involves environmental activation, reducing agent secretion, protease release, peptide/amino acid uptake, and metabolic processes. Sulfite has emerged as a critical activator of keratinase catalysis, while cysteine serves as a regulatory mediator. qRT-PCR assay results for 11 selected gene subset corroborated the RNA-seq findings. This study enhances our understanding of the transcriptomic responses of P. aeruginosa Gxun-7 to feather degradation and offers insights into potential degradation mechanisms, thereby aiding in the formulation of effective feather waste management strategies in poultry farming.

19.
Foods ; 13(7)2024 Mar 31.
Article En | MEDLINE | ID: mdl-38611376

During the storage and transportation processes, the occurrence of core browning in 'Yali' pear fruit due to adversity injury can be easily mitigated by implementing different cooling methods, especially in advanced maturity fruits. In this study, 'Yali' pears at an advanced maturity stage were subjected to slow cooling and rapid cooling treatment. The quality-related physiological percentage and severity, and the rate of good fruits were determined, and RNA-seq was used to explore the effects of different cooling methods on pathways related to core browning in advanced-maturity pears at the transcriptional level. The results indicated that, compared with slow cooling treatment, rapid cooling significantly inhibited core browning in advanced-maturity 'Yali' pears. Measurements of quality-related physiological indexes suggested that rapid cooling treatment led to higher SSC content, firmness, L* value, and b* value, indicating better brightness, coloration, and higher soluble solid content, which are desirable for commercial sale. Rapid cooling effectively suppressed the physiological metabolism of 'Yali' pears, delaying fruit senescence compared with slow-cooling treatment. Furthermore, the RNA-Seq sequencing results revealed that pathways related to browning are involved in hormone signal transduction pathways, which are associated with resistance and aging processes of pear fruit. In summary, rapid cooling treatment delayed the core browning of advanced maturity of 'Yali' pears, indicating that the core browning of 'Yali' pears is related to the cooling method, and the mechanism of rapid cooling in reducing the core browning of advanced maturity of 'Yali' pears was by delaying the aging process of the fruit. This provides a new perspective for alleviating the core browning of advanced-maturity 'Yali' pears during storage and transportation, and provides a theoretical reference for studying the mechanism of core browning of 'Yali' pears.

20.
Spectrochim Acta A Mol Biomol Spectrosc ; 315: 124236, 2024 Jul 05.
Article En | MEDLINE | ID: mdl-38615415

In this work, a colorimetric aptasensor based on magnetic beads (MBs), gold nanoparticles (AuNPs) and Horseradish Peroxidase (HRP) was prepared for the detection of mucin 1 (MUC1). Complementary DNA of the MUC1 aptamer (Apt) immobilized on the MBs was combined with the prepared AuNPs-Apt-HRP complex (AuNPs@Apt-HRP). In the presence of MUC1, it specifically bound to Apt, resulting in the detachment of gold nanoparticles from the MBs. After magnetic separation, AuNPs@Apt-HRP was separated into the supernatant and reacted with 3,3',5,5'-Tetramethylbenzidine (TMB) to produce color reaction from colorless to blue. The linear range of MUC1 was from 75 to 500 µg/mL (R2 = 0.9878), and the detection limit was 41.95 µg/mL. The recovery rate of MUC1 in human serum was 99.18 %∼101.15 %. This method is simple and convenient. Moreover, it does not require complex and expensive equipment for detection of MUC1. It provides value for the development of MUC1 colorimetric sensors and a promising strategy for the determination of MUC1 in clinical diagnosis.


Aptamers, Nucleotide , Benzidines , Biosensing Techniques , Colorimetry , Gold , Limit of Detection , Metal Nanoparticles , Mucin-1 , Mucin-1/analysis , Mucin-1/blood , Colorimetry/methods , Gold/chemistry , Aptamers, Nucleotide/chemistry , Metal Nanoparticles/chemistry , Humans , Biosensing Techniques/methods , Horseradish Peroxidase/chemistry , Horseradish Peroxidase/metabolism
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