PubMed Health⌕ Search

Biomedical subjects

Rui Ma

Publications and source records attributed to Rui Ma.

At least 19 recordsLinked to original sources
PubMed2026

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.

BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom 3 improved the neutral detergent fiber degradation (NDFD) by 20.39% averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom 3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF, + 11.47%). Genomic analysis revealed that the SynCom 3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.

Animals↗
PubMed2025

SHICEDO: single-cell Hi-C data enhancement with reduced over-smoothing.

MOTIVATION: Single-cell Hi-C (scHi-C) technologies have significantly advanced our understanding of the 3D genome organization. However, scHi-C data are often sparse and noisy, leading to substantial computational challenges in downstream analyses. RESULTS: In this study, we introduce SHICEDO, a novel deep-learning model specifically designed to enhance scHi-C contact matrices by imputing missing or sparsely captured chromatin contacts through a generative adversarial framework. SHICEDO leverages the unique structural characteristics of scHi-C matrices to derive customized features that enable effective data enhancement. Additionally, the model incorporates a channel-wise attention mechanism to mitigate the over-smoothing issue commonly associated with scHi-C enhancement methods. Through simulations and real-data applications, we demonstrate that SHICEDO outperforms the state-of-the-art methods, achieving superior quantitative and qualitative results. Moreover, SHICEDO enhances key structural features in scHi-C data, thus enabling more precise delineation of chromatin structures such as A/B compartments, TAD-like domains, and chromatin loops. AVAILABILITY AND IMPLEMENTATION: SHICEDO is publicly available at https://github.com/wmalab/SHICEDO.

Single-Cell Analysis↗
PubMed2025

Adipocyte-specific IGF1R knockout activates the β-catenin/apelin axis to combat diet-induced obesity in male mice.

AIMS: Obesity, driven by complex genetic and environmental interactions, remains a global health crisis with limited therapeutic options. The insulin-like growth factor 1 receptor (IGF1R) plays dual roles in metabolism and growth, but its tissue-specific functions in adipose biology are controversial. This study investigates how adipose-specific IGF1R knockout impacts systemic metabolism under high-fat diet (HFD) stress and explores the underlying mechanisms. METHODS: Adipose-specific IGF1R knockout mice (AdIGF1RKO) were generated by crossing Igf1rfl/fl mice with Adipoq-Cre transgenics. Mice were fed a normal chow diet (NCD) or HFD for 20 weeks. Metabolic phenotyping included glucose/insulin tolerance tests, body composition analysis and serum profiling. RNA-seq, Western blot and quantitative real-time reverse transcriptase PCR were used to identify molecular pathways. In vitro studies with stromal vascular fraction (SVF) cells validated β-catenin/apelin interactions. RESULTS: AdIGF1RKO male mice exhibited reduced adipose mass under NCD and resisted HFD-induced obesity, showing attenuated hepatic lipid deposition and improved glucose metabolism. Mechanistically, IGF1R knockout enhanced INSR and Akt phosphorylation, driving GSK3β-β-catenin activation and apelin upregulation. Apelin activated AMPK, suppressing lipogenesis and enhancing fatty acid oxidation. Notably, β-catenin's role shifted from inhibiting adipogenesis in precursors to promoting metabolic adaptation in mature adipocytes. CONCLUSION: We unveil a β-catenin/apelin-driven endocrine axis that reprograms energy metabolism under obesogenic stress. Therapeutically, targeting adipose IGF1R or apelin signalling could combat obesity while avoiding systemic toxicity. Limitations include unresolved β-catenin/Apln transcriptional mechanisms, APJ function and tissue-specific AMPK effects. Our findings redefine IGF1R's metabolic role and propose novel strategies for obesity-related disorders.

Animals↗
PubMed2006

Specific receptor subtype mediation of LPA-induced dual effects in cardiac fibroblasts.

Lysophosphatidic acid (LPA) is a phospholipid messenger with diverse effects mediated via receptors LPA1, LPA2 and LPA3. Our previous study revealed that serum LPA level is elevated after myocardial infarction (MI). However, very little is known about the effects of LPA on cardiac fibroblasts (CFs) that play a crucial role in left ventricular remodeling after MI. Here we demonstrated that LPA dose-dependently induced proliferation and collagen synthesis with the maximum stimulation at 10 microM that was preferentially mediated by LPA3. LPA also dose-dependently induced apoptotic cell death, as estimated by MTT assay, hoechst staining, TUNEL and flow cytometric analysis, with an IC(50) of 50 microM. Moreover, apoptotic cell death may involve mitochondrial dysfunction and activation of caspase-3. Apoptosis induced by LPA might be mediated by LPA1. These data suggest that LPA exerts dual proliferative and proapoptotic actions mediated by specific LPA receptor subtypes.

Animals↗
PubMed2006

Immunization with SARS-CoV S DNA vaccine generates memory CD4+ and CD8+ T cell immune responses.

An effective vaccine for severe acute respiratory syndrome (SARS) will probably require the generation and maintenance of both humoral and cellular immune responses. It has been reported that after natural infection in humans and immunization in animals with SARS-CoV vaccine, antibody is produced and persistent for a long period of time. In the present study, mice were immunized i.m. with SARS-CoV S DNA vaccine, and three different methods (ELISA, ELISPOT and FACS) were used to evaluate the immune responses when the cells were stimulated in vitro with a pool of peptides overlapping entire SARS spike protein. The results show that prime-immunization with SARS-CoV S DNA vaccine can induce both CD4(+) and CD8(+) T cell responses. Boosting with the same vaccine enhances CD4(+) and CD8(+) T cell responses in both lymphoid and nonlymphoid organs and were persistent over two months. The SARS-CoV S-specific CD4(+) and CD8(+) T cells were CD62L(-), a marker for memory cells, and -30 to 50% of the cells expressed IL-7Ralpha (CD127), a marker for the capacity of effector cells to develop into memory cells. In addition, immunization with the DNA vaccine elicited high levels of antibody production. Taken together, these data demonstrate that immunization with SARS-CoV S DNA vaccine can generate antigen-specific humoral and cellular immune responses that may contribute to long-term protection.

Animals↗
PubMed2006

Apoptosis of human breast carcinoma cells in the presence of cis-platin and L-/D-PPMP: IV. Modulation of replication complexes and glycolipid: Glycosyltransferases.

Apoptosis of human breast carcinoma cells (SKBR-3, MCF-7, and MDA-468) has been observed after treatment of these cells with anti-cancer drug cis-platin and glycosphingolipid biosynthesis inhibitor L- and D-PPMP, respectively. These drugs initiated apoptosis in a dose-dependent manner as measured by phenotypic morphological changes, by binding of a fluorescent phophatidyl serine-specific dye (PSS-380) onto the outer leaflet of the cell membranes, and by activation of caspases, -3, -8, and -9. It was observed that in two hours very little apoptotic process had started but predominant biochemical changes occurred after 6 h. DNA degradation started after 24 hours of drug treatment. However, very little is known about the stability of the ';Replication Complexes'' during the apoptotic process. DNA helicases are motor proteins that catalyze the melting of genomic DNA during its replication, repair, and recombination processes. Previously, DNA helicase-III was characterized as a component of the replication complexes isolated from embryonic chicken brains as well as breast and colon carcinoma cells. Helicase activities were measured by a novel method (ROME assay), and DNA polymerase-alpha activities were determined by regular chain extension of the nicked ACT-DNA, by determining values obtained from +/- aphidicolin-treated incubation mixtures. In all three breast carcinoma cell lines, a common trend was observed: a decrease of activities of DNA polymerase-alpha and Helicase III. A sharp decrease of activities of the glycolipid sialyltransferases: SAT-2 (CMP-NeuAc; GD3 alpha2-8 sialyltransferase) and SAT-4 (CMP-NeuAc: GM1a alpha2-3 sialyltransferase) was observed in the apoptotic carcinoma cells treated with L-PPMP compared with cis-platin.

Acetyltransferases↗
PubMed2006

Development of in vitro techniques for the important medicinal plant Veratrum californicum.

VERATRUM CALIFORNICUM (Liliaceae) is an important monocotyledonous medicinal plant which is the only source of the anticancer compound cyclopamine. An IN VITRO culture system for somatic embryogenesis and green plant regeneration of VERATRUM CALIFORNICUM was developed. Embryogenic calli were induced from mature embryos on induction medium. Five basal media supplemented with different growth regulators were evaluated for embryogenic callus induction, modified MS medium with 4 mg/L picloram showing the best result for embryogenic callus production. Fine suspension cell lines were established by employing friable embryogenic calli as starting material and AA medium and L2 medium as culture media. The suspension cell lines cultured in AA medium with 4 mg/L NAA appeared to be fresh yellow and fast growing. The suspension cells were cryopreserved successfully and recovered at a high rate. Green plants were regenerated from embryogenic calli maintained on solid medium with 73 % regeneration ability (green plants/100 calli) in 27-month-old culture. The IN VITRO plantlets contained the steroid alkaloids cyclopamine and veratramine. This IN VITRO system will form the basis for metabolic engineering of VERATRUM cells in the context of biotechnological production of pharmaceutically important secondary metabolites. DMSO:dimethyl sulfoxide fw:fresh weight NAA:naphthaleneacetic acid 2,4-D:2,4-dichlorophenoxyacetic acid picloram:4-amino-3,5,6-trichloro-2-pyridinecarboxylic acid dicamba:3,6-dichloro-2-methoxybenzoic acid.

Cryopreservation↗
PubMed2006

[Effect of cyclosporin A on the production of IFN-gamma by murine splenocytes].

AIM: To explore the effect of cyclosporine A (CsA) on the production of IFN-gamma by murine splenocytes after stimulation with different reagents. METHODS: Mouse splenocytes were prepared and cultured with anti-CD3 mAb alone, anti-CD3 mAb plus anti-CD28 mAb or anti-CD3 mAb plus IL-12, in the presence or absence of different concentrations of CsA. After stimulating for 3 days, the content of INF-gamma in the culture supernatant was assayed by ELISA. The effects of CsA on the expression of activated molecules on T cells and intracellular IFN-gamma production were examined at the single cell level by flow cytometry. RESULTS: The mouse splenocytes stimulated with anti-CD3 mAb, anti-CD3 mAb + anti-CD28 mAb or anti-CD3 mAb + IL-12 could produce high level of IFN-gamma, but CsA inhibited INF-gamma production in a dose-dependent manner. The inhibitory mechanism of CsA was related to the activation of splenocytes. CONCLUSION: CsA can inhibit the expressions of CD25 and CD69 on splenocytes, as well as INF-gamma production by splenocytes in a dose dependent manner.

Animals↗
PubMed2006

[Effects of chitosans with different molecular weights on Streptococcus sanguis biofilm].

PURPOSE: To investigate the effects of chitosan on Streptococcus sanguis biofilm. METHODS: Streptococcus sanguis biofilm was formed on saliva-coated glass (SCG) in a flow culture system, then exposed to 2% chitosans with different molecular weights (5 cps, 80 cps, 600 cps) for 3, 10, 30 minutes. Confocal laser scanning microscope and Vital/Dead fluorescent staining technique (vital stained green, dead stained red) were combined to observe the biofilm thickness, bacterial density. Analysis of variance was used for comparison. RESULTS: The biofilm thickness and bacterial density reduced significantly after treatment by 2% chitosan. Of all the treatment groups, 5 cps (low molecular weight) chitosan is most effective (P<0.01). CONCLUSIONS: 5 cps (low molecular weight) chitosan seems to be most effective in detaching biofilm.

Biofilms↗
PubMed2005

Photonic band gap effect and structural color from silver nanoparticle gelatin emulsion.

We have fabricated planar structures of silver nanoparticles in monochromatic gelatin emulsion with a continuous spacing ranging from 0.15-0.40 micron using a two-beam interference of a single laser source. Our planar holograms display a colorful "rainbow" pattern and photonic bandgaps covering the visible and IR ranges. We model the planar silver nanoparticle-gelatin composite system using an effective medium approach and good agreement is obtained between theory and experiment.

Journal Article↗
PubMed2005

Chronic morphine exposure affects the visual response properties of V1 neurons in cat.

Chronic opiate exposure leads to maladaptive changes in brain function. In view of the localization of opiate receptors in mammalian visual system, chronic opiate exposure is likely to affect the visual responses properties of V1 neurons. Using in vivo single-unit recording, we here showed that chronic morphine treatment resulted in the functional abnormality of primary visual cortical cells. When compared with saline-treated (as control) cats, cortical neurons in morphine-treated cats exhibited higher spontaneous activity, lower signal-to-noise ratios and weaker orientation and direction selectivity. However, re-exposure with morphine could significantly improve the function of V1 neurons in morphine-treated cats. These findings demonstrated that chronic morphine treatment could significantly degrade the response properties of V1 neurons and may lead to a function dependence on morphine in visual cortical cells.

Animals↗
PubMed2005

Effects of allitridi on cell cycle arrest of human gastric cancer cells.

AIM: To determine the effect of allitridi on cell cycle of human gastric cancer (HGC) cell lines MGC803 and SGC7901 and its possible mechanism. METHODS: Trypan blue dye exclusion was used to evaluate the proliferation, inhibition of cells and damages of these cells were detected with electron microscope. Flow cytometry and cell mitotic index were used to analyze the change of cell cycle, immunohistochemistry, and RT-PCR was used to examine expression of the p21(WAF1) gene. RESULTS: MGC803 cell growth was inhibited by allitridi with 24 h IC50 being 6.4 microg/mL. SGC7901 cell growth was also inhibited by allitridi with 24 h IC50 being 7.3 microg/mL. After being treated with allitridi at the concentration of 12 microg/mL for 24 h, cells were found to have direct cytotoxic effects, including broken cellular membrane, swollen and vesiculated mitochondria and rough endoplasmic reticula, and mass lipid droplet. When cells were treated with allitridi at the concentration of 3, 6, and 9 microg/mL for 24 h, the percentage of G0/G1 phase cells was decreased and that of G2/M phase cells was significantly increased (P = 0.002) compared with those in the group. When cells were treated with allitridi at the concentration of 6 microg/mL, cell mitotic index was much higher (P = 0.003) than that of control group, indicating that allitridi could cause gastric cancer cell arrest in M phase. Besides, the expression levels of p21(WAF1) gene of MGC803 cells and p21(WAF1) gene of SGC7901 cells were remarkably upregulated after treatment. CONCLUSION: Allitridi can cause gastric cancer cell arrest in M phase, and this may be one of the mechanisms for inhibiting cell proliferation. Effect of allitridi on cells in M phase may be associated with the upregulation of p21(WAF1) genes. This study provides experimental data for clinical use of allitridi in the treatment of gastric carcinoma.

Adenocarcinoma, Mucinous↗
PubMed2005

Serotonin transporter promoter polymorphism and monoamine oxidase type A VNTR allelic variants together influence alcohol binge drinking risk in young women.

The short allelic variant of the serotonin transporter protein promoter polymorphism (5HTTLPR) appears to influence binge drinking in college students. Both monoamine oxidase type A (MAOA) and the serotonin transporter protein are involved in the processing of serotonin, and allelic variants are both associated with differences in the efficiency of expression. We hypothesized that a significant gene x gene interaction would further stratify the risk of binge drinking in this population. Participants were college students (n = 412) who completed the College Alcohol Study, used to measure binge drinking behaviors. Genomic DNA was extracted from saliva for PCR based genotyping. The risk function for binge drinking was modeled using logistic regression, with final model fit P < 0.0005. This model was valid only for Caucasian females (n = 223), but the power to detect sex and ethnic effects was small. Young Caucasian women carrying higher expression MAOA VNTR alleles homozygous for the short allelic variant of the 5HTTLPR demonstrated the highest rate of binge drinking by self-report, odds ratio (genotype odds: population odds) and 95% confidence intervals, 3.11 (1.14-18.10). Individuals carrying higher expression MAOA VNTR alleles carrying at least one long 5HTTLPR allelic variant had the lowest risk of binge drinking 0.46 (0.28-0.71). These results support the hypothesis that binge drinking behavior in young adulthood may be influenced by neurobiological differences in serotonergic function conferred by functional polymorphisms in genes involved in serotonin processing.

Adolescent↗
PubMed2005

[Regulation of androgen receptor mRNA expression by testosterone in cultured vascular smooth muscle cells].

OBJECTIVE: To investigate the effects of testosterone exposure on androgen receptor (AR) mRNA expression in cultured vascular smooth muscle cells (VSMCs). METHODS: VSMCs were cultured from the thoracic aorta of male SD rats using explant method. The total RNA was extracted by one-step guanidine isothiocyanate method and subjected to Northern blotting analysis for determining AR mRNA level. The effect of testosterone on the viability and growth of VSMCs were studied by means of cell counting and tritiated thymidine incorporation assay. RESULTS: Testosterone treatment of the synchronized VSMCs for 24 h increased intracellular AR mRNA expression in a dose-dependent manner, with relative mRNA level of 97.67+/-7.22, 98.00+/-13.58, 143.33+/-10.99, 177.67+/-14.62 and 185.67+/-19.97 corresponding to testosterone doses of 0, 4 nmol/L, 40 nmol/L, 400 nmol/L and 4 micromol/L, respectively. Incubation of synchronized VSMCs with testosterone at a physiological level of 40 nmol/L for 24 h resulted in a mean of 30% up-regulation of AR mRNA level, compared with that of untreated cells. During AR up-regulation, testosterone had no significant effects on the cell number and DNA synthesis of VSMCs as measured by cell counting and tritiated thymidine incorporation assay. CONCLUSION: Self-initiated up-regulation of AR mRNA expression occurs in synchronized VSMCs, which is independent of testosterone that influences apoptosis or growth rate of the cells, suggesting the involvement of AR in androgen regulational at the transcription level in VSMCs.

Animals↗
PubMed2005

[Experimental study of pilots' scan and performance, workloads].

OBJECTIVE: To study the problems of pilots' scan, performance, workload. METHOD: An experimental system for evaluating pilots' scan, performance, workload was built up based on previous studies. RESULT: After theoretical consideration and analysis of experimental results, the difference between expert pilots and novice pilots were disclosed preliminarily. CONCLUSION: Expert pilots demonstrates more frequent fixations with shorter dwell time than novice pilots do; to both pilots, the conclusion can be drawn that the variation between workloads and performance is not fixed.

Aerospace Medicine↗
PubMed2005

MUC5AC expression up-regulation goblet cell hyperplasia in the airway of patients with chronic obstructive pulmonary disease.

OBJECTIVE: To determine the number of goblet cells, the change of MUC5AC expression in chronic obstructive pulmonary disease (COPD) patients and the relationship of smoking with goblet cell, MUC5AC, and lung function. METHODS: Eighteen patients undergoing lung resections for a solitary peripheral carcinoma were classified by lung function as having COPD. Twenty patients with normal lung function served as the control group. Normal lobe bronchioles far away from the lesion site were taken for paraffin section. Goblet cells were identified by AB/PAS staining and the expression of MUC5AC in the paraffin's section was tested by immunohistochemistry. RESULTS: Goblet cell hyperplasia was observed in the COPD group. The positive rate of goblet cell in COPD group (0.20% +/- 0.10%) was significantly higher than that in the normal lung function group (0.13% +/- 0.06%, P < 0.05). The positive rate of MUC5AC expression in the COPD group (0.27% +/- 0.09%) was higher than that in the normal lung function group (0.20% +/- 0.10%, P < 0.05). The positive rate of goblet cell in smokers (27.93% +/- 9.00%) of the COPD group and normal lung function group was higher than that in non-smokers (17.70% +/- 9.37%, P < 0.05), while MUC5AC expression had no significant difference between smokers and non-smokers (17.88% +/- 6.44% and 10.88% +/- 7.10%, respectively). CONCLUSION: For COPD patients with declined lung function, there were goblet cell hyperplasia and increased expression of MUC5AC. MUC5AC expression up-regulation may due to goblet cell hyperplasia. Smoking may be an important factor for goblet cell hyperplasia.

Aged↗
PubMed2005

[The effect of sodium doecyl sulfate on Streptococcus sanguis biofilm].

PURPOSE: To investigate the effects of sodium doecyl sulfate on Streptococcus sanguis biofilm. METHODS: Streptococcus sanguis biofilm was formed on saliva-coated glass(SCG) in a flow culture system, then exposed to different dental plaque control agents for 3,10,30 minutes including A: 300 mmol.L(-1) sodium doecyl sulfate (SDS); B: 2% chlorhexidine combined with 300 mmol.L(-1) SDS; C: 0.3%triclosan combined with 300 mmol.L(-1) SDS. Confocal laser scanning microscopy and vital/dead fluorescent staining technique (vital stained green, dead stained red) were combined to observe biofilm thickness, bacterial density and viability, analysis of variance was used for comparison. RESULTS: The biofilm thickness and bacteria density reduced after treatment by 300 mmol.L(-1) SDS. However, there was no significant difference after treatment by 2% chlorhexidine combined with 300 mmol.L(-1)SDS; When treated by 0.3% triclosan combined with 300 mmol.L(-1) SDS, most or all of the bacteria detached from the surface and dispersed. CONCLUSIONS: The combination of SDS (aimed at detachment) and triclosan (aimed at killing bacteria) may be most effective in controlling biofilm.

Biofilms↗